Commit c532a10a authored by Mathieu's avatar Mathieu

2.0 beta 1

parent 5b3b8753
......@@ -417,7 +417,7 @@ class Analysis(object):
def _check_protein(self):
"""
This function checks that the provided file is protein
:raises SystemExit: if only ACGT is found over a reasonable amount of lines
:raises SystemExit: if only ACGTN is found over a reasonable amount of lines
"""
aas = set(Analysis.CODONS.values())
aas.remove('A')
......@@ -781,7 +781,7 @@ class Analysis(object):
:param out: a file to which the header will be added
:type out: file
"""
out.write('# BUSCO version is %s and the dataset is %s\n' % (VERSION, self._clade_path))
out.write('# BUSCO version is: %s \n# The lineage dataset is: %s\n' % (VERSION, self._clade_name))
out.write('# To reproduce this run: %s\n#\n' % _rerun_cmd)
def _blast(self, missing_and_frag_only=False, ancestral_variants=False):
......@@ -1188,7 +1188,7 @@ class Analysis(object):
# Extract fasta files from augustus output
_logger.info('Extracting predicted proteins ...')
self._no_predictions = []
for entry in self._missing_busco_list:
for entry in self._missing_busco_list + self._fragmented_busco_list:
if entry in self._location_dic:
for location in self._location_dic[entry]:
output_index = self._location_dic[entry].index(location) + 1
......@@ -1841,7 +1841,7 @@ class GenomeAnalysis(Analysis):
"""
super(GenomeAnalysis, self).cleanup()
Analysis.p_open(['rm %s*%s%s_.temp' % (self._tmp, self._abrev, self._random)], 'bash', shell=True)
Analysis.p_open(['rm %(tmp)s%(abrev)s.ns? %(tmp)s%(abrev)s.nin %(tmp)s%(abrev)s.nhr'
Analysis.p_open(['rm %(tmp)s%(abrev)s.*ns? %(tmp)s%(abrev)s.*nin %(tmp)s%(abrev)s.*nhr'
% {'tmp': self._tmp, 'abrev': self._abrev + str(self._random)}], 'bash', shell=True)
def _run_tarzip(self):
......@@ -2134,7 +2134,7 @@ class TranscriptomeAnalysis(Analysis):
"""
super(TranscriptomeAnalysis, self).cleanup()
Analysis.p_open(['rm %s*%s%s_.temp' % (self._tmp, self._abrev, self._random)], 'bash', shell=True)
Analysis.p_open(['rm %(tmp)s%(abrev)s.ns? %(tmp)s%(abrev)s.nin %(tmp)s%(abrev)s.nhr'
Analysis.p_open(['rm %(tmp)s%(abrev)s.*ns? %(tmp)s%(abrev)s.*nin %(tmp)s%(abrev)s.*nhr'
% {'tmp': self._tmp, 'abrev': self._abrev + str(self._random)}], 'bash', shell=True)
def _run_tarzip(self):
......@@ -2416,7 +2416,7 @@ class GeneSetAnalysis(Analysis):
# end of classes definition, now module code
VERSION = 'beta 2.0'
VERSION = '2.0 beta 1'
CONTACT = 'mailto:[email protected]'
......@@ -2469,7 +2469,8 @@ def _parse_args():
'transcriptome assemblies (DNA)\n- prot or proteins, for annotated gene sets (protein)')
required.add_argument(
'-l', '--lineage', dest='clade', required=True, metavar='LINEAGE',
help='Specify which BUSCO lineage data to use.\nVisit http://busco.ezlab.org for available lineages.')
help='Specify location of the BUSCO lineage data to be used.\n'
'Visit http://busco.ezlab.org for available lineages.')
optional.add_argument(
'-f', '--force', action='store_true', required=False, default=False, dest='force',
......@@ -2601,7 +2602,7 @@ def _define_parameters(args):
else:
target_species = args['species']
_logger.info('The dataset is %s (%s)' % (clade_name, domain))
_logger.info('The lineage dataset is: %s (%s)' % (clade_name, domain))
# Set up the number of cores to be used
# Augustus uses the python 'threading' library to be run in parallel, blast and HMMer allow this by default
......
This diff is collapsed.
......@@ -8,9 +8,9 @@ NOTE: This public repository is being set up. It provides the **beta version of
**BUSCO - Benchmarking sets of Universal Single-Copy Orthologs.**
To get help, ``python3 BUSCO.py -h`` and ``python3 BUSCO_plot.py -h``.
To get help, ``python BUSCO.py -h`` and ``python BUSCO_plot.py -h``.
See also the user guide: http://busco.ezlab.org/files/BUSCO_userguide.pdf
See also the user guide: BUSCO_userguide.pdf
You can download BUSCO datasets on http://busco.ezlab.org
......@@ -24,4 +24,4 @@ the Free Software Foundation, either version 3 of the License, or
BUSCO is distributed in the hope that it will be useful,
but WITHOUT ANY WARRANTY; without even the implied warranty of
MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
GNU General Public License for more details.
\ No newline at end of file
GNU General Public License for more details.
Markdown is supported
0%
or
You are about to add 0 people to the discussion. Proceed with caution.
Finish editing this message first!
Please register or to comment