Commit 6b4b3e39 by Eric Coissac

various small bugs

parent f87e9208
......@@ -79,13 +79,14 @@ def addSolexaPairEndOptions(optionManager):
const='illumina',
help="input file is in fastq nucleic format produced by old solexa sequencer")
optionManager.add_option('--proba',
action="store", dest="proba",
metavar="<FILENAME>",
type="str",
default=None,
help="null ditribution data file")
# optionManager.add_option('--proba',
# action="store", dest="proba",
# metavar="<FILENAME>",
# type="str",
# default=None,
# help="null ditribution data file")
optionManager.add_option('--score-min',
action="store", dest="smin",
metavar="#.###",
......@@ -93,12 +94,12 @@ def addSolexaPairEndOptions(optionManager):
default=None,
help="minimum score for keeping aligment")
optionManager.add_option('--pvalue',
action="store", dest="pvalue",
metavar="#.###",
type="float",
default=None,
help="maximum pvalue for keeping aligment")
# optionManager.add_option('--pvalue',
# action="store", dest="pvalue",
# metavar="#.###",
# type="float",
# default=None,
# help="maximum pvalue for keeping aligment")
......@@ -207,6 +208,10 @@ if __name__ == '__main__':
)
(options, direct) = optionParser()
#WARNING TO REMOVE : DIRTY PATCH !
options.proba = None
options.sminL = None
options.sminR = None
......
......@@ -246,7 +246,8 @@ if __name__ == '__main__':
sequence = node['_sequence']
### Should be removed ?
sequence['clean']=status
tmp = sequence.get('clean',{})
tmp.update(status)
tmp = sequence.get('head',{})
tmp[ratio]=h
......
......@@ -50,6 +50,7 @@ if __name__ == '__main__':
writer(s)
i+=1
else:
print >>sys.stderr,""
sys.exit(0)
......
......@@ -145,7 +145,10 @@ if __name__=='__main__':
if type(k) is str:
if k not in omit:
if k in seq:
s = '%s%s%s'%(s,OFS,seq[k])
v = seq[k]
if v is None:
v=options.NA
s = '%s%s%s'%(s,OFS,v)
else:
s = '%s%s%s'%(s,OFS,options.NA)
else:
......@@ -155,7 +158,10 @@ if __name__=='__main__':
else:
sk={}
if k[1] in sk:
s = '%s%s%s'%(s,OFS,sk[k[1]])
v = sk[k[1]]
if v is None:
v=options.NA
s = '%s%s%s'%(s,OFS,v)
else:
if k[0][0:7]=='merged_':
s = '%s%s0'%(s,OFS)
......
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