Commit a4401677 authored by Mathieu's avatar Mathieu

2.0 beta 3

parent 455d5d51
......@@ -309,6 +309,13 @@ class Analysis(object):
'Please clean the header of your input file.' % (char, header.strip()))
raise SystemExit
for char in FORBIDDEN_HEADER_CHARS_BEFORE_SPLIT:
if char in header.split()[0]:
_logger.error('The character \'%s\' is present in the fasta header %s, '
'which will crash BUSCO. '
'Please clean the header of your input file.' % (char, header.split()[0].strip()))
raise SystemExit
@staticmethod
def _check_blast():
"""
......@@ -440,8 +447,9 @@ class Analysis(object):
n += 1
if '>' not in line:
for aa in aas:
if aa in line:
_logger.error('Please provide a nucleotide file as input, it should not contains \'%s\'' % aa)
if aa.upper() in line or aa.lower() in line:
_logger.error('Please provide a nucleotide file as input, it should not contains \'%s or %s\''
% (aa.upper(), aa.lower()))
file.close()
raise SystemExit
file.close()
......@@ -466,7 +474,7 @@ class Analysis(object):
n += 1
if '>' not in line:
for aa in aas:
if aa in line:
if aa.lower() in line or aa.upper() in line:
is_aa = True
break
file.close()
......@@ -787,6 +795,9 @@ class Analysis(object):
self._target_species = params['target_species']
self._augustus_config_path = params['augustus_config_path']
self._tarzip = params['tarzip']
self._dataset_creation_date = params['dataset_creation_date']
self._dataset_nb_species = params['dataset_nb_species']
self._dataset_nb_buscos = params['dataset_nb_buscos']
self.mainout = None
self._totalbuscos = 0
self._total = 0
......@@ -882,7 +893,10 @@ class Analysis(object):
:param out: a file to which the header will be added
:type out: file
"""
out.write('# BUSCO version is: %s \n# The lineage dataset is: %s\n' % (VERSION, self._clade_name))
out.write('# BUSCO version is: %s \n# The lineage dataset is: %s (Creation date: %s,'
' number of species: %s, number of BUSCOs: %s)\n'
% (VERSION, self._clade_name, self._dataset_creation_date, self._dataset_nb_species,
self._dataset_nb_buscos))
out.write('# To reproduce this run: %s\n#\n' % _rerun_cmd)
@staticmethod
......@@ -1075,6 +1089,7 @@ class Analysis(object):
# to a FASTA file ('run_XXXX/augustus_output/extracted_proteins').
_logger.info('Extracting predicted proteins...')
files = os.listdir('%saugustus_output/predicted_genes' % self.mainout)
files.sort()
for entry in files:
Analysis.p_open(['sed -i.bak \'1,3d\' %saugustus_output/predicted_genes/%s;'
'rm %saugustus_output/predicted_genes/%s.bak'
......@@ -1735,6 +1750,7 @@ class Analysis(object):
"""
hmmer_results = os.listdir('%shmmer_output' % self.mainout)
hmmer_results.sort()
hmmer_results_files = []
for entry in hmmer_results:
hmmer_results_files.append(entry)
......@@ -2203,6 +2219,7 @@ class GenomeAnalysis(Analysis):
_logger.info('Running HMMER to confirm orthology of predicted proteins:')
files = os.listdir('%saugustus_output/extracted_proteins' % self.mainout)
files.sort()
if not os.path.exists(self.mainout + 'hmmer_output'):
Analysis.p_open(['mkdir', '%shmmer_output' % self.mainout], 'bash', shell=False)
......@@ -2426,6 +2443,7 @@ class TranscriptomeAnalysis(Analysis):
if not os.path.exists('%stranslated_proteins' % self.mainout):
Analysis.p_open(['mkdir', '%stranslated_proteins' % self.mainout], 'bash', shell=False)
files = os.listdir(self._tmp)
files.sort()
lista = []
for entry in files:
if entry.endswith(self._abrev + str(self._random) + '_.temp'):
......@@ -2434,9 +2452,8 @@ class TranscriptomeAnalysis(Analysis):
_logger.info('Translating candidate transcripts...')
for entry in lista:
raw_seq = open(self._tmp + entry)
name = entry.split(self._abrev)[0]
if name == '': # if the contig name is _abrev, might happen :)
name = self._abrev
name = self._abrev.join(entry.replace('_.temp', '')
.split(self._abrev)[:-1]) # this works even if the runname is in the header
trans_seq = open(self.mainout + 'translated_proteins/' + name + '.faa', 'w')
nucl_seq = ''
header = ''
......@@ -2470,6 +2487,7 @@ class TranscriptomeAnalysis(Analysis):
"""
_logger.info('Running HMMER to confirm transcript orthology:')
files = os.listdir('%stranslated_proteins/' % self.mainout)
files.sort()
if not os.path.exists('%shmmer_output' % self.mainout):
Analysis.p_open(['mkdir', '%shmmer_output' % self.mainout], 'bash', shell=False)
......@@ -2552,6 +2570,7 @@ class GeneSetAnalysis(Analysis):
if not os.path.exists(self.mainout + 'hmmer_output'):
Analysis.p_open(['mkdir', '%shmmer_output' % self.mainout], 'bash', shell=False)
files = os.listdir(self._clade_path + '/hmms')
files.sort()
f2 = open('%sscores_cutoff' % self._clade_path) # open target scores file
# Load dictionary of HMM expected scores and full list of groups
score_dic = {}
......@@ -2580,13 +2599,15 @@ class GeneSetAnalysis(Analysis):
# end of classes definition, now module code
VERSION = '2.0 beta 2'
VERSION = '2.0 beta 3'
CONTACT = 'mailto:[email protected]'
ROOT_FOLDER = os.getcwd()
FORBIDDEN_HEADER_CHARS = ['/', 'ç', '¬', '¢', '\'', '´', 'ê', 'î', 'ô', 'ŵ', 'ẑ', 'û', 'â', 'ŝ', 'ĝ', 'ĥ', 'ĵ', 'ŷ',
FORBIDDEN_HEADER_CHARS_BEFORE_SPLIT = ['/', '\'']
FORBIDDEN_HEADER_CHARS = ['ç', '¬', '¢', '´', 'ê', 'î', 'ô', 'ŵ', 'ẑ', 'û', 'â', 'ŝ', 'ĝ', 'ĥ', 'ĵ', 'ŷ',
'ĉ', 'é', 'ï', 'ẅ', 'ë', 'ẅ', 'ë', 'ẗ,', 'ü', 'í', 'ö', 'ḧ', 'é', 'ÿ', 'ẍ', 'è', 'é',
'à', 'ä', '¨', '€', '£', 'á']
......@@ -2720,6 +2741,9 @@ def _define_parameters(args):
target_species = None
clade_name = None
domain = None
dataset_creation_date = "N/A"
dataset_nb_buscos = "N/A"
dataset_nb_species = "N/A"
# load the dataset config, or warn the user if not present
try:
target_species_file = open('%sdataset.cfg' % args['clade'])
......@@ -2730,6 +2754,12 @@ def _define_parameters(args):
target_species = l.strip().split("=")[1]
elif l.split("=")[0] == "domain":
domain = l.strip().split("=")[1]
elif l.split("=")[0] == "creation_date":
dataset_creation_date = l.strip().split("=")[1]
elif l.split("=")[0] == "number_of_BUSCOs":
dataset_nb_buscos = l.strip().split("=")[1]
elif l.split("=")[0] == "number_of_species":
dataset_nb_species = l.strip().split("=")[1]
if domain != 'prokaryota' and domain != 'eukaryota':
_logger.error('Corrupted dataset.cfg file: domain is %s, should be eukaryota or prokaryota' % domain)
raise SystemExit
......@@ -2847,7 +2877,10 @@ def _define_parameters(args):
"force": args['force'], "sequences": args['in'], "cpus": cpus, "clade_name": clade_name,
"clade_path": args['clade'], "ev_cutoff": ev_cutoff, "domain": domain, "restart": args['restart'],
"augustus_config_path": augustus_config_path, "tarzip": args['tarzip'],
"region_limit": region_limit, "flank": flank, "long": args['long']}
"region_limit": region_limit, "flank": flank, "long": args['long'],
"dataset_creation_date": dataset_creation_date, "dataset_nb_species": dataset_nb_species,
"dataset_nb_buscos": dataset_nb_buscos
}
def _check_path_exist(path):
......
Beta 3
- Improve the detection of problematic special characters in the fasta header and sequences
name=sample dataset BUSCO 2.0
species=fly
domain=eukaryota
creation_date=07.10.2016
number_of_BUSCOs=10
number_of_species=23
Warning: Block unknown_D is not significant enough, removed from profile.
Warning: Block unknown_G is not significant enough, removed from profile.
Warning: Block unknown_C is not significant enough, removed from profile.
Warning: Block unknown_A is not significant enough, removed from profile.
Warning: Block unknown_B is not significant enough, removed from profile.
Warning: Block unknown_C is not significant enough, removed from profile.
Will create parameters for a EUKARYOTIC species!
creating directory /home/xxx/augustus-3.2.2/config/species/BUSCO_SAMPLE_3715919971/ ...
creating /home/xxx/augustus-3.2.2/config/species/BUSCO_SAMPLE_3715919971/BUSCO_SAMPLE_3715919971_parameters.cfg ...
creating /home/xxx/augustus-3.2.2/config/species/BUSCO_SAMPLE_3715919971/BUSCO_SAMPLE_3715919971_weightmatrix.txt ...
creating /home/xxx/augustus-3.2.2/config/species/BUSCO_SAMPLE_3715919971/BUSCO_SAMPLE_3715919971_metapars.cfg ...
The necessary files for training BUSCO_SAMPLE_3715919971 have been created.
Now, either run etraining or optimize_parameters.pl with --species=BUSCO_SAMPLE_3715919971.
creating directory /home/xxx/augustus-3.2.2/config/species/BUSCO_SAMPLE_1214242381/ ...
creating /home/xxx/augustus-3.2.2/config/species/BUSCO_SAMPLE_1214242381/BUSCO_SAMPLE_1214242381_parameters.cfg ...
creating /home/xxx/augustus-3.2.2/config/species/BUSCO_SAMPLE_1214242381/BUSCO_SAMPLE_1214242381_weightmatrix.txt ...
creating /home/xxx/augustus-3.2.2/config/species/BUSCO_SAMPLE_1214242381/BUSCO_SAMPLE_1214242381_metapars.cfg ...
The necessary files for training BUSCO_SAMPLE_1214242381 have been created.
Now, either run etraining or optimize_parameters.pl with --species=BUSCO_SAMPLE_1214242381.
etraining quickly estimates the parameters from a file with training genes.
optimize_augustus.pl alternates running etraining and augustus to find optimal metaparameters.
......@@ -56,4 +56,4 @@ taa: 3 (0.375)
tga: 1 (0.125)
end *EXON*
Storing parameters to file...
Writing exon model parameters [1] to file /home/xxx/augustus-3.2.2/config/species/BUSCO_SAMPLE_3715919971/BUSCO_SAMPLE_3715919971_exon_probs.pbl.
Writing exon model parameters [1] to file /home/xxx/augustus-3.2.2/config/species/BUSCO_SAMPLE_1214242381/BUSCO_SAMPLE_1214242381_exon_probs.pbl.
