47 lines
1.7 KiB
Python
47 lines
1.7 KiB
Python
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from obitools.format.genericparser import GenericParser
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from obitools.utils import universalOpen
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from obitools.fasta import parseFastaDescription
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from obitools import NucSequence
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import sys
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_contigIterator=GenericParser('^CO ')
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_contigIterator.addParseAction('AF', '\nAF +(\S+) +([UC]) +(-?[0-9]+)')
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_contigIterator.addParseAction('RD', '\nRD +(\S+) +([0-9]+) +([0-9]+) +([0-9]+) *\n([A-Za-z\n*]+?)\n\n')
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_contigIterator.addParseAction('DS', '\nDS +(.+)')
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_contigIterator.addParseAction('CO', '^CO (\S+)')
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def contigIterator(file):
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file = universalOpen(file)
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for entry in _contigIterator(file):
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contig=[]
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for rd,ds,af in map(None,entry['RD'],entry['DS'],entry['AF']):
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id = rd[0]
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shift = int(af[2])
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if shift < 0:
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print >> sys.stderr,"Sequence %s in contig %s has a negative paddng value %d : skipped" % (id,entry['CO'][0],shift)
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#continue
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definition,info = parseFastaDescription(ds)
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info['shift']=shift
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seq = rd[4].replace('\n','').replace('*','-').strip()
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contig.append(NucSequence(id,seq,definition,**info))
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maxlen = max(len(x)+x['shift'] for x in contig)
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minshift=min(x['shift'] for x in contig)
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rep = []
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for s in contig:
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info = s.getTags()
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info['shift']-=minshift-1
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head = '-' * (info['shift']-1)
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tail = (maxlen + minshift - len(s) - info['shift'] - 1)
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info['tail']=tail
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newseq = NucSequence(s.id,head + str(s)+ '-' * tail,s.definition,**info)
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rep.append(newseq)
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yield entry['CO'][0],rep
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