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obi annotate: now defaults to setting str if expression is not valid

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This commit is contained in:
Celine Mercier
2020-04-24 11:35:20 +02:00
parent 67bdee105a
commit 60bfd3ae8d
2 changed files with 42 additions and 51 deletions
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41
python/obitools3/commands/annotate.pyx
View File

@ -190,58 +190,50 @@ def sequenceTaggerGenerator(config, taxo=None):
seq['seq_rank']=counter[0] seq['seq_rank']=counter[0]
for i,v in toSet: for i,v in toSet:
#try: try:
if taxo is not None: if taxo is not None:
environ = {'taxonomy' : taxo, 'sequence':seq, 'counter':counter[0], 'math':math} environ = {'taxonomy' : taxo, 'sequence':seq, 'counter':counter[0], 'math':math}
else: else:
environ = {'sequence':seq, 'counter':counter[0], 'math':math} environ = {'sequence':seq, 'counter':counter[0], 'math':math}
val = eval(v, environ, seq) val = eval(v, environ, seq)
#except Exception,e: # TODO discuss usefulness of this except Exception: # set string if not a valid expression
# if options.onlyValid: val = v
# raise e
# val = v
seq[i]=val seq[i]=val
if length: if length:
seq['seq_length']=len(seq) seq['seq_length']=len(seq)
if newId is not None: if newId is not None:
# try: try:
if taxo is not None: if taxo is not None:
environ = {'taxonomy' : taxo, 'sequence':seq, 'counter':counter[0], 'math':math} environ = {'taxonomy' : taxo, 'sequence':seq, 'counter':counter[0], 'math':math}
else: else:
environ = {'sequence':seq, 'counter':counter[0], 'math':math} environ = {'sequence':seq, 'counter':counter[0], 'math':math}
val = eval(newId, environ, seq) val = eval(newId, environ, seq)
# except Exception,e: except Exception: # set string if not a valid expression
# if options.onlyValid: val = newId
# raise e
# val = newId
seq.id=val seq.id=val
if newDef is not None: if newDef is not None:
# try: try:
if taxo is not None: if taxo is not None:
environ = {'taxonomy' : taxo, 'sequence':seq, 'counter':counter[0], 'math':math} environ = {'taxonomy' : taxo, 'sequence':seq, 'counter':counter[0], 'math':math}
else: else:
environ = {'sequence':seq, 'counter':counter[0], 'math':math} environ = {'sequence':seq, 'counter':counter[0], 'math':math}
val = eval(newDef, environ, seq) val = eval(newDef, environ, seq)
# except Exception,e: except Exception: # set string if not a valid expression
# if options.onlyValid: val = newDef
# raise e
# val = newDef
seq.definition=val seq.definition=val
#
if newSeq is not None: if newSeq is not None:
# try: try:
if taxo is not None: if taxo is not None:
environ = {'taxonomy' : taxo, 'sequence':seq, 'counter':counter[0], 'math':math} environ = {'taxonomy' : taxo, 'sequence':seq, 'counter':counter[0], 'math':math}
else: else:
environ = {'sequence':seq, 'counter':counter[0], 'math':math} environ = {'sequence':seq, 'counter':counter[0], 'math':math}
val = eval(newSeq, environ, seq) val = eval(newSeq, environ, seq)
# except Exception,e: except Exception: # set string if not a valid expression
# if options.onlyValid: val = newSeq
# raise e
# val = newSeq
seq.seq=val seq.seq=val
if 'seq_length' in seq: if 'seq_length' in seq:
seq['seq_length']=len(seq) seq['seq_length']=len(seq)
@ -251,15 +243,14 @@ def sequenceTaggerGenerator(config, taxo=None):
seq.view.delete_column(QUALITY_COLUMN) seq.view.delete_column(QUALITY_COLUMN)
if run is not None: if run is not None:
# try: try:
if taxo is not None: if taxo is not None:
environ = {'taxonomy' : taxo, 'sequence':seq, 'counter':counter[0], 'math':math} environ = {'taxonomy' : taxo, 'sequence':seq, 'counter':counter[0], 'math':math}
else: else:
environ = {'sequence':seq, 'counter':counter[0], 'math':math} environ = {'sequence':seq, 'counter':counter[0], 'math':math}
eval(run, environ, seq) eval(run, environ, seq)
# except Exception,e: except Exception,e:
# if options.onlyValid: raise e
# raise e
return sequenceTagger return sequenceTagger

2
python/obitools3/version.py
View File

@ -1,5 +1,5 @@
major = 3 major = 3
minor = 0 minor = 0
serial= '0-beta14b' serial= '0-beta1c'
version ="%d.%02d.%s" % (major,minor,serial) version ="%d.%02d.%s" % (major,minor,serial)