>g1[sample:25227-28731]
atggaggcatctgctgccaaaatcacacccatggccagttccacgtccacttccggatccataaactccccttccagtgacaaaatgaactacgcactccaagtggcgctgcaaactatcaaggagcggtgcatccagctgcagcgccgcgtggccagcatggaggaggagaaccagcgactgagggaagcctccagcaggtcagaaggtgctccaactgcaaaggaaatcggggtcactggggatgtactctccctcaaagcccaggtctctgagctgcagcgccaaaaggagcagctggaggagcacattagcatggtgtccaacgagaacagacgcctctggtcccgtctgtcgcagatctccaaggatcagcagctaaacgcagtgcccagctcatccgactcgcgtgcccagcaaaaccagaacctggtgcgctccaagacctttacgcaacactcccccaatcctcaccttcgccaaaagatgctgtcagacgggataaaggatctcagcctggaggaaatagccttggatgacttcggtgccagtagcggggaactaggttacccttacaacctgcaaaaggtggaggaaaccaccagtgaacctgatgccaatgtggatgccaaaagatgtatggatggactgcaggagatgaggcgagaggccatgaagcagcagcaggagctcagttcggctctgactttactagaaagtcgcatagcactgaagccctgtccggaatgtgcccagaaaaccttcaaaaagccggagatggccgacaaaagtctggaaacggacgacagcctgaccagcgaactgaagaactatgagagccagcacaatggacacaatggaacaccgcccagccagagaatcaatatcatacaagagaaaatcaaagcagacgcagccgatgcaatggagaagatctgccctatgtgcggcaagcagtactccagccaagtgtctttcaatgccttccgcgagcacgtcgagatgcacttcatcgacgatgcactggagttggaatccgagaacagcatggagcgccagttcgagtttgtttcccatgcg
>g2[sample:28912-30181]
atgttttgcggcaagagtttagtcaataatttctacaaatataagagaaagatgtggcagaatgtagtcccaataatacagcgtggcaagggaacttaccacccactaaaaattctctttttcggcaccgattacttttccttgcccagcttacaggcgctacacaaaaactgcggtgaccacttgggagttgttacctccttcaaaaatcccgccaactgtgtgaggacctatgcggaaaaggagaagcttcccctgcaaaagtggcccatagatccatctgtgtgtcctaagtttgacctgggcgtcgtggtttcctttggccacctgattcctgctaatatcatacatggatttcctaatggaatgatcaatgttcatgctagtctattgcccaggtggcgaggagctgctcccatcatatatgcgatcatgaagggagatgccatcactggggtttccatcatgaaaatcgaacctcaccggtttgatattggtgcaattttagctcagcgggaggtggcgattgagcccaatgtcttcatgccggacttgcacgcatctttggcgtcgttaggggcagatttactagtggatacggttaacaacctgtcagtacgacttaaggaagccaaaccccaggatagtacaaagaccagctatgctcccaagatcaccagtaaaataacagaagtcaattggtcggagctgagtgcccttgacatatacacgcgtcatagagctttgtttggctacaaaaaccttaccaccagctttttgagcaagcaagtgcagctgctagagctacctgaggaaggcgagatccctggtaattggatgtgctcagcacagccagttggaggtgcttcaattacgcgtagaaggtag
>g3[sample:30184-31421]
atgtccagaaatttgtttttatcaattacaaacttatttaggaacttggagagcctgttcctgccacatggaggacaccctcctgctctagcgttggccggttttcagcatgatcacagccatagatcctcccaggaattcagtttgaagcagcttattggcgacggaatgctgtgggctgttccgaaacacaggagatccgtggagaaacgcctgaagcggaagttcggatatccggaatacaattggaagcctctgagggagaagaggaacatccgctcctgtctgcaatgtggccatgaccacgagatgggggttctttgtcctttctgctaccaaaaagtcctgaaggagactgagctcatgcagtcgaaaatccaggagacactgggtctagatcccgtggacaaggaagtaatcgttctttatgagggcgagaaagccgaacagtcctcagatgagctgaaaaacaaacgcatcgtggagatgaagaagcctcgtcccatgtggttcaccaagaatctgctccaaaaatccacgcagcaattgtccgaaaccaaggaagtcaagccctccgacttggcctag
>g4[sample:31632-32490]
atggcctgcttgagcacttccggtcgcgtcgtctgcggctcccgtcgccagcagacgcacaagctgctctaccagctattcggatcccggccaggatatacagccccatccaccgcgaccggattattcagtccgcccaaagtccaacagcaggccatgcgactctgccacggattaagcttcagcttgggcaaggattaccccgatctgctggtaagttcattgccggatgaagcctacaccgcgaaaaaatag
>g1[sample:27021-28665]
atggaggcatctgctgccaaaatcacacccatggccagttccacgtccacttccggatccataaactccccttccagtgacaaaatgaactacgcactccaagtggcgctgcaaactatcaaggagcggtgcatccagctgcagcgccgcgtggccagcatggaggaggagaaccagcgactgagggaagcctccagcaggtcagaaggtgctccaactgcaaaggaaatcggggtcactggggatgtactctccctcaaagcccaggtctctgagctgcagcgccaaaaggagcagctggaggagcacattagcatggtgtccaacgagaacagacgcctctggtcccgtctgtcgcagatctccaaggatcagcagctaaacgcagtgcccagctcatccgactcgcgtgcccagcaaaaccagaacctggtgcgctccaagacctttacgcaacactcccccaatcctcaccttcgccaaaagatgctgtcagacgggataaaggatctcagcctggaggaaatagccttggatgacttcggtgccagtagcggggaactaggttacccttacaacctgcaaaaggtggaggaaaccaccagtgaacctgatgccaatgtggatgccaaaagatgtatggatggactgcaggagatgaggcgagaggccatgaagcagcagcaggagctcagttcggctctgactttactagaaagtcgcatagcactgaagccctgtccggaatgtgcccagaaaaccttcaaaaagccggagatggccgacaaaagtctggaaacggacgacagcctgaccagcgaactgaagaactatgagagccagcacaatggacacaatggaacaccgcccagccagagaatcaatatcatacaagagaaaatcaaagcagacgcagccgatgcaatggagaagatctgccctatgtgcggcaagcagtactccagccaagtgtctttcaatgccttccgcgagcacgtcgagatgcacttcatcgacgatgcactggagttggaatccgagaacagcatggagcgccagttcgagtttgtttcccatgcggtgggtgacttctga
>g2[sample:28906-30181]
atgttttgcggcaagagtttagtcaataatttctacaaatataagagaaagatgtggcagaatgtagtcccaataatacagcgtggcaagggaacttaccacccactaaaaattctctttttcggcaccgattacttttccttgcccagcttacaggcgctacacaaaaactgcggtgaccacttgggagttgttacctccttcaaaaatcccgccaactgtgtgaggacctatgcggaaaaggagaagcttcccctgcaaaagtggcccatagatccatctgtgtgtcctaagtttgacctgggcgtcgtggtttcctttggccacctgattcctgctaatatcatacatggatttcctaatggaatgatcaatgttcatgctagtctattgcccaggtggcgaggagctgctcccatcatatatgcgatcatgaagggagatgccatcactggggtttccatcatgaaaatcgaacctcaccggtttgatattggtgcaattttagctcagcgggaggtggcgattgagcccaatgtcttcatgccggacttgcacgcatctttggcgtcgttaggggcagatttactagtggatacggttaacaacctgtcagtacgacttaaggaagccaaaccccaggatagtacaaagaccagctatgctcccaagatcaccagtaaaataacagaagtcaattggtcggagctgagtgcccttgacatatacacgcgtcatagagctttgtttggctacaaaaaccttaccaccagctttttgagcaagcaagtgcagctgctagagctacctgaggaaggcgagatccctggtaattggatgtgctcagcacagccagttggaggtgcttcaattacgcgtagaaggtag
>g3[sample:30184-31415]
atgtccagaaatttgtttttatcaattacaaacttatttaggaacttggagagcctgttcctgccacatggaggacaccctcctgctctagcgttggccggttttcagcatgatcacagccatagatcctcccaggaattcagtttgaagcagcttattggcgacggaatgctgtgggctgttccgaaacacaggagatccgtggagaaacgcctgaagcggaagttcggatatccggaatacaattggaagcctctgagggagaagaggaacatccgctcctgtctgcaatgtggccatgaccacgagatgggggttctttgtcctttctgctaccaaaaagtcctgaaggagactgagctcatgcagtcgaaaatccaggagacactgggtctagatcccgtggacaaggaagtaatcgttctttatgagggcgagaaagccgaacagtcctcagatgagctgaaaaacaaacgcatcgtggagatgaagaagcctcgtcccatgtggttcaccaagaatctgctccaaaaatccacgcagcaattgtccgaaaccaaggaagtcaagccctccgacttggcctag
>g4[sample:31646-47625]
atggcctgcttgagcacttccggtcgcgtcgtctgcggctcccgtcgccagcagacgcacaagctgctctaccagctattcggatcccggccaggatatacagccccatccaccgcgaccggattattcagtccgcccaaagtccaacagcaggccatgcgactctgccacggattaagcttcagcttgggcaaggattaccccgatctgctgcaaagctcccacaagtgcagccaaacgctgcagtactcccaaagttccaaggcgaatctgaggcagcacagctcggtccacacacaacagccagccggtcctgtgagggagttccagatcgatccctacatcatactcgacgacgacctcaagtacttctacgacgatgtgagatatctgctgaaatcgggcacatcccagccagagttggacaccatcgccagctattatttcgatggccaggggaaggctctgcgacccatggttaccatgctgatggccaaggcgataaactaccacctgaacaacgagtcacaccaattagtacacaaacagcgacagatcgccctcttttcggagatggtgcactcggccagcttggtccacgacgatgtcatcgatcagtcggacttccgacgcggcaagcccagcgtgaatgctctttggaaccacaaaaaggtcacaatggctggtgattatatcttatcgattgcctcgattatgatagctcgtctgcgcagcgatgatgtgacgatcgtgctgagtcagatcttgaccgatttggtccaaggcgagttcatgcagctgggctcaagggagacggagaacgagcgcttcgcccattacctgaccaagacgtacaggaagaccgcatcgctgatcgccaacgcactgaaggcgaccgccgtgattgcccaggccgacgacaacgtggccgaggtggccttccagtacggacgcaacatcggcttggcctttcagctggtcgacgacatgctggacttcgtctcctccaccgagcagatgggcaagccgacggcggcagatctgaaactgggtctggccaccgcccccgtcctctttgcatgcgaaaagtaccccgagctgaatcccatggtgatgcggcgcttcagcgagcccggcgacgtggagcgagccttcgagctggtgcacaagtcgcacggtctggaacagacccggttcctggccaagaagcactgcaacgaggcgatacggctggcccaggagctcacggagtcgccctaccagaagggcctccaggtggtcgccgacttagtcatcaaccgcatgaagtag
>g5[sample:48236-51425]
atgacgactagcgatgaaatgggcatgggcggcaacttctgccacgaccacatccagcatccgctgatgtggtgcgatgagaagaagcgtctggtggagcgcaagaatgcagaagagagtcttcgcatgtggcgtcgcaggaaggcggaggagtgtgctcgcaaggagaaggataagcaggagcatgtggactcagcactaaccacttttgtggacaacacaaggttcttcagggaaattgcagagttcgtgtccgatttcagtgatgggcaaatccagcagctgctggaggaaagcgctcgtctgcgcgttgagcacgccgagaatctcatccgtgtgaagagcaagcaccagtcactcagccaggtgatgcagcaggtccagaactcgagctccaccatcgaggagcttgaggaaaactggaagaagcgctccaaagcggaggaacagaagcgcatcaatgtcaagaacatagccgagtttaagaacttcaagaaaactgtggaatctgcagctggccatgtaggtgcggaggtcaatagtcaagcgaatggcgccgcccaggatgaggaccttattatcgaaggaatcgaagagaccggcggcgggatcttctcgctctacgatccctggtccaaggccctaatgaagaaccccgtgcgcaacgagaagtgcggtcacatctacgaccgcgattcggtgatgctgattataaaggacaacattggcatccgatgtcccgtgctcggctgtggcaacacgacctacatccagcctgcgcacctggtcgaggatgccaaagtccggcaaatgtactacgacctgtttcaccaacattgtccttggggtcgacctggtggtggtgcacccaatgtagaagtgcggcgcaaggacatcacagccgtaggccttcactccacgcccacagtgaccaatgcccaccgaatgaatctgctgcagccgtgtcgctacaacgacttcttctcgatgcagaagaagtgtcacaacaacccgctggccgcctaccaccaccaccaccaccatgcccctcctgcccctccgccgggtggtcgccttggccacgcccactcagttcatcacctgcaggaaagtggtcccaggagcagcaccgtcacgatttgcgagcgggagattccccacaagcccggagcgggagttggtgtcaatgttgccaaaaacgccaacggtgagagccttcacatcgagctgaaagagcatccttcaatgtcgtttcgcaataaaggccatgtagacatagaattgcgatacaagccctctcctccgtgcaagggcaagcctcttctggagaagattgtggttagcgagagtgaacagcgatgtcctttgcaggaaaagctggccacacagaagaagcgcctgcaggccaaactagaaaagccggtgagcggca
>g1[sample:62761-68675]
atgttcgtgtcgacagtctctcgcattgcccccgttgccaggagcgccttcctcgccaactccaagcagtacctgcgaccattgagcagcgccatcatcagccagagccagactttggccgctcagaacacaacccccgttgcattgctgccacagatcaggtcattccagacctcgccagtcacgcgtgacattgactcggccgccaaattcattggcgctggtgccgcaacagtcggtgtcgctggatccggtgctggtatcggaacagtattcggttccctcatcatcggctacgccaggaacccatcgctgaaacagcagctgttctcctacgccattctgggcttcgccctgtccgaggccatgggtctgttctgtttgatgatggccttcctgctgttgttcgccttctaa
>g2[sample:69313-70561]
atggatttcgccaagaaaatacttggaaagtacggctggaaggagggcgacggcttgggcaagaacaacacgggaattgcagctccattgaaggccagtctgaagttcgataacgcgggtctgggagtggatcgcgcccaggaattcaatgaccattggtgggagcgctgctttaacgaggccgccagcaatgtggacgtccagattcagcaagacggacaggtgtccacctcccgcaggaaaggcgaggaagcggtggagatctccaccagcggattctccgcgcgtaagctgaagaaagccaaggagcagcacgccagcgatggaaagaccacctacgacaacttcctgcagacttcgctgctcacccaaggcggcaacgaagttgagacctccgagcgcatcaaggtggaggagattgaggtcgccaaggtggcggtgctcacagatgaagaactctttaaagcctgcggaggaaggactgcgcacaaaggagcacggcatggcttaaagttaagcggaaagatcgcccgcttggagcagcaggagcgcgagatgctggagaagcttcagagcaagctgaagactacgcctgaaaccactctggttccgaaaagcggaaagttgattgaggagacccagcacaaagtagcagattcagtggattgcagtgtggagcaggctacgaagcccaaaaagaagaaaaagtctaggactgaggagtccgtcgaggaaattgcgcctgcccaactggaagagcccataaaatccaagaaaaagaagaaagacaaggctgagaaggcggcaaaggaatactcaacacatcaggctcaagacgaccccgtccagatcaagaggagaaaaaataagacagggaagctagaagaggaagtccaagatgttacggaagtcgaagaggcagtgaagataaaaaagaaggacaagaggcagcaaggggtagaagcaactgaagccttaagcattgaaactgatgaacatgtaaaatccaaaaagaagcggaaaacggaagactcctcagaggaaaccgaaactcccacaaaaaccaaaaagaaaagaaagaacaaggaactcgtgtaa
>g3[sample:70677-71872]
atgtcggactttgaaatggaggacagcgcctcggggtacgattcaggtgataactcagatgccgagctgcaagcggcatttgaacgaggcgacttaaaaccaggcctaaacttggagttcaatggccagagagacaaagtgaatgatgtgaccaaactgctggcaaaaacagaggctatcaagatgcaacttccttggctggagcgcctggacatgatcaacacactggctcccctggccccggaactcgctgtacagctggagaagcacgagcaaaagcgggccaatctcttcaaaggcaacgccaagctgccctacattcggcccgaggaggatcccgttctgaacgatttcaagagggagatgctcttccatcgacaggcgcaaagtgctgttctagaggccattccccgcctgcacgagctgggcataaagacccgtcggccagatgactacttcgccgaaatggccaagtctgacgagcacatgcagaaggtccgcgccaacctgatggccaaacagcaaggacaggcgaaatccgagcgcatcaagcagatccgcgaacagcgcaaaatgggcaagatgctggccaaacagaccaaggtccaacgcgaggccgagaagaaggacatgctggacaaattgaagaaattccgcaagggcaagctgaagaacctggacttcctggaggacgccaaggcgctggagtccaagcagaagcagtcagccgagaatcgcaagaagcgcaacaagaagttcggctttggaggcaagaagaagggcctcaagaggaacacaaagtcctcctccgcgggattggatggcgacaagtccacaaggcggcagcggggcgtgaaggcgggtgcttcggtcaacaaacgtcttggcaaatcgcgacgcattaaggccaagggcagaaagtag
