Commit 89aa1ab2 by Rob Waterhouse Committed by Mathieu

BUSCO 2.0.1

parent 623f5a65
......@@ -7,7 +7,7 @@
.. moduleauthor:: Robert M. Waterhouse <robert.waterhouse@unige.ch>
.. moduleauthor:: Mathieu Seppey <mathieu.seppey@unige.ch>
.. versionadded:: 1.0
.. versionchanged:: 2.0
.. versionchanged:: 2.0.1
BUSCO - Benchmarking Universal Single-Copy Orthologs.
......@@ -981,8 +981,13 @@ class Analysis(object):
try:
if "processed" not in open('%sblast_output/tblastn_%s%s.tsv' % (self.mainout, self._abrev, output_suffix),
'r').readlines()[-1]:
_logger.warning('tblastn might have ended prematurely (the result file lacks the expected final line), '
'which could produce incomplete results in the next steps !')
_logger.error('tblastn has ended prematurely (the result file lacks the expected final line), '
'which will produce incomplete results in the next steps ! '
'This problem likely appeared in blast+ 2.4 and seems not fully fixed in 2.6. '
'It happens only when using multiple cores. You can use a single core (-c 1) or '
'downgrade to blast+ 2.2.x, a safe choice regarding this issue. '
'See blast+ documentation for more information.')
raise SystemExit
except IndexError:
pass # if the tblastn result file is empty, for example in phase 2 if 100% was found in phase 1
......@@ -1199,11 +1204,13 @@ class Analysis(object):
Analysis.p_open(['new_species.pl --species=BUSCO_%s%s 1>>%s'
' 2>&1'
% (self._abrev, self._random, augustus_log)], 'new_species.pl', shell=True)
Analysis.p_open(['cat %saugustus_output/gb/*.gb > %saugustus_output/training_set_%s.txt'
% (self.mainout, self.mainout, self._abrev)],
'bash',
shell=True)
Analysis.p_open(
['find %saugustus_output/gb/ -type f -name "*.gb" -exec cat {} \; > %saugustus_output/training_set_%s.txt'
% (self.mainout, self.mainout, self._abrev)],
'bash',
shell=True)
# train on new training set (complete single copy buscos)
Analysis.p_open(['etraining --species=BUSCO_%s%s %saugustus_output/training_set_%s.txt 1>>%s 2>&1' %
(self._abrev, self._random, self.mainout, self._abrev, augustus_log)], 'augustus etraining',
......@@ -2653,7 +2660,7 @@ class GeneSetAnalysis(Analysis):
# end of classes definition, now module code
VERSION = '2.0'
VERSION = '2.0.1'
CONTACT = 'mailto:support@orthodb.org'
......
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2.0.1
- Stop the execution when tblastn crashes, instead of just warning the user
- Issue #16 fixed
- Issue #9 fixed
2.0
- Minor changes, similar to beta 4
......
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