>g4[sample:72303-73243]
atgtcggcttctgcgaatttggcgaacgtttacgcggagctaatgcgccggtgtggtgattcgtacacgatctcctatggagcaccacccacttacttggtgagcacggtgggagctgcagaagctggtaagaagattgtgctggtcttcaaggaggatcgcaatggtgcctggaccaaaaacccgaccacaccgaccaggacagtaccaaaaaaagagggctcggcggatttggatctgacgggtagtcctttaaaggacgactgcttggtggacgccatagctgacttgtccatcaacttgcagctggaccatccgatggcgtggaagctggaggaggagtaccagcgtgggatacccgtggacaaggcgaggtccattatgtgctccgagttcctgcagctggctgaaggactcggatccgtgtggtttctttgcgacggcagcgatcctgggcagactcagttgctccagtatgagttcaatcctacgcacttctccagaggaatcctaagctaccagggggtgcaccctgctttcttggtgaccccacagtccctggtgcgcc
>g1[sample:66254-68675]
atgttcgtgtcgacagtctctcgcattgcccccgttgccaggagcgccttcctcgccaactccaagcagtacctgcgaccattgagcagcgccatcatcagccagagccagactttggccgctcagaacacaacccccgttgcattgctgccacagatcaggtcattccagacctcgccagtcacgcgtgacattgactcggccgccaaattcattggcgctggtgccgcaacagtcggtgtcgctggatccggtgctggtatcggaacagtattcggttccctcatcatcggctacgccaggaacccatcgctgaaacagcagctgttctcctacgccattctgggcttcgccctgtccgaggccatgggtctgttctgtttgatgatggccttcctgctgttgttcgccttctaa
>g2[sample:69310-70561]
atggatttcgccaagaaaatacttggaaagtacggctggaaggagggcgacggcttgggcaagaacaacacgggaattgcagctccattgaaggccagtctgaagttcgataacgcgggtctgggagtggatcgcgcccaggaattcaatgaccattggtgggagcgctgctttaacgaggccgccagcaatgtggacgtccagattcagcaagacggacaggtgtccacctcccgcaggaaaggcgaggaagcggtggagatctccaccagcggattctccgcgcgtaagctgaagaaagccaaggagcagcacgccagcgatggaaagaccacctacgacaacttcctgcagacttcgctgctcacccaaggcggcaacgaagttgagacctccgagcgcatcaaggtggaggagattgaggtcgccaaggtggcggtgctcacagatgaagaactctttaaagcctgcggaggaaggactgcgcacaaaggagcacggcatggcttaaagttaagcggaaagatcgcccgcttggagcagcaggagcgcgagatgctggagaagcttcagagcaagctgaagactacgcctgaaaccactctggttccgaaaagcggaaagttgattgaggagacccagcacaaagtagcagattcagtggattgcagtgtggagcaggctacgaagcccaaaaagaagaaaaagtctaggactgaggagtccgtcgaggaaattgcgcctgcccaactggaagagcccataaaatccaagaaaaagaagaaagacaaggctgagaaggcggcaaaggaatactcaacacatcaggctcaagacgaccccgtccagatcaagaggagaaaaaataagacagggaagctagaagaggaagtccaagatgttacggaagtcgaagaggcagtgaagataaaaaagaaggacaagaggcagcaaggggtagaagcaactgaagccttaagcattgaaactgatgaacatgtaaaatccaaaaagaagcggaaaacggaagactcctcagaggaaaccgaaactcccacaaaaaccaaaaagaaaagaaagaacaaggaactcgtgtaa
>g3[sample:70677-71839]
atgtcggactttgaaatggaggacagcgcctcggggtacgattcaggtgataactcagatgccgagctgcaagcggcatttgaacgaggcgacttaaaaccaggcctaaacttggagttcaatggccagagagacaaagtgaatgatgtgaccaaactgctggcaaaaacagaggctatcaagatgcaacttccttggctggagcgcctggacatgatcaacacactggctcccctggccccggaactcgctgtacagctggagaagcacgagcaaaagcgggccaatctcttcaaaggcaacgccaagctgccctacattcggcccgaggaggatcccgttctgaacgatttcaagagggagatgctcttccatcgacaggcgcaaagtgctgttctagaggccattccccgcctgcacgagctgggcataaagacccgtcggccagatgactacttcgccgaaatggccaagtctgacgagcacatgcagaaggtccgcgccaacctgatggccaaacagcaaggacaggcgaaatccgagcgcatcaagcagatccgcgaacagcgcaaaatgggcaagatgctggccaaacagaccaaggtccaacgcgaggccgagaagaaggacatgctggacaaattgaagaaattccgcaagggcaagctgaagaacctggacttcctggaggacgccaaggcgctggagtccaagcagaagcagtcagccgagaatcgcaagaagcgcaacaagaagttcggctttggaggcaagaagaagggcctcaagaggaacacaaagtcctcctccgcgggattggatggcgacaagtccacaaggcggcagcggggcgtgaaggcgggtgcttcggtcaacaaacgtcttggcaaatcgcgacgcattaaggccaagggcagaaagtag
>g4[sample:72260-74808]
atgtcggcttctgcgaatttggcgaacgtttacgcggagctaatgcgccggtgtggtgattcgtacacgatctcctatggagcaccacccacttacttggtgagcacggtgggagctgcagaagctggtaagaagattgtgctggtcttcaaggaggatcgcaatggtgcctggaccaaaaacccgaccacaccgaccaggacagtaccaaaaaaagagggctcggcggatttggatctgacgggtagtcctttaaaggacgactgcttggtggacgccatagctgacttgtccatcaacttgcagctggaccatccgatggcgtggaagctggaggaggagtaccagcgtgggatacccgtggacaaggcgaggtccattatgtgctccgagttcctgcagctggctgaaggactcggatccgtgtggtttctttgcgacggcagcgatcctgggcagactcagttgctccagtatgagttcaatcctacgcacttctccagaggaatcctaagctaccagggggtgcaccctgctttcttggtgaccccacagtccctggtgcgccaacatggcaaggatccggatgaaaccatgatcgaaaactgctaccaggtcaatacccacatgaaactgcgctgctcctggacctctagtgcttcacttccccttctggtgaacctaaacgactgcgatgttgccttgaatcacaaatttcgcgtaggcgactgcagtgctttgacacaggacttcatgaaccagctgcgcattttggtctacatacgcgaagatatcgtctcctaccacacggatgtcaagcagggcgtctcacgggaacccacctatcgttgtggcagtgggattgacatggacgagctgcgcgagtctattaatcagacaatgacagatgtaaccagcctcattggtcattatagcataagcaatgcggagtttgacatcgaagatgtcatacagagggccaaggtgcgtcggctcacggatctgaccgataagctttgggagctgctcaagtgctgtcactcgtacaaggatcttaaaatggcctttagcatgctctttcaatgtgctgcacgatgtaacatagtaaacacgccgactaataaaaatcgactggccaagattatcaccgagttggccaatcgtcgtctggccatgccctgcttaagtggggccgagcctttggaactgcttttggagattggcctggagaagttgtacaaggactacgaattcatctataccgagagcaagatgtgcagcaccaatctgctgaaggaggactctagcgaagcaacgtcggacggtggctcccccaagaatctgccccagcttcgaaaatccctgcataatgcggtcaggggtgatccgaccccaggagcaggaatgcggaagacgctgctgcacaaccacggcgctgccaattcgcggattacaaaatatgccggtaacgacgatgatgccgggttcaaaaacagccacttcgacgagctcgagagtacggagagaatctccaagttgtttcagattcattgcaccttggaacatctgctgatgatgcacatccacttaaaccttgcaaacgtttacaacgatgtctgttctgagttgctgaagaaaccgccgaaattagtggaatccatcgatgatcagctaagtgatgtaatggacattcgcctgtctgcccactatgtcagggatcatttggatggtaaggatccctactcccggcacattaccatgcgttcgtacaacaagttccgcgaactgaagacaaccttctatttcgcttcggaaaacgtttgtccgcccaacttggctcagtgtttccagtgtgatgacaaggagatggtcaaggagcgcacctatcattcctggatatatcgcaagattcgctcacttaagtaa
>g1[sample:66254-68675]
atgttcgtgtcgacagtctctcgcattgcccccgttgccaggagcgccttcctcgccaactccaagcagtacctgcgaccattgagcagcgccatcatcagccagagccagactttggccgctcagaacacaacccccgttgcattgctgccacagatcaggtcattccagacctcgccagtcacgcgtgacattgactcggccgccaaattcattggcgctggtgccgcaacagtcggtgtcgctggatccggtgctggtatcggaacagtattcggttccctcatcatcggctacgccaggaacccatcgctgaaacagcagctgttctcctacgccattctgggcttcgccctgtccgaggccatgggtctgttctgtttgatgatggccttcctgctgttgttcgccttctaa
>g2[sample:69313-70561]
atggatttcgccaagaaaatacttggaaagtacggctggaaggagggcgacggcttgggcaagaacaacacgggaattgcagctccattgaaggccagtctgaagttcgataacgcgggtctgggagtggatcgcgcccaggaattcaatgaccattggtgggagcgctgctttaacgaggccgccagcaatgtggacgtccagattcagcaagacggacaggtgtccacctcccgcaggaaaggcgaggaagcggtggagatctccaccagcggattctccgcgcgtaagctgaagaaagccaaggagcagcacgccagcgatggaaagaccacctacgacaacttcctgcagacttcgctgctcacccaaggcggcaacgaagttgagacctccgagcgcatcaaggtggaggagattgaggtcgccaaggtggcggtgctcacagatgaagaactctttaaagcctgcggaggaaggactgcgcacaaaggagcacggcatggcttaaagttaagcggaaagatcgcccgcttggagcagcaggagcgcgagatgctggagaagcttcagagcaagctgaagactacgcctgaaaccactctggttccgaaaagcggaaagttgattgaggagacccagcacaaagtagcagattcagtggattgcagtgtggagcaggctacgaagcccaaaaagaagaaaaagtctaggactgaggagtccgtcgaggaaattgcgcctgcccaactggaagagcccataaaatccaagaaaaagaagaaagacaaggctgagaaggcggcaaaggaatactcaacacatcaggctcaagacgaccccgtccagatcaagaggagaaaaaataagacagggaagctagaagaggaagtccaagatgttacggaagtcgaagaggcagtgaagataaaaaagaaggacaagaggcagcaaggggtagaagcaactgaagccttaagcattgaaactgatgaacatgtaaaatccaaaaagaagcggaaaacggaagactcctcagaggaaaccgaaactcccacaaaaaccaaaaagaaaagaaagaacaaggaactcgtgtaa
>g3[sample:70677-71872]
atgtcggactttgaaatggaggacagcgcctcggggtacgattcaggtgataactcagatgccgagctgcaagcggcatttgaacgaggcgacttaaaaccaggcctaaacttggagttcaatggccagagagacaaagtgaatgatgtgaccaaactgctggcaaaaacagaggctatcaagatgcaacttccttggctggagcgcctggacatgatcaacacactggctcccctggccccggaactcgctgtacagctggagaagcacgagcaaaagcgggccaatctcttcaaaggcaacgccaagctgccctacattcggcccgaggaggatcccgttctgaacgatttcaagagggagatgctcttccatcgacaggcgcaaagtgctgttctagaggccattccccgcctgcacgagctgggcataaagacccgtcggccagatgactacttcgccgaaatggccaagtctgacgagcacatgcagaaggtccgcgccaacctgatggccaaacagcaaggacaggcgaaatccgagcgcatcaagcagatccgcgaacagcgcaaaatgggcaagatgctggccaaacagaccaaggtccaacgcgaggccgagaagaaggacatgctggacaaattgaagaaattccgcaagggcaagctgaagaacctggacttcctggaggacgccaaggcgctggagtccaagcagaagcagtcagccgagaatcgcaagaagcgcaacaagaagttcggctttggaggcaagaagaagggcctcaagaggaacacaaagtcctcctccgcgggattggatggcgacaagtccacaaggcggcagcggggcgtgaaggcgggtgcttcggtcaacaaacgtcttggcaaatcgcgacgcattaaggccaagggcagaaagtag
>g4[sample:72303-76647]
atgtcggcttctgcgaatttggcgaacgtttacgcggagctaatgcgccggtgtggtgattcgtacacgatctcctatggagcaccacccacttacttggtgagcacggtgggagctgcagaagctggtaagaagattgtgctggtcttcaaggaggatcgcaatggtgcctggaccaaaaacccgaccacaccgaccaggacagtaccaaaaaaagagggctcggcggatttggatctgacgggtagtcctttaaaggacgactgcttggtggacgccatagctgacttgtccatcaacttgcagctggaccatccgatggcgtggaagctggaggaggagtaccagcgtgggatacccgtggacaaggcgaggtccattatgtgctccgagttcctgcagctggctgaaggactcggatccgtgtggtttctttgcgacggcagcgatcctgggcagactcagttgctccagtatgagttcaatcctacgcacttctccagaggaatcctaagctaccagggggtgcaccctgctttcttggtgaccccacagtccctggtgcgccaacatggcaaggatccggatgaaaccatgatcgaaaactgctaccaggtcaatacccacatgaaactgcgctgctcctggacctctagtgcttcacttccccttctggtgaacctaaacgactgcgatgttgccttgaatcacaaatttcgcgtaggcgactgcagtgctttgacacaggacttcatgaaccagctgcgcattttggtctacatacgcgaagatatcgtctcctaccacacggatgtcaagcagggcgtctcacgggaacccacctatcgttgtggcagtgggattgacatggacgagctgcgcgagtctattaatcagacaatgacagatgtaaccagcctcattggtcattatagcataagcaatgcggagtttgacatcgaagatgtcatacagagggccaaggtgcgtcggctcacggatctgaccgataagctttgggagctgctcaagtgctgtcactcgtacaaggatcttaaaatggcctttagcatgctctttcaatgtgctgcacgatgtaacatagtaaacacgccgactaataaaaatcgactggccaagattatcaccgagttggccaatcgtcgtctggccatgccctgcttaagtggggccgagcctttggaactgcttttggagattggcctggagaagttgtacaaggactacgaattcatctataccgagagcaagatgtgcagcaccaatctgctgaaggaggactctagcgaagcaacgtcggacggtggctcccccaagaatctgccccagcttcgaaaatccctgcataatgcggtcaggggtgatccgaccccaggagcaggaatgcggaagacgctgctgcacaaccacggcgctgccaattcgcggattacaaaatatgccggtaacgacgatgatgccgggttcaaaaacagccacttcgacgagctcgagagtacggagagaatctccaagttgtttcagattcattgcaccttggaacatctgctgatgatgcacatccacttaaaccttgcaaacgtttacaacgatgtctgttctgagttgctgaagaaaccgccgaaattagtggaatccatcgatgatcagctaagtgatgtaatggacattcgcctgtctgcccactatgtcagggatcatttggatggtaaggatccctactcccggcacattaccatgcgttcgtacaacaagttccgcgaactgaagacaaccttctatttcgcttcggaaaacgtttgtccgcccaacttggctcagtgtttccagtgtgatgacaaggagatggtcaaggagcgcacctatcattcctggatatatcgcaagattcgctcacttaaatacccctttggtctagtcaccccaacttattctcagaaacttttccagacacaccacctaatccttttggcaaagtcgtcgggcctcgagtttttctttaagttcggctatgccttcctgacaataaccctcatgatcatgatctggatgtcgctggcccgtgcctcgatgttcgatcgagagatggaggaaacgcactacccgccctgcacctacaacgtgatgtgcacctgctccaagtcctctacggatctggggatagtgcactgcaagaatgttccgtttccggcactgccgcgcatggtgaaccagtcaaaggtcttcatgctgcacatggagaacacgggtctgcgcgagattgagccctacttcctgcagtccacgggcatgtaccgcttaaagatctctg
>g1[sample:77357-81759]
ggagatctacatgcgctattgcggcctgaccaacatctcgcctgtggcctttgacagcctggtgaacagcctccagatcctggatttgtctgggaacaatctcaccaagctgcatcacaagctcttcaacaatttcgatgtcttgagggtcatcagcatgcgggacaataagatcaagattcagaagcccacggagaccttcaatgcggtgcactacacgctcctgaaactggacctgagtggtgaccgcaacgaccccaccaatctgcagacccttcgcaaaatgcggaacatgcgatcactgtcgatctcgcgcctgggatcctcctccgttgggcctgaggacttcaaggacttcggcgtggagctggaggacctgcaaatcaccagggccagtctctccgggattcaatcacacgctttcaagcatgtcaggggtctgaaaaggctggacttcagcgagaacggaatatctagcattgagaacgatgccttccatgagattggtcactcgctcatctctctgaagatgtcgcacggctactctggcagttccctgccagctgaacctctgagacatctgacttcccttcaagagctggactttagcaacaatcacatcagcagcatgagcgacaccagtttccatttcctgaagaacttgcgtctcctagagcttcatgacaacaggatcgaacaggttttaaagggcactttccagggcgacattcactcaaagctggaggagatctcgcttcgcttcaaccacctgacctccatttcccagcataccttcttcgatctggaagccctgagaaaactgcacctggatgacaataagattgacaagattgagcgaagagcctttatgaatctggatgaactggagtatcttagtttgaggggcaacaagataaacaacctggctgacgagtccttccagaaccttccaaaactggagatccttgacatggcttttaatcagctacccaacttcaactttgactacttcgatcaagtgggcaccttgtcgaatcttaatgtgaaccttcggttcttaggtggcatgtatcactcgaacatcaagacattggatctttcccacaacaacatatctattattcatcctggatacttccggcctgccgaaatttcactgacacacttgcatctgggctacaattcgctgatgaacacgactcgagatgtcttcggcaacatgccccacttgcaatggctggacctcagctacaattggatccacgaactggactttgatgcctttaaaaacaccaagcagctccagttggtcttctttgatcacaattacctcactgatattccccaggatatattcaaacctgtccagagcctgcgcatcgtcgatttctcgcacaatcacttgaggggcctgcccgacaatctcttctataatggaggaatggaaaaattggatgtgtcgcacaacatgatgctgaagatcccctcctcatcgctgtccagtttggctgcgttgacgctttgtgaattgcacctgtccaacaactttatctctaccattcacagcatggatttgtccaacaagtttagatcacttcgctacctggacatctcatacaactatctgctgcgaattgatgatgccgtttttgcaaccatgccaaaattggccgttctggatctctcccacaatcgggatctgaaggtgatggataagtcgtttatgggtttggagaactcgctgatcaaactgggtctggagaacgtttctctgagcacagtgcccgagattcgactgaagtatctgcgggagttccgtttgggttacaatgaactgccttcgattccgcaggaactagcccacaatatgactaatctgcgcatgctggacctctccaacaacgacttaacaaatgtgccactgatgacccaagctctcccccacttgagacgcctgatgctctccggcaatcccataacctcgctgaacaacaacagtttcgatggcgtgaacgaggatcttgagatgctggatatatcgaatttccggttgcactatttcgagtatggctgtctggactcgttgccccacttgcgatcccttaagcttactgcgtactcccatctggagcacttcaatatcccacatctgttgcgccatcattataatatccgccagttgtggatcgaggccccacagcccttcacccgcattgttaagaagggatctggacccacccaggagatgcagacccttcagctgggcaatcccaccgacttgctgcgcgaaatggagggccatctgccctccaagctgaccaacatcaccttcagtggtcctcagttcactaacctgaatgaacgcattttaagaggcatgcgttctccatacctctacatgcaactattcaatacctctctgcaagccttgcctcctaacttctttaagtacatgggccgagttcggaacatttcgctggacattcgctaccacaatcggaacctgaagaagattccaaatccaaacacaggagctgttccctatctgccgaatagtgtgttcctcacggacttgaagatgtctcacactgatctcaactgcgactgcgacctggggtgggtggagttctggcaacgcaagaggcgccagtacatctgctcctcccaaacctggaccgacaccgttttccgcactttcatgaactctccttgccaggtgtacggtcgccacaactgcgacgaacatgatgatgacctgagggagacgcgctgtgaaaacaaaggagggcagcagctgatggaggccctcaaattcgatctggagtgcgggtgggacaatgcaaactgccgggaggccgcctttgtggtggtgatggtgtgcgtggccatggtcttctggatgtga
>g2[sample:81792-89171]
atgttgcgctatctggcactttcggaggcgaaaatcgcaagactgccacgccctctatcgcgatgctatcacagcgaaaaaggcgtttggggctataagccagttgcacagcgtgaatatcaagtggccgaggatgtgcgggcctccaggaactcgcaggccaacgtctatcgctttgtggaggcctttcgccagcacgggcacaaattggcagccgtaaatcccatcagcatcaggacgaggcagccggagctgcaggaattaagtcccgcattttatggactgcagacacaggagccggtgcgcaccgatggccttttaagtggtccgcaggtggcccagaatgtcgcccagctggagcagctgctcaaggacatttactgcggccgctcaaccagcgccgagttctcctatgtcgaggacatcgaggagcgcgagtggctggcccggaactttgagacgctggaccagcagcagctggcaaacagcgagcgttgcgaaatcgccgagctgttaattaagtcgcaggcctgggagaatttcatggcactcaagtttcccacattcaagagatacggaggcgaaggtgccgagtccatgctggccttcttctggcaactgctccgtgacagtgtccaagagctcgtgcgtgtggaccgcttcttaaacgcgattagcgaaacgcggaatcgcgcacccatttcaaggcgccaaactttgtctcgtgacagtccgcaggcaggctcacatatcatcgcacgcttacttaaccctaatctgctttcccaaaacttttccctctcgcatgcaaccccgaaaaacggaaacaacggaaacgacgacgacaacgataaaaaattctacaatggaatgacagcgaacatcgagcacgtggtcctggcgatgccccatcgaggaaggacttcgctgcaggcggcgctcttcaacatgcggccggcgaaagttttccgcaaactcagcggcgcatccgagtttcccgaagacgtcgaggccatgtccgacgtcataagtcatttccatgtttccgagcagctggaagtactgggcaagaagctgaactttactatggtgcggaatccctcccatctggaggctgccaatcctgtggccatgggaaaaacgcgatcgaagcagcaagcaagaggtgaaggagccttcggggatagtggtcagcccttggggcaacacgtgctcaacgtaatccttcatggagatggtgcgttcgccggccagggagtcaaccaggagtgcctcaacatggcctacgtgccccactttgaggtgggcggaagtgtgcacttgattgtcaacaaccaggtgggattcaccacgccaggagatcgcggacgatccactgcctacccgtcggacttggccaagtccattcaggctcctgtgttccatgtcaatggctgtgatcccgaggctgtggccaggatcacaaacttggcctttagatatcagagagagttccgcaaggacatctttattgatttgaactgcttcagaagatggggtcacaatgaattggacgaccccacctttaccagtcccatggtgtataagatagtcccccagctgggattggtcccagacgtgtacgcccagcagttggccaaggagcaggttctcccggagtcgaaggccaaagaaattagggaggagttcatgaaatatctgggtgaggaacttgccttggctcctacctaccagccaccaccttcttacttcgaaagtcagtggaaggagcttcagttggctccctccaaggaactaacctattgggacactggcttggattactcgctacttcattacattggtcagcagagtgtgactttcccagaagactttaacgtccacccccacctgctgaaaacgcatgtcaatgcccgactcaagaaactggaaaacggagtcaagatcgattggtctacagccgaagccatggccattggcagcctgatgtaccagggacacaatgtgaggatcagtggcgaggacgtgggccgaggaaccttctcccatcgccatgccatgctggtggatcagcagaccaacgagatgtacattcccttgaacaacatggagggcggaaacggtggaaaactggaggtagctcacagtactttgtcggaggaggcggtgctgggattcgagtacggcatggccattgacaaccccaacaatctgattatctgggaagcgcagtttggcgactttgccaatggagcacaaattataatcgacaccttcattgtcacgggagaaaccaggtggatggagtccaatgccttagtgatgctactgccccatggatacgatggcggtgcatcggagcacagttcctgtcgcatcgagcgcttcctgcagctcagcgactccaaggaaacgtccgccgatggcgattccgtcaacgtgcacgtcgtgaaccccaccacgcccgcccaatactatcacgtactgcgtcgccaactggcaaggaacttccgcaagcccctcgtggtggtggcccccaaaacgctgctccgccttcctgtggccacatccacgcacgaggacttccagccgggcacgctcttccaaaatgtcctgggagacaccactgcgaagccggagcaggtgcgcaaggtcatcctgtgcagtggaaagcactactacgctctcgccgaggagcgcgagaagcgtcaggcctacgacacggccatcctgcgcctggagtccctgagtcctttccccgtccaggagctgcaggcccagctggcccaatacggcaacgtgcaatcttttgtttggagccaggaggagcatcgcaacatgggcgcctggacgtttgtgcggccacgttttgaaaatttaattggccaaaagctccactacagcggtcgctgcgaggcacccaccaacgccactggaatcggaaatgtgcataagcgggaagttgatgagattcttgctggcccatttgaactttga
>g3[sample:90522-91693]
atgcgtttcaaactgtttgtggtttgtgcgctggcctgcggctttatggcctatgtcctggctaacgagaatatatcgacggaggagtttgaggatcaaataatcaatgcagttccggaaccggtcaaggtgactaagcccaaatctcaggcggaatttgttgaggttccaaaggccacgcccgcgcccaagaaagcggtggaggaaaagccaaaaaccaatcccctggccctgcagaagcccactctgattcccgtggtgcatgtcaccagtcggggcacagatgatgtcctcaccgtcgcgggattgaagcccgagaaaatgtttggagccctcgtaatgcaaaatgagtacttgggcgagctgtacgacgtggacaacagcggctacaattgggaacagctcagtgggtttcagttcggtttagtttaccaatatttgctcgataacctgtgctcgggccttcaggtgtag
>g1[sample:164350-165618]
atggcggtggcaagtgccgccaactctggtcgggactacctgccacgcccccaggccagagcctatgtctacggcacgcccccgcccagcacgatggcccagctgcggcggataatccaaggtcacctggagcgcttccagcaggctgagcagacccacttttcccgccgcgccaacgtgcagctggggaaatcggaactgccggcggagagaaaaccgctggcgatgcaactgtgggtggttcgcacgcccgccgtttccggcgcggcctcggataacgtcctcgattacgccctgccgcccaacacacccactccgaaggactacgcgcacaaattcctgcccgagggcaaggatgtggtacccggaagctcttacataccgctgcggttggtggtgataaagcgctga
>g2[sample:168309-169293]
atggcgcgtctctacgattcccgcaccacgatcttttcgcctgagggccgactgtaccaggtagagtacgcgatggaggccgcttcgcagtcgaacacttgcctgggcatcctggccaagaacggagtcattttggctacggagcgaagcgtggacaagctcttggactcgagcattcctgcgcccaggatctgcaggctgaacgaggacgctgcctgttgcgccacgggcaacaaggcggatggaaacgtgctgaccaccgaattgcgcctgatcgcccaacaatatgttagcacctacggtgagatgattccttgcgagcagctggtcacgaacctgtgtgacatcaaacaggcgtatacgcaatacggcggcaagcgacccttcggggtatcctttctgtacatgggctgggactgccgcttcgggttccagctgtatcagtccgatcccagtgggaactacagtggctggaaggccacatgcattggccgcaaatcaggggcggccatggaaatgcttcagaaggaactattcagcaagggctacgcaagtccctcgctcgaggaagccaaggatgtagccatcaaggtcatgggcatgaccttggatagagatagcttgacccctgcgaagctggaaatggctgtactacagcgcttctataacaccaccatatttcatatcttagagaaaattgaggtacacaacctaattcagaagcataacattttgcagtttcaaatcgccaggcgaaagtattaa
>g1[sample:228113-231702]
atggagctgcgcgtgggtaacaaataccgcctgggccgtaagataggatcgggatcgttcggcgacatctacctgggaaccacgatcaacactggcgaggaggtggccatcaagctggagtgcatccgcaccaagcacccccagctgcacatcgagtcgaagttctacaagacgatgcagggcggcataggtataccccgcataatctggtgcggcagcgagggcgactacaatgtgatggtgatggagctactcggaccctcgctggaggacctcttcaacttttgttcgcgccgcttttcgttgaagacggttctgctgctggcggaccagatgatctcccgcatcgattacatacactcgcgggacttcatccatcgcgacattaagccggataacttcctcatgggtcttggcaagaagggcaacctggtgtacatcattgactttgggctggccaagaagttccgggatgcccggtcgctgaagcacattccctatcgggaaaacaagaacctcacgggcactgcccgctatgcctccatcaacacacatttgggcattgagcaatcgcgtcgcgacgacctggaatctcttggctatgtcctcatgtacttcaatctgggagccttgccctggcagggcctaaaggcagccaacaagaggcaaaagtacgagaggatctccgagaagaagctgtccacttcgattgtggtgctgtgcaagggcttccccagcgagttcgtcaactatctgaacttctgtcgccagatgcatttcgaccagcgtccagattactgccacctgcgcaagctcttccggaacctgttccaccgattgggcttcacttatgactatgtgtttgactggaacctgcttaagtttggcggaccacggaatcctcaggccattcagcaggcgcaggacggcgcggacggtcaggcgggacatgatgccgtggccgcagcagcggcagtggcagcagcggcagccgcctcctcgcatcaacagcagcagcacaaggtcaatgcggcgcttggcggcggagggggcagtgcagcgcaacagcaactccagggcggccaaacgctggcgatgctgggcggcaatggaggcggaaacggcagccaactgatcggcggcaacggactcaacatggacgactcgatggcggccaccaactcgtcgagaccgccctacgacacgccggagcgtcggccctcgatacggatgcgccagggaggcggagcaggcggcggtggagtgggtgtgggcggtatgcagagcggcggagggggcggtggcgtggggaacgccaaataa
>g2[sample:232880-234117]
atgggagcccgacagtctcaatcccgcgaggcccgatccgtttcgatggaaaacccaactcctgccggcgttattgatatatccgacgatgtggtcaagcgattgaaggcgggaatatcccagcaggctcgtgagcacgcagccgctgcggaggactcgaagccggcgcccaagccaacggcaaaggctgctgccaagccagccgcatcctcgccagctgctcctgctccgaaagtatcctcctatcccgctgcagtgcccatttacgtccagggaggaggacacaccatcagcgcggctgatgtgcagcgccagatgaaccaggagctgattaagaacgacgagctgtggaaggagcgcatggccaagttggaggagaacctcaagaagaccaacaccatcctggagaaggagtatgccaatgctgtagacaatgtgcacaagcgattcgtcagcaccgcgtcgtcgcacaaagtgcctccctgccaggacctgaaatcccagctgctcgcctgctaccgcgcgcatcccggagagaccttgaaatgcatggaggaggtggcccagttccgacagtgcatcgatctgcatcgcgtccagaagctggatgcggaaccagagacgctgaaagttgccaaggcggcctag
>g3[sample:234179-238509]
atgcattccgaggtactagtcggattcctgtgggctggcctgctggcgttcagctgggcaggagtcaccacccagccgccgccactgattcgcaccctgagtgccggaggagacataggaccccagtttgatgtgggcaagcacaaggaacccgaagatgcggaattctggcacaaagtgggcctgcggcagctggagaagaccattaagcaggcccagcgggtgaaggagcactcctaccagaagaaggcccggaacatcatcatcttcatcggggacggcatgggagtatccacgatcagtgctgggcgcatctacaagggacagtacctgaagcacggccacggcgaggaggaacatctcgtcttcgacgatttcccaaacactggaatggccaagacttacaatgtggacaaacaggttccggactcggcgggcactgccactgcgatcttctcgggatcgaaaacccactacggagccattggaatggatgccacccgctccaagaagaacggccagcagggcagggtccaaagcgtcatggagtgggcccagaaggagggcaagcgtactggagtggtcaccacaaccaggatcacccatgccacgcctgccgccacgtacgcccacatctacgaccgggattgggagtgcgacacggaagtgcccgcggaatcggtgggcattcatgttgatattgcccgtcagttggtggaaaatgctcctggaaatcgattcaatgtaatcctgggcggaggaatgtcccccatgggcatcctgaatgcctccgaggtgaagactacgatttttgaaggacccacggaaacaatttgcagccgaggtgataaacggaatcttccggccgagtggttggctcatcacgccaacgatacagttcctccagcattggtacacaaccggaacgatctgctcaatgtgaatgttaaggaggtggaccacttgatggggctgttccgaaacaatcacatcacttactccatagccagagaggaaggagagccttccctgcaggagatgacggagacggccttgggaatcctagaaagaggcgacgagtcaaagggttatgtgctcctagtagaaggcggtcgcattgaccagggtcaccacatgaactatgcccgtgctgcccttcatgagctgtacgaattcgatttggcaatccaagcggccgtgaacaacacagatcccgaagaaacgttgatcctggtgaccgccgaccattcccacgcggttaccttcaatggttacgccctccgaggagctgatatcctgggaacagccaattcgcacgagaaaaacgatcccatgttctacgagaccatctcgtatgccaatggtcctggatattgggatcacttggcgaatgactccagacctcagaacagttccaacatgtggatgcccttgaagcattttacggaagaggagaggactgcacccacctatcgccacttggcaacggtgccgagaaaggatgaaacccacggcggcgaggatgtggctgtttttgcatatggccctggatccagtttggttcgcggggtcttcgagcagaactatttggcctatgtgatgagctacgcgggctgcttgggtcccgccaaggacttcgacgactcttgcgaggatcataaggatgagcaaagggagaggccgctgaacaaaccgaatcccaagagaagtggtgcctctgatttgggaacctccttgatccccatcgtgactgcagccactgcgggtattttatgcggtcacaggctgtaa
......@@ -6,7 +6,7 @@
# Using protein profile unknown
# --[0..111]--> unknown_A (17) <--[0..101]--
# fly version. Use default transition matrix.
# Looks like ./tmp/sampleSAMPLE_3715919971_.temp is in fasta format.
# Looks like ./tmp/sampleSAMPLE_1214242381_.temp is in fasta format.
# We have hints for 0 sequences and for 0 of the sequences in the input set.
#
# ----- prediction on sequence number 1 (length = 10482, name = sample) -----
......@@ -25,6 +25,18 @@ sample AUGUSTUS CDS 27827 28553 0.85 - 0 transcript_id "g1.t1"; gene_id "g1";
sample AUGUSTUS exon 27827 28731 . - . transcript_id "g1.t1"; gene_id "g1";
sample AUGUSTUS start_codon 28551 28553 . - 0 transcript_id "g1.t1"; gene_id "g1";
sample AUGUSTUS tss 28731 28731 . - . transcript_id "g1.t1"; gene_id "g1";
# coding sequence = [atggaggcatctgctgccaaaatcacacccatggccagttccacgtccacttccggatccataaactccccttccagtg
# acaaaatgaactacgcactccaagtggcgctgcaaactatcaaggagcggtgcatccagctgcagcgccgcgtggccagcatggaggaggagaaccag
# cgactgagggaagcctccagcaggtcagaaggtgctccaactgcaaaggaaatcggggtcactggggatgtactctccctcaaagcccaggtctctga
# gctgcagcgccaaaaggagcagctggaggagcacattagcatggtgtccaacgagaacagacgcctctggtcccgtctgtcgcagatctccaaggatc
# agcagctaaacgcagtgcccagctcatccgactcgcgtgcccagcaaaaccagaacctggtgcgctccaagacctttacgcaacactcccccaatcct
# caccttcgccaaaagatgctgtcagacgggataaaggatctcagcctggaggaaatagccttggatgacttcggtgccagtagcggggaactaggtta
# cccttacaacctgcaaaaggtggaggaaaccaccagtgaacctgatgccaatgtggatgccaaaagatgtatggatggactgcaggagatgaggcgag
# aggccatgaagcagcagcaggagctcagttcggctctgactttactagaaagtcgcatagcactgaagccctgtccggaatgtgcccagaaaaccttc
# aaaaagccggagatggccgacaaaagtctggaaacggacgacagcctgaccagcgaactgaagaactatgagagccagcacaatggacacaatggaac
# accgcccagccagagaatcaatatcatacaagagaaaatcaaagcagacgcagccgatgcaatggagaagatctgccctatgtgcggcaagcagtact
# ccagccaagtgtctttcaatgccttccgcgagcacgtcgagatgcacttcatcgacgatgcactggagttggaatccgagaacagcatggagcgccag
# ttcgagtttgtttcccatgcg]
# protein sequence = [MEASAAKITPMASSTSTSGSINSPSSDKMNYALQVALQTIKERCIQLQRRVASMEEENQRLREASSRSEGAPTAKEIG
# VTGDVLSLKAQVSELQRQKEQLEEHISMVSNENRRLWSRLSQISKDQQLNAVPSSSDSRAQQNQNLVRSKTFTQHSPNPHLRQKMLSDGIKDLSLEEI
# ALDDFGASSGELGYPYNLQKVEETTSEPDANVDAKRCMDGLQEMRREAMKQQQELSSALTLLESRIALKPCPECAQKTFKKPEMADKSLETDDSLTSE
......@@ -52,6 +64,16 @@ sample AUGUSTUS CDS 30008 30091 0.93 + 0 transcript_id "g2.t1"; gene_id "g2";
sample AUGUSTUS exon 30008 30181 . + . transcript_id "g2.t1"; gene_id "g2";
sample AUGUSTUS stop_codon 30089 30091 . + 0 transcript_id "g2.t1"; gene_id "g2";
sample AUGUSTUS tts 30181 30181 . + . transcript_id "g2.t1"; gene_id "g2";
# coding sequence = [atgttttgcggcaagagtttagtcaataatttctacaaatataagagaaagatgtggcagaatgtagtcccaataatac
# agcgtggcaagggaacttaccacccactaaaaattctctttttcggcaccgattacttttccttgcccagcttacaggcgctacacaaaaactgcggt
# gaccacttgggagttgttacctccttcaaaaatcccgccaactgtgtgaggacctatgcggaaaaggagaagcttcccctgcaaaagtggcccataga
# tccatctgtgtgtcctaagtttgacctgggcgtcgtggtttcctttggccacctgattcctgctaatatcatacatggatttcctaatggaatgatca
# atgttcatgctagtctattgcccaggtggcgaggagctgctcccatcatatatgcgatcatgaagggagatgccatcactggggtttccatcatgaaa
# atcgaacctcaccggtttgatattggtgcaattttagctcagcgggaggtggcgattgagcccaatgtcttcatgccggacttgcacgcatctttggc
# gtcgttaggggcagatttactagtggatacggttaacaacctgtcagtacgacttaaggaagccaaaccccaggatagtacaaagaccagctatgctc
# ccaagatcaccagtaaaataacagaagtcaattggtcggagctgagtgcccttgacatatacacgcgtcatagagctttgtttggctacaaaaacctt
# accaccagctttttgagcaagcaagtgcagctgctagagctacctgaggaaggcgagatccctggtaattggatgtgctcagcacagccagttggagg
# tgcttcaattacgcgtagaaggtag]
# protein sequence = [MFCGKSLVNNFYKYKRKMWQNVVPIIQRGKGTYHPLKILFFGTDYFSLPSLQALHKNCGDHLGVVTSFKNPANCVRTY
# AEKEKLPLQKWPIDPSVCPKFDLGVVVSFGHLIPANIIHGFPNGMINVHASLLPRWRGAAPIIYAIMKGDAITGVSIMKIEPHRFDIGAILAQREVAI
# EPNVFMPDLHASLASLGADLLVDTVNNLSVRLKEAKPQDSTKTSYAPKITSKITEVNWSELSALDIYTRHRALFGYKNLTTSFLSKQVQLLELPEEGE
......@@ -76,6 +98,13 @@ sample AUGUSTUS exon 31215 31421 . - . transcript_id "g3.t1"; gene_id "g3";
sample AUGUSTUS tss 31421 31421 . - . transcript_id "g3.t1"; gene_id "g3";
sample AUGUSTUS protein_match 30482 30486 2.3 - 2 target "unknown_A[16..17]"; target_start 93; transcript_id "g3.t1"; gene_id "g3";
sample AUGUSTUS protein_match 30543 30588 8.96 - 0 target "unknown_A[1..16]"; target_start 93; transcript_id "g3.t1"; gene_id "g3";
# coding sequence = [atgtccagaaatttgtttttatcaattacaaacttatttaggaacttggagagcctgttcctgccacatggaggacacc
# ctcctgctctagcgttggccggttttcagcatgatcacagccatagatcctcccaggaattcagtttgaagcagcttattggcgacggaatgctgtgg
# gctgttccgaaacacaggagatccgtggagaaacgcctgaagcggaagttcggatatccggaatacaattggaagcctctgagggagaagaggaacat
# ccgctcctgtctgcaatgtggccatgaccacgagatgggggttctttgtcctttctgctaccaaaaagtcctgaaggagactgagctcatgcagtcga
# aaatccaggagacactgggtctagatcccgtggacaaggaagtaatcgttctttatgagggcgagaaagccgaacagtcctcagatgagctgaaaaac
# aaacgcatcgtggagatgaagaagcctcgtcccatgtggttcaccaagaatctgctccaaaaatccacgcagcaattgtccgaaaccaaggaagtcaa
# gccctccgacttggcctag]
# protein sequence = [MSRNLFLSITNLFRNLESLFLPHGGHPPALALAGFQHDHSHRSSQEFSLKQLIGDGMLWAVPKHRRSVEKRLKRKFGY
# PEYNWKPLREKRNIRSCLQCGHDHEMGVLCPFCYQKVLKETELMQSKIQETLGLDPVDKEVIVLYEGEKAEQSSDELKNKRIVEMKKPRPMWFTKNLL
# QKSTQQLSETKEVKPSDLA]
......@@ -90,9 +119,12 @@ sample AUGUSTUS start_codon 32021 32023 . + 0 transcript_id "g4.t1"; gene_id "g4
sample AUGUSTUS CDS 32021 32275 0.67 + 0 transcript_id "g4.t1"; gene_id "g4";
sample AUGUSTUS stop_codon 32273 32275 . + 0 transcript_id "g4.t1"; gene_id "g4";
sample AUGUSTUS tts 32490 32490 . + . transcript_id "g4.t1"; gene_id "g4";
# coding sequence = [atggcctgcttgagcacttccggtcgcgtcgtctgcggctcccgtcgccagcagacgcacaagctgctctaccagctat
# tcggatcccggccaggatatacagccccatccaccgcgaccggattattcagtccgcccaaagtccaacagcaggccatgcgactctgccacggatta
# agcttcagcttgggcaaggattaccccgatctgctggtaagttcattgccggatgaagcctacaccgcgaaaaaatag]
# protein sequence = [MACLSTSGRVVCGSRRQQTHKLLYQLFGSRPGYTAPSTATGLFSPPKVQQQAMRLCHGLSFSLGKDYPDLLVSSLPDE
# AYTAKK]
# end gene g4
###
# command line:
# augustus --proteinprofile=sample_data/example/prfl/BUSCO_1.prfl --predictionStart=25227 --predictionEnd=35708 --species=fly ./tmp/sampleSAMPLE_3715919971_.temp
# augustus --codingseq=1 --proteinprofile=sample_data/example/prfl/BUSCO_1.prfl --predictionStart=25227 --predictionEnd=35708 --species=fly ./tmp/sampleSAMPLE_1214242381_.temp
......@@ -6,7 +6,7 @@
# Using protein profile unknown
# --[0..348]--> unknown_A (44) <--[0..8]--> unknown_B (36) <--[0..13]--> unknown_C (16) <--[1..27]--> unknown_D (73) <--[0..15]--
# fly version. Use default transition matrix.
# Looks like ./tmp/sampleSAMPLE_3715919971_.temp is in fasta format.
# Looks like ./tmp/sampleSAMPLE_1214242381_.temp is in fasta format.
# We have hints for 0 sequences and for 0 of the sequences in the input set.
#
# ----- prediction on sequence number 1 (length = 24405, name = sample) -----
......@@ -26,6 +26,18 @@ sample AUGUSTUS CDS 27827 28553 0.82 - 0 transcript_id "g1.t1"; gene_id "g1";
sample AUGUSTUS exon 27827 28665 . - . transcript_id "g1.t1"; gene_id "g1";
sample AUGUSTUS start_codon 28551 28553 . - 0 transcript_id "g1.t1"; gene_id "g1";
sample AUGUSTUS tss 28665 28665 . - . transcript_id "g1.t1"; gene_id "g1";
# coding sequence = [atggaggcatctgctgccaaaatcacacccatggccagttccacgtccacttccggatccataaactccccttccagtg
# acaaaatgaactacgcactccaagtggcgctgcaaactatcaaggagcggtgcatccagctgcagcgccgcgtggccagcatggaggaggagaaccag
# cgactgagggaagcctccagcaggtcagaaggtgctccaactgcaaaggaaatcggggtcactggggatgtactctccctcaaagcccaggtctctga
# gctgcagcgccaaaaggagcagctggaggagcacattagcatggtgtccaacgagaacagacgcctctggtcccgtctgtcgcagatctccaaggatc
# agcagctaaacgcagtgcccagctcatccgactcgcgtgcccagcaaaaccagaacctggtgcgctccaagacctttacgcaacactcccccaatcct
# caccttcgccaaaagatgctgtcagacgggataaaggatctcagcctggaggaaatagccttggatgacttcggtgccagtagcggggaactaggtta
# cccttacaacctgcaaaaggtggaggaaaccaccagtgaacctgatgccaatgtggatgccaaaagatgtatggatggactgcaggagatgaggcgag
# aggccatgaagcagcagcaggagctcagttcggctctgactttactagaaagtcgcatagcactgaagccctgtccggaatgtgcccagaaaaccttc
# aaaaagccggagatggccgacaaaagtctggaaacggacgacagcctgaccagcgaactgaagaactatgagagccagcacaatggacacaatggaac
# accgcccagccagagaatcaatatcatacaagagaaaatcaaagcagacgcagccgatgcaatggagaagatctgccctatgtgcggcaagcagtact
# ccagccaagtgtctttcaatgccttccgcgagcacgtcgagatgcacttcatcgacgatgcactggagttggaatccgagaacagcatggagcgccag
# ttcgagtttgtttcccatgcggtgggtgacttctga]
# protein sequence = [MEASAAKITPMASSTSTSGSINSPSSDKMNYALQVALQTIKERCIQLQRRVASMEEENQRLREASSRSEGAPTAKEIG
# VTGDVLSLKAQVSELQRQKEQLEEHISMVSNENRRLWSRLSQISKDQQLNAVPSSSDSRAQQNQNLVRSKTFTQHSPNPHLRQKMLSDGIKDLSLEEI
# ALDDFGASSGELGYPYNLQKVEETTSEPDANVDAKRCMDGLQEMRREAMKQQQELSSALTLLESRIALKPCPECAQKTFKKPEMADKSLETDDSLTSE
......@@ -53,6 +65,16 @@ sample AUGUSTUS CDS 30008 30091 0.92 + 0 transcript_id "g2.t1"; gene_id "g2";
sample AUGUSTUS exon 30008 30181 . + . transcript_id "g2.t1"; gene_id "g2";
sample AUGUSTUS stop_codon 30089 30091 . + 0 transcript_id "g2.t1"; gene_id "g2";
sample AUGUSTUS tts 30181 30181 . + . transcript_id "g2.t1"; gene_id "g2";
# coding sequence = [atgttttgcggcaagagtttagtcaataatttctacaaatataagagaaagatgtggcagaatgtagtcccaataatac
# agcgtggcaagggaacttaccacccactaaaaattctctttttcggcaccgattacttttccttgcccagcttacaggcgctacacaaaaactgcggt
# gaccacttgggagttgttacctccttcaaaaatcccgccaactgtgtgaggacctatgcggaaaaggagaagcttcccctgcaaaagtggcccataga
# tccatctgtgtgtcctaagtttgacctgggcgtcgtggtttcctttggccacctgattcctgctaatatcatacatggatttcctaatggaatgatca
# atgttcatgctagtctattgcccaggtggcgaggagctgctcccatcatatatgcgatcatgaagggagatgccatcactggggtttccatcatgaaa
# atcgaacctcaccggtttgatattggtgcaattttagctcagcgggaggtggcgattgagcccaatgtcttcatgccggacttgcacgcatctttggc
# gtcgttaggggcagatttactagtggatacggttaacaacctgtcagtacgacttaaggaagccaaaccccaggatagtacaaagaccagctatgctc
# ccaagatcaccagtaaaataacagaagtcaattggtcggagctgagtgcccttgacatatacacgcgtcatagagctttgtttggctacaaaaacctt
# accaccagctttttgagcaagcaagtgcagctgctagagctacctgaggaaggcgagatccctggtaattggatgtgctcagcacagccagttggagg
# tgcttcaattacgcgtagaaggtag]
# protein sequence = [MFCGKSLVNNFYKYKRKMWQNVVPIIQRGKGTYHPLKILFFGTDYFSLPSLQALHKNCGDHLGVVTSFKNPANCVRTY
# AEKEKLPLQKWPIDPSVCPKFDLGVVVSFGHLIPANIIHGFPNGMINVHASLLPRWRGAAPIIYAIMKGDAITGVSIMKIEPHRFDIGAILAQREVAI
# EPNVFMPDLHASLASLGADLLVDTVNNLSVRLKEAKPQDSTKTSYAPKITSKITEVNWSELSALDIYTRHRALFGYKNLTTSFLSKQVQLLELPEEGE
......@@ -75,6 +97,13 @@ sample AUGUSTUS exon 30837 30936 . - . transcript_id "g3.t1"; gene_id "g3";
sample AUGUSTUS start_codon 30919 30921 . - 0 transcript_id "g3.t1"; gene_id "g3";
sample AUGUSTUS exon 31215 31415 . - . transcript_id "g3.t1"; gene_id "g3";
sample AUGUSTUS tss 31415 31415 . - . transcript_id "g3.t1"; gene_id "g3";
# coding sequence = [atgtccagaaatttgtttttatcaattacaaacttatttaggaacttggagagcctgttcctgccacatggaggacacc
# ctcctgctctagcgttggccggttttcagcatgatcacagccatagatcctcccaggaattcagtttgaagcagcttattggcgacggaatgctgtgg
# gctgttccgaaacacaggagatccgtggagaaacgcctgaagcggaagttcggatatccggaatacaattggaagcctctgagggagaagaggaacat
# ccgctcctgtctgcaatgtggccatgaccacgagatgggggttctttgtcctttctgctaccaaaaagtcctgaaggagactgagctcatgcagtcga
# aaatccaggagacactgggtctagatcccgtggacaaggaagtaatcgttctttatgagggcgagaaagccgaacagtcctcagatgagctgaaaaac
# aaacgcatcgtggagatgaagaagcctcgtcccatgtggttcaccaagaatctgctccaaaaatccacgcagcaattgtccgaaaccaaggaagtcaa
# gccctccgacttggcctag]
# protein sequence = [MSRNLFLSITNLFRNLESLFLPHGGHPPALALAGFQHDHSHRSSQEFSLKQLIGDGMLWAVPKHRRSVEKRLKRKFGY
# PEYNWKPLREKRNIRSCLQCGHDHEMGVLCPFCYQKVLKETELMQSKIQETLGLDPVDKEVIVLYEGEKAEQSSDELKNKRIVEMKKPRPMWFTKNLL
# QKSTQQLSETKEVKPSDLA]
......@@ -114,6 +143,20 @@ sample AUGUSTUS protein_match 45270 45401 10.4 + 0 target "unknown_A[1..44]"; ta
sample AUGUSTUS protein_match 45550 45657 8.91 + 0 target "unknown_B[1..36]"; target_start 298; transcript_id "g4.t1"; gene_id "g4";
sample AUGUSTUS protein_match 45694 45741 11.9 + 0 target "unknown_C[1..16]"; target_start 346; transcript_id "g4.t1"; gene_id "g4";
sample AUGUSTUS protein_match 46207 46425 9.82 + 0 target "unknown_D[1..73]"; target_start 363; transcript_id "g4.t1"; gene_id "g4";
# coding sequence = [atggcctgcttgagcacttccggtcgcgtcgtctgcggctcccgtcgccagcagacgcacaagctgctctaccagctat
# tcggatcccggccaggatatacagccccatccaccgcgaccggattattcagtccgcccaaagtccaacagcaggccatgcgactctgccacggatta
# agcttcagcttgggcaaggattaccccgatctgctgcaaagctcccacaagtgcagccaaacgctgcagtactcccaaagttccaaggcgaatctgag
# gcagcacagctcggtccacacacaacagccagccggtcctgtgagggagttccagatcgatccctacatcatactcgacgacgacctcaagtacttct
# acgacgatgtgagatatctgctgaaatcgggcacatcccagccagagttggacaccatcgccagctattatttcgatggccaggggaaggctctgcga
# cccatggttaccatgctgatggccaaggcgataaactaccacctgaacaacgagtcacaccaattagtacacaaacagcgacagatcgccctcttttc
# ggagatggtgcactcggccagcttggtccacgacgatgtcatcgatcagtcggacttccgacgcggcaagcccagcgtgaatgctctttggaaccaca
# aaaaggtcacaatggctggtgattatatcttatcgattgcctcgattatgatagctcgtctgcgcagcgatgatgtgacgatcgtgctgagtcagatc
# ttgaccgatttggtccaaggcgagttcatgcagctgggctcaagggagacggagaacgagcgcttcgcccattacctgaccaagacgtacaggaagac
# cgcatcgctgatcgccaacgcactgaaggcgaccgccgtgattgcccaggccgacgacaacgtggccgaggtggccttccagtacggacgcaacatcg
# gcttggcctttcagctggtcgacgacatgctggacttcgtctcctccaccgagcagatgggcaagccgacggcggcagatctgaaactgggtctggcc
# accgcccccgtcctctttgcatgcgaaaagtaccccgagctgaatcccatggtgatgcggcgcttcagcgagcccggcgacgtggagcgagccttcga
# gctggtgcacaagtcgcacggtctggaacagacccggttcctggccaagaagcactgcaacgaggcgatacggctggcccaggagctcacggagtcgc
# cctaccagaagggcctccaggtggtcgccgacttagtcatcaaccgcatgaagtag]
# protein sequence = [MACLSTSGRVVCGSRRQQTHKLLYQLFGSRPGYTAPSTATGLFSPPKVQQQAMRLCHGLSFSLGKDYPDLLQSSHKCS
# QTLQYSQSSKANLRQHSSVHTQQPAGPVREFQIDPYIILDDDLKYFYDDVRYLLKSGTSQPELDTIASYYFDGQGKALRPMVTMLMAKAINYHLNNES
# HQLVHKQRQIALFSEMVHSASLVHDDVIDQSDFRRGKPSVNALWNHKKVTMAGDYILSIASIMIARLRSDDVTIVLSQILTDLVQGEFMQLGSRETEN
......@@ -137,6 +180,21 @@ sample AUGUSTUS CDS 50740 50856 1 + 0 transcript_id "g5.t1"; gene_id "g5";
sample AUGUSTUS exon 50740 50856 . + . transcript_id "g5.t1"; gene_id "g5";
sample AUGUSTUS CDS 50924 51425 0.38 + 0 transcript_id "g5.t1"; gene_id "g5";
sample AUGUSTUS exon 50924 51425 . + . transcript_id "g5.t1"; gene_id "g5";
# coding sequence = [atgacgactagcgatgaaatgggcatgggcggcaacttctgccacgaccacatccagcatccgctgatgtggtgcgatg
# agaagaagcgtctggtggagcgcaagaatgcagaagagagtcttcgcatgtggcgtcgcaggaaggcggaggagtgtgctcgcaaggagaaggataag
# caggagcatgtggactcagcactaaccacttttgtggacaacacaaggttcttcagggaaattgcagagttcgtgtccgatttcagtgatgggcaaat
# ccagcagctgctggaggaaagcgctcgtctgcgcgttgagcacgccgagaatctcatccgtgtgaagagcaagcaccagtcactcagccaggtgatgc
# agcaggtccagaactcgagctccaccatcgaggagcttgaggaaaactggaagaagcgctccaaagcggaggaacagaagcgcatcaatgtcaagaac
# atagccgagtttaagaacttcaagaaaactgtggaatctgcagctggccatgtaggtgcggaggtcaatagtcaagcgaatggcgccgcccaggatga
# ggaccttattatcgaaggaatcgaagagaccggcggcgggatcttctcgctctacgatccctggtccaaggccctaatgaagaaccccgtgcgcaacg
# agaagtgcggtcacatctacgaccgcgattcggtgatgctgattataaaggacaacattggcatccgatgtcccgtgctcggctgtggcaacacgacc
# tacatccagcctgcgcacctggtcgaggatgccaaagtccggcaaatgtactacgacctgtttcaccaacattgtccttggggtcgacctggtggtgg
# tgcacccaatgtagaagtgcggcgcaaggacatcacagccgtaggccttcactccacgcccacagtgaccaatgcccaccgaatgaatctgctgcagc
# cgtgtcgctacaacgacttcttctcgatgcagaagaagtgtcacaacaacccgctggccgcctaccaccaccaccaccaccatgcccctcctgcccct
# ccgccgggtggtcgccttggccacgcccactcagttcatcacctgcaggaaagtggtcccaggagcagcaccgtcacgatttgcgagcgggagattcc
# ccacaagcccggagcgggagttggtgtcaatgttgccaaaaacgccaacggtgagagccttcacatcgagctgaaagagcatccttcaatgtcgtttc
# gcaataaaggccatgtagacatagaattgcgatacaagccctctcctccgtgcaagggcaagcctcttctggagaagattgtggttagcgagagtgaa
# cagcgatgtcctttgcaggaaaagctggccacacagaagaagcgcctgcaggccaaactagaaaagccggtgagcggca]
# protein sequence = [MTTSDEMGMGGNFCHDHIQHPLMWCDEKKRLVERKNAEESLRMWRRRKAEECARKEKDKQEHVDSALTTFVDNTRFFR
# EIAEFVSDFSDGQIQQLLEESARLRVEHAENLIRVKSKHQSLSQVMQQVQNSSSTIEELEENWKKRSKAEEQKRINVKNIAEFKNFKKTVESAAGHVG
# AEVNSQANGAAQDEDLIIEGIEETGGGIFSLYDPWSKALMKNPVRNEKCGHIYDRDSVMLIIKDNIGIRCPVLGCGNTTYIQPAHLVEDAKVRQMYYD
......@@ -146,4 +204,4 @@ sample AUGUSTUS exon 50924 51425 . + . transcript_id "g5.t1"; gene_id "g5";
# end gene g5
###
# command line:
# augustus --proteinprofile=sample_data/example/prfl/BUSCO_2.prfl --predictionStart=27021 --predictionEnd=51425 --species=fly ./tmp/sampleSAMPLE_3715919971_.temp
# augustus --codingseq=1 --proteinprofile=sample_data/example/prfl/BUSCO_2.prfl --predictionStart=27021 --predictionEnd=51425 --species=fly ./tmp/sampleSAMPLE_1214242381_.temp
......@@ -6,7 +6,7 @@
# Using protein profile unknown
# --[15..26]--> unknown_C (6) <--[15..40]--> unknown_D (32) <--[1..45]--> unknown_E (13) <--[0..2]--> unknown_F (28) <--[0..6]--> unknown_G (9) <--[3..810]--
# fly version. Use default transition matrix.
# Looks like ./tmp/sampleSAMPLE_3715919971_.temp is in fasta format.
# Looks like ./tmp/sampleSAMPLE_1214242381_.temp is in fasta format.
# We have hints for 0 sequences and for 0 of the sequences in the input set.
#
# ----- prediction on sequence number 1 (length = 10906, name = sample) -----
......@@ -34,6 +34,11 @@ sample AUGUSTUS protein_match 67446 67541 8.63 + 0 target "unknown_D[1..32]"; ta
sample AUGUSTUS protein_match 68136 68174 7.31 + 0 target "unknown_E[1..13]"; target_start 85; transcript_id "g1.t1"; gene_id "g1";
sample AUGUSTUS protein_match 68175 68258 8.64 + 0 target "unknown_F[1..28]"; target_start 98; transcript_id "g1.t1"; gene_id "g1";
sample AUGUSTUS protein_match 68259 68285 12.5 + 0 target "unknown_G[1..9]"; target_start 126; transcript_id "g1.t1"; gene_id "g1";
# coding sequence = [atgttcgtgtcgacagtctctcgcattgcccccgttgccaggagcgccttcctcgccaactccaagcagtacctgcgac
# cattgagcagcgccatcatcagccagagccagactttggccgctcagaacacaacccccgttgcattgctgccacagatcaggtcattccagacctcg
# ccagtcacgcgtgacattgactcggccgccaaattcattggcgctggtgccgcaacagtcggtgtcgctggatccggtgctggtatcggaacagtatt
# cggttccctcatcatcggctacgccaggaacccatcgctgaaacagcagctgttctcctacgccattctgggcttcgccctgtccgaggccatgggtc
# tgttctgtttgatgatggccttcctgctgttgttcgccttctaa]
# protein sequence = [MFVSTVSRIAPVARSAFLANSKQYLRPLSSAIISQSQTLAAQNTTPVALLPQIRSFQTSPVTRDIDSAAKFIGAGAAT
# VGVAGSGAGIGTVFGSLIIGYARNPSLKQQLFSYAILGFALSEAMGLFCLMMAFLLLFAF]
# end gene g1
......@@ -47,6 +52,18 @@ sample AUGUSTUS start_codon 69425 69427 . + 0 transcript_id "g2.t1"; gene_id "g2
sample AUGUSTUS CDS 69425 70522 1 + 0 transcript_id "g2.t1"; gene_id "g2";
sample AUGUSTUS stop_codon 70520 70522 . + 0 transcript_id "g2.t1"; gene_id "g2";
sample AUGUSTUS tts 70561 70561 . + . transcript_id "g2.t1"; gene_id "g2";
# coding sequence = [atggatttcgccaagaaaatacttggaaagtacggctggaaggagggcgacggcttgggcaagaacaacacgggaattg
# cagctccattgaaggccagtctgaagttcgataacgcgggtctgggagtggatcgcgcccaggaattcaatgaccattggtgggagcgctgctttaac
# gaggccgccagcaatgtggacgtccagattcagcaagacggacaggtgtccacctcccgcaggaaaggcgaggaagcggtggagatctccaccagcgg
# attctccgcgcgtaagctgaagaaagccaaggagcagcacgccagcgatggaaagaccacctacgacaacttcctgcagacttcgctgctcacccaag
# gcggcaacgaagttgagacctccgagcgcatcaaggtggaggagattgaggtcgccaaggtggcggtgctcacagatgaagaactctttaaagcctgc
# ggaggaaggactgcgcacaaaggagcacggcatggcttaaagttaagcggaaagatcgcccgcttggagcagcaggagcgcgagatgctggagaagct
# tcagagcaagctgaagactacgcctgaaaccactctggttccgaaaagcggaaagttgattgaggagacccagcacaaagtagcagattcagtggatt
# gcagtgtggagcaggctacgaagcccaaaaagaagaaaaagtctaggactgaggagtccgtcgaggaaattgcgcctgcccaactggaagagcccata
# aaatccaagaaaaagaagaaagacaaggctgagaaggcggcaaaggaatactcaacacatcaggctcaagacgaccccgtccagatcaagaggagaaa
# aaataagacagggaagctagaagaggaagtccaagatgttacggaagtcgaagaggcagtgaagataaaaaagaaggacaagaggcagcaaggggtag
# aagcaactgaagccttaagcattgaaactgatgaacatgtaaaatccaaaaagaagcggaaaacggaagactcctcagaggaaaccgaaactcccaca
# aaaaccaaaaagaaaagaaagaacaaggaactcgtgtaa]
# protein sequence = [MDFAKKILGKYGWKEGDGLGKNNTGIAAPLKASLKFDNAGLGVDRAQEFNDHWWERCFNEAASNVDVQIQQDGQVSTS
# RRKGEEAVEISTSGFSARKLKKAKEQHASDGKTTYDNFLQTSLLTQGGNEVETSERIKVEEIEVAKVAVLTDEELFKACGGRTAHKGARHGLKLSGKI
# ARLEQQEREMLEKLQSKLKTTPETTLVPKSGKLIEETQHKVADSVDCSVEQATKPKKKKKSRTEESVEEIAPAQLEEPIKSKKKKKDKAEKAAKEYST
......@@ -68,6 +85,16 @@ sample AUGUSTUS CDS 71718 71783 0.79 - 0 transcript_id "g3.t1"; gene_id "g3";
sample AUGUSTUS exon 71718 71872 . - . transcript_id "g3.t1"; gene_id "g3";
sample AUGUSTUS start_codon 71781 71783 . - 0 transcript_id "g3.t1"; gene_id "g3";
sample AUGUSTUS tss 71872 71872 . - . transcript_id "g3.t1"; gene_id "g3";
# coding sequence = [atgtcggactttgaaatggaggacagcgcctcggggtacgattcaggtgataactcagatgccgagctgcaagcggcat
# ttgaacgaggcgacttaaaaccaggcctaaacttggagttcaatggccagagagacaaagtgaatgatgtgaccaaactgctggcaaaaacagaggct
# atcaagatgcaacttccttggctggagcgcctggacatgatcaacacactggctcccctggccccggaactcgctgtacagctggagaagcacgagca
# aaagcgggccaatctcttcaaaggcaacgccaagctgccctacattcggcccgaggaggatcccgttctgaacgatttcaagagggagatgctcttcc
# atcgacaggcgcaaagtgctgttctagaggccattccccgcctgcacgagctgggcataaagacccgtcggccagatgactacttcgccgaaatggcc
# aagtctgacgagcacatgcagaaggtccgcgccaacctgatggccaaacagcaaggacaggcgaaatccgagcgcatcaagcagatccgcgaacagcg
# caaaatgggcaagatgctggccaaacagaccaaggtccaacgcgaggccgagaagaaggacatgctggacaaattgaagaaattccgcaagggcaagc
# tgaagaacctggacttcctggaggacgccaaggcgctggagtccaagcagaagcagtcagccgagaatcgcaagaagcgcaacaagaagttcggcttt
# ggaggcaagaagaagggcctcaagaggaacacaaagtcctcctccgcgggattggatggcgacaagtccacaaggcggcagcggggcgtgaaggcggg
# tgcttcggtcaacaaacgtcttggcaaatcgcgacgcattaaggccaagggcagaaagtag]
# protein sequence = [MSDFEMEDSASGYDSGDNSDAELQAAFERGDLKPGLNLEFNGQRDKVNDVTKLLAKTEAIKMQLPWLERLDMINTLAP
# LAPELAVQLEKHEQKRANLFKGNAKLPYIRPEEDPVLNDFKREMLFHRQAQSAVLEAIPRLHELGIKTRRPDDYFAEMAKSDEHMQKVRANLMAKQQG
# QAKSERIKQIREQRKMGKMLAKQTKVQREAEKKDMLDKLKKFRKGKLKNLDFLEDAKALESKQKQSAENRKKRNKKFGFGGKKKGLKRNTKSSSAGLD
......@@ -81,10 +108,16 @@ sample AUGUSTUS tss 72303 72303 . + . transcript_id "g4.t1"; gene_id "g4";
sample AUGUSTUS exon 72303 73243 . + . transcript_id "g4.t1"; gene_id "g4";
sample AUGUSTUS start_codon 72676 72678 . + 0 transcript_id "g4.t1"; gene_id "g4";
sample AUGUSTUS CDS 72676 73243 0.97 + 0 transcript_id "g4.t1"; gene_id "g4";
# coding sequence = [atgtcggcttctgcgaatttggcgaacgtttacgcggagctaatgcgccggtgtggtgattcgtacacgatctcctatg
# gagcaccacccacttacttggtgagcacggtgggagctgcagaagctggtaagaagattgtgctggtcttcaaggaggatcgcaatggtgcctggacc
# aaaaacccgaccacaccgaccaggacagtaccaaaaaaagagggctcggcggatttggatctgacgggtagtcctttaaaggacgactgcttggtgga
# cgccatagctgacttgtccatcaacttgcagctggaccatccgatggcgtggaagctggaggaggagtaccagcgtgggatacccgtggacaaggcga
# ggtccattatgtgctccgagttcctgcagctggctgaaggactcggatccgtgtggtttctttgcgacggcagcgatcctgggcagactcagttgctc
# cagtatgagttcaatcctacgcacttctccagaggaatcctaagctaccagggggtgcaccctgctttcttggtgaccccacagtccctggtgcgcc]
# protein sequence = [MSASANLANVYAELMRRCGDSYTISYGAPPTYLVSTVGAAEAGKKIVLVFKEDRNGAWTKNPTTPTRTVPKKEGSADL
# DLTGSPLKDDCLVDAIADLSINLQLDHPMAWKLEEEYQRGIPVDKARSIMCSEFLQLAEGLGSVWFLCDGSDPGQTQLLQYEFNPTHFSRGILSYQGV
# HPAFLVTPQSLVR]
# end gene g4
###
# command line:
# augustus --proteinprofile=sample_data/example/prfl/BUSCO_3.prfl --predictionStart=62338 --predictionEnd=73243 --species=fly ./tmp/sampleSAMPLE_3715919971_.temp
# augustus --codingseq=1 --proteinprofile=sample_data/example/prfl/BUSCO_3.prfl --predictionStart=62338 --predictionEnd=73243 --species=fly ./tmp/sampleSAMPLE_1214242381_.temp
......@@ -6,7 +6,7 @@
# Using protein profile unknown
# --[0..26]--> unknown_A (25) <--[4..13]--> unknown_B (16) <--[40..496]--
# fly version. Use default transition matrix.
# Looks like ./tmp/sampleSAMPLE_3715919971_.temp is in fasta format.
# Looks like ./tmp/sampleSAMPLE_1214242381_.temp is in fasta format.
# We have hints for 0 sequences and for 0 of the sequences in the input set.
#
# ----- prediction on sequence number 1 (length = 10546, name = sample) -----
......@@ -28,6 +28,11 @@ sample AUGUSTUS CDS 68134 68297 0.7 + 2 transcript_id "g1.t1"; gene_id "g1";
sample AUGUSTUS exon 68134 68675 . + . transcript_id "g1.t1"; gene_id "g1";
sample AUGUSTUS stop_codon 68295 68297 . + 0 transcript_id "g1.t1"; gene_id "g1";
sample AUGUSTUS tts 68675 68675 . + . transcript_id "g1.t1"; gene_id "g1";
# coding sequence = [atgttcgtgtcgacagtctctcgcattgcccccgttgccaggagcgccttcctcgccaactccaagcagtacctgcgac
# cattgagcagcgccatcatcagccagagccagactttggccgctcagaacacaacccccgttgcattgctgccacagatcaggtcattccagacctcg
# ccagtcacgcgtgacattgactcggccgccaaattcattggcgctggtgccgcaacagtcggtgtcgctggatccggtgctggtatcggaacagtatt
# cggttccctcatcatcggctacgccaggaacccatcgctgaaacagcagctgttctcctacgccattctgggcttcgccctgtccgaggccatgggtc
# tgttctgtttgatgatggccttcctgctgttgttcgccttctaa]
# protein sequence = [MFVSTVSRIAPVARSAFLANSKQYLRPLSSAIISQSQTLAAQNTTPVALLPQIRSFQTSPVTRDIDSAAKFIGAGAAT
# VGVAGSGAGIGTVFGSLIIGYARNPSLKQQLFSYAILGFALSEAMGLFCLMMAFLLLFAF]
# end gene g1
......@@ -43,6 +48,18 @@ sample AUGUSTUS stop_codon 70520 70522 . + 0 transcript_id "g2.t1"; gene_id "g2"
sample AUGUSTUS tts 70561 70561 . + . transcript_id "g2.t1"; gene_id "g2";
sample AUGUSTUS protein_match 69473 69547 6.49 + 0 target "unknown_A[1..25]"; target_start 16; transcript_id "g2.t1"; gene_id "g2";
sample AUGUSTUS protein_match 69572 69619 7.89 + 0 target "unknown_B[1..16]"; target_start 49; transcript_id "g2.t1"; gene_id "g2";
# coding sequence = [atggatttcgccaagaaaatacttggaaagtacggctggaaggagggcgacggcttgggcaagaacaacacgggaattg
# cagctccattgaaggccagtctgaagttcgataacgcgggtctgggagtggatcgcgcccaggaattcaatgaccattggtgggagcgctgctttaac
# gaggccgccagcaatgtggacgtccagattcagcaagacggacaggtgtccacctcccgcaggaaaggcgaggaagcggtggagatctccaccagcgg
# attctccgcgcgtaagctgaagaaagccaaggagcagcacgccagcgatggaaagaccacctacgacaacttcctgcagacttcgctgctcacccaag
# gcggcaacgaagttgagacctccgagcgcatcaaggtggaggagattgaggtcgccaaggtggcggtgctcacagatgaagaactctttaaagcctgc
# ggaggaaggactgcgcacaaaggagcacggcatggcttaaagttaagcggaaagatcgcccgcttggagcagcaggagcgcgagatgctggagaagct
# tcagagcaagctgaagactacgcctgaaaccactctggttccgaaaagcggaaagttgattgaggagacccagcacaaagtagcagattcagtggatt
# gcagtgtggagcaggctacgaagcccaaaaagaagaaaaagtctaggactgaggagtccgtcgaggaaattgcgcctgcccaactggaagagcccata
# aaatccaagaaaaagaagaaagacaaggctgagaaggcggcaaaggaatactcaacacatcaggctcaagacgaccccgtccagatcaagaggagaaa
# aaataagacagggaagctagaagaggaagtccaagatgttacggaagtcgaagaggcagtgaagataaaaaagaaggacaagaggcagcaaggggtag
# aagcaactgaagccttaagcattgaaactgatgaacatgtaaaatccaaaaagaagcggaaaacggaagactcctcagaggaaaccgaaactcccaca
# aaaaccaaaaagaaaagaaagaacaaggaactcgtgtaa]
# protein sequence = [MDFAKKILGKYGWKEGDGLGKNNTGIAAPLKASLKFDNAGLGVDRAQEFNDHWWERCFNEAASNVDVQIQQDGQVSTS
# RRKGEEAVEISTSGFSARKLKKAKEQHASDGKTTYDNFLQTSLLTQGGNEVETSERIKVEEIEVAKVAVLTDEELFKACGGRTAHKGARHGLKLSGKI
# ARLEQQEREMLEKLQSKLKTTPETTLVPKSGKLIEETQHKVADSVDCSVEQATKPKKKKKSRTEESVEEIAPAQLEEPIKSKKKKKDKAEKAAKEYST
......@@ -64,6 +81,16 @@ sample AUGUSTUS CDS 71718 71783 0.77 - 0 transcript_id "g3.t1"; gene_id "g3";
sample AUGUSTUS exon 71718 71839 . - . transcript_id "g3.t1"; gene_id "g3";
sample AUGUSTUS start_codon 71781 71783 . - 0 transcript_id "g3.t1"; gene_id "g3";
sample AUGUSTUS tss 71839 71839 . - . transcript_id "g3.t1"; gene_id "g3";
# coding sequence = [atgtcggactttgaaatggaggacagcgcctcggggtacgattcaggtgataactcagatgccgagctgcaagcggcat
# ttgaacgaggcgacttaaaaccaggcctaaacttggagttcaatggccagagagacaaagtgaatgatgtgaccaaactgctggcaaaaacagaggct
# atcaagatgcaacttccttggctggagcgcctggacatgatcaacacactggctcccctggccccggaactcgctgtacagctggagaagcacgagca
# aaagcgggccaatctcttcaaaggcaacgccaagctgccctacattcggcccgaggaggatcccgttctgaacgatttcaagagggagatgctcttcc
# atcgacaggcgcaaagtgctgttctagaggccattccccgcctgcacgagctgggcataaagacccgtcggccagatgactacttcgccgaaatggcc
# aagtctgacgagcacatgcagaaggtccgcgccaacctgatggccaaacagcaaggacaggcgaaatccgagcgcatcaagcagatccgcgaacagcg
# caaaatgggcaagatgctggccaaacagaccaaggtccaacgcgaggccgagaagaaggacatgctggacaaattgaagaaattccgcaagggcaagc
# tgaagaacctggacttcctggaggacgccaaggcgctggagtccaagcagaagcagtcagccgagaatcgcaagaagcgcaacaagaagttcggcttt
# ggaggcaagaagaagggcctcaagaggaacacaaagtcctcctccgcgggattggatggcgacaagtccacaaggcggcagcggggcgtgaaggcggg
# tgcttcggtcaacaaacgtcttggcaaatcgcgacgcattaaggccaagggcagaaagtag]
# protein sequence = [MSDFEMEDSASGYDSGDNSDAELQAAFERGDLKPGLNLEFNGQRDKVNDVTKLLAKTEAIKMQLPWLERLDMINTLAP
# LAPELAVQLEKHEQKRANLFKGNAKLPYIRPEEDPVLNDFKREMLFHRQAQSAVLEAIPRLHELGIKTRRPDDYFAEMAKSDEHMQKVRANLMAKQQG
# QAKSERIKQIREQRKMGKMLAKQTKVQREAEKKDMLDKLKKFRKGKLKNLDFLEDAKALESKQKQSAENRKKRNKKFGFGGKKKGLKRNTKSSSAGLD
......@@ -88,6 +115,26 @@ sample AUGUSTUS CDS 74706 74773 1 + 2 transcript_id "g4.t1"; gene_id "g4";
sample AUGUSTUS exon 74706 74808 . + . transcript_id "g4.t1"; gene_id "g4";
sample AUGUSTUS stop_codon 74771 74773 . + 0 transcript_id "g4.t1"; gene_id "g4";
sample AUGUSTUS tts 74808 74808 . + . transcript_id "g4.t1"; gene_id "g4";
# coding sequence = [atgtcggcttctgcgaatttggcgaacgtttacgcggagctaatgcgccggtgtggtgattcgtacacgatctcctatg
# gagcaccacccacttacttggtgagcacggtgggagctgcagaagctggtaagaagattgtgctggtcttcaaggaggatcgcaatggtgcctggacc
# aaaaacccgaccacaccgaccaggacagtaccaaaaaaagagggctcggcggatttggatctgacgggtagtcctttaaaggacgactgcttggtgga
# cgccatagctgacttgtccatcaacttgcagctggaccatccgatggcgtggaagctggaggaggagtaccagcgtgggatacccgtggacaaggcga
# ggtccattatgtgctccgagttcctgcagctggctgaaggactcggatccgtgtggtttctttgcgacggcagcgatcctgggcagactcagttgctc
# cagtatgagttcaatcctacgcacttctccagaggaatcctaagctaccagggggtgcaccctgctttcttggtgaccccacagtccctggtgcgcca
# acatggcaaggatccggatgaaaccatgatcgaaaactgctaccaggtcaatacccacatgaaactgcgctgctcctggacctctagtgcttcacttc
# cccttctggtgaacctaaacgactgcgatgttgccttgaatcacaaatttcgcgtaggcgactgcagtgctttgacacaggacttcatgaaccagctg
# cgcattttggtctacatacgcgaagatatcgtctcctaccacacggatgtcaagcagggcgtctcacgggaacccacctatcgttgtggcagtgggat
# tgacatggacgagctgcgcgagtctattaatcagacaatgacagatgtaaccagcctcattggtcattatagcataagcaatgcggagtttgacatcg
# aagatgtcatacagagggccaaggtgcgtcggctcacggatctgaccgataagctttgggagctgctcaagtgctgtcactcgtacaaggatcttaaa
# atggcctttagcatgctctttcaatgtgctgcacgatgtaacatagtaaacacgccgactaataaaaatcgactggccaagattatcaccgagttggc
# caatcgtcgtctggccatgccctgcttaagtggggccgagcctttggaactgcttttggagattggcctggagaagttgtacaaggactacgaattca
# tctataccgagagcaagatgtgcagcaccaatctgctgaaggaggactctagcgaagcaacgtcggacggtggctcccccaagaatctgccccagctt
# cgaaaatccctgcataatgcggtcaggggtgatccgaccccaggagcaggaatgcggaagacgctgctgcacaaccacggcgctgccaattcgcggat
# tacaaaatatgccggtaacgacgatgatgccgggttcaaaaacagccacttcgacgagctcgagagtacggagagaatctccaagttgtttcagattc
# attgcaccttggaacatctgctgatgatgcacatccacttaaaccttgcaaacgtttacaacgatgtctgttctgagttgctgaagaaaccgccgaaa
# ttagtggaatccatcgatgatcagctaagtgatgtaatggacattcgcctgtctgcccactatgtcagggatcatttggatggtaaggatccctactc
# ccggcacattaccatgcgttcgtacaacaagttccgcgaactgaagacaaccttctatttcgcttcggaaaacgtttgtccgcccaacttggctcagt
# gtttccagtgtgatgacaaggagatggtcaaggagcgcacctatcattcctggatatatcgcaagattcgctcacttaagtaa]
# protein sequence = [MSASANLANVYAELMRRCGDSYTISYGAPPTYLVSTVGAAEAGKKIVLVFKEDRNGAWTKNPTTPTRTVPKKEGSADL
# DLTGSPLKDDCLVDAIADLSINLQLDHPMAWKLEEEYQRGIPVDKARSIMCSEFLQLAEGLGSVWFLCDGSDPGQTQLLQYEFNPTHFSRGILSYQGV
# HPAFLVTPQSLVRQHGKDPDETMIENCYQVNTHMKLRCSWTSSASLPLLVNLNDCDVALNHKFRVGDCSALTQDFMNQLRILVYIREDIVSYHTDVKQ
......@@ -98,4 +145,4 @@ sample AUGUSTUS tts 74808 74808 . + . transcript_id "g4.t1"; gene_id "g4";
# end gene g4
###
# command line:
# augustus --proteinprofile=sample_data/example/prfl/BUSCO_4.prfl --predictionStart=64425 --predictionEnd=74970 --species=fly ./tmp/sampleSAMPLE_3715919971_.temp
# augustus --codingseq=1 --proteinprofile=sample_data/example/prfl/BUSCO_4.prfl --predictionStart=64425 --predictionEnd=74970 --species=fly ./tmp/sampleSAMPLE_1214242381_.temp
......@@ -6,7 +6,7 @@
# Using protein profile unknown
# --[0..48]--> unknown_A (7) <--[9..17]--> unknown_B (13) <--[0..5]--> unknown_C (23) <--[11..39]--> unknown_E (104) <--[0..1]--> unknown_F (11) <--[17..768]--
# fly version. Use default transition matrix.
# Looks like ./tmp/sampleSAMPLE_3715919971_.temp is in fasta format.
# Looks like ./tmp/sampleSAMPLE_1214242381_.temp is in fasta format.
# We have hints for 0 sequences and for 0 of the sequences in the input set.
#
# ----- prediction on sequence number 1 (length = 10570, name = sample) -----
......@@ -28,6 +28,11 @@ sample AUGUSTUS CDS 68134 68297 0.57 + 2 transcript_id "g1.t1"; gene_id "g1";
sample AUGUSTUS exon 68134 68675 . + . transcript_id "g1.t1"; gene_id "g1";
sample AUGUSTUS stop_codon 68295 68297 . + 0 transcript_id "g1.t1"; gene_id "g1";
sample AUGUSTUS tts 68675 68675 . + . transcript_id "g1.t1"; gene_id "g1";
# coding sequence = [atgttcgtgtcgacagtctctcgcattgcccccgttgccaggagcgccttcctcgccaactccaagcagtacctgcgac
# cattgagcagcgccatcatcagccagagccagactttggccgctcagaacacaacccccgttgcattgctgccacagatcaggtcattccagacctcg
# ccagtcacgcgtgacattgactcggccgccaaattcattggcgctggtgccgcaacagtcggtgtcgctggatccggtgctggtatcggaacagtatt
# cggttccctcatcatcggctacgccaggaacccatcgctgaaacagcagctgttctcctacgccattctgggcttcgccctgtccgaggccatgggtc
# tgttctgtttgatgatggccttcctgctgttgttcgccttctaa]
# protein sequence = [MFVSTVSRIAPVARSAFLANSKQYLRPLSSAIISQSQTLAAQNTTPVALLPQIRSFQTSPVTRDIDSAAKFIGAGAAT
# VGVAGSGAGIGTVFGSLIIGYARNPSLKQQLFSYAILGFALSEAMGLFCLMMAFLLLFAF]
# end gene g1
......@@ -41,6 +46,18 @@ sample AUGUSTUS start_codon 69425 69427 . + 0 transcript_id "g2.t1"; gene_id "g2
sample AUGUSTUS CDS 69425 70522 1 + 0 transcript_id "g2.t1"; gene_id "g2";
sample AUGUSTUS stop_codon 70520 70522 . + 0 transcript_id "g2.t1"; gene_id "g2";
sample AUGUSTUS tts 70561 70561 . + . transcript_id "g2.t1"; gene_id "g2";
# coding sequence = [atggatttcgccaagaaaatacttggaaagtacggctggaaggagggcgacggcttgggcaagaacaacacgggaattg
# cagctccattgaaggccagtctgaagttcgataacgcgggtctgggagtggatcgcgcccaggaattcaatgaccattggtgggagcgctgctttaac
# gaggccgccagcaatgtggacgtccagattcagcaagacggacaggtgtccacctcccgcaggaaaggcgaggaagcggtggagatctccaccagcgg
# attctccgcgcgtaagctgaagaaagccaaggagcagcacgccagcgatggaaagaccacctacgacaacttcctgcagacttcgctgctcacccaag
# gcggcaacgaagttgagacctccgagcgcatcaaggtggaggagattgaggtcgccaaggtggcggtgctcacagatgaagaactctttaaagcctgc
# ggaggaaggactgcgcacaaaggagcacggcatggcttaaagttaagcggaaagatcgcccgcttggagcagcaggagcgcgagatgctggagaagct
# tcagagcaagctgaagactacgcctgaaaccactctggttccgaaaagcggaaagttgattgaggagacccagcacaaagtagcagattcagtggatt
# gcagtgtggagcaggctacgaagcccaaaaagaagaaaaagtctaggactgaggagtccgtcgaggaaattgcgcctgcccaactggaagagcccata
# aaatccaagaaaaagaagaaagacaaggctgagaaggcggcaaaggaatactcaacacatcaggctcaagacgaccccgtccagatcaagaggagaaa
# aaataagacagggaagctagaagaggaagtccaagatgttacggaagtcgaagaggcagtgaagataaaaaagaaggacaagaggcagcaaggggtag
# aagcaactgaagccttaagcattgaaactgatgaacatgtaaaatccaaaaagaagcggaaaacggaagactcctcagaggaaaccgaaactcccaca
# aaaaccaaaaagaaaagaaagaacaaggaactcgtgtaa]
# protein sequence = [MDFAKKILGKYGWKEGDGLGKNNTGIAAPLKASLKFDNAGLGVDRAQEFNDHWWERCFNEAASNVDVQIQQDGQVSTS
# RRKGEEAVEISTSGFSARKLKKAKEQHASDGKTTYDNFLQTSLLTQGGNEVETSERIKVEEIEVAKVAVLTDEELFKACGGRTAHKGARHGLKLSGKI
# ARLEQQEREMLEKLQSKLKTTPETTLVPKSGKLIEETQHKVADSVDCSVEQATKPKKKKKSRTEESVEEIAPAQLEEPIKSKKKKKDKAEKAAKEYST
......@@ -69,6 +86,16 @@ sample AUGUSTUS protein_match 71501 71515 2.92 - 0 target "unknown_B[9..13]"; ta
sample AUGUSTUS protein_match 71573 71596 4.47 - 0 target "unknown_B[1..8]"; target_start 42; transcript_id "g3.t1"; gene_id "g3";
sample AUGUSTUS protein_match 71639 71656 5.37 - 0 target "unknown_A[2..7]"; target_start 21; transcript_id "g3.t1"; gene_id "g3";