obitools/ecopcr
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git-svn-id: https://www.grenoble.prabi.fr/svn/LECASofts/ecoPCR/branches/refactoring@67 60f365c0-8329-0410-b2a4-ec073aeeaa1d

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This commit is contained in:
Eric Coissac
2007-06-15 13:40:14 +00:00
parent 8455ed0a99
commit fc26a9fda3
1 changed files with 51 additions and 6 deletions
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55
tools/ecoPCRFormat.py
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@ -267,6 +267,30 @@ def genbankEntryParser(entry):
Tx = None Tx = None
return {'id':Id,'taxid':Tx,'definition':De,'sequence':Sq} return {'id':Id,'taxid':Tx,'definition':De,'sequence':Sq}
######################
_cleanDef = re.compile('[\nDE]')
def cleanDef(definition):
return _cleanDef.sub('',definition)
_emblParseID = re.compile('(?<=^ID {3})[^ ]+(?=;)',re.MULTILINE)
_emblParseDE = re.compile('(?<=^DE {3}).+?\. *$(?=[^ ])',re.MULTILINE+re.DOTALL)
_emblParseSQ = re.compile('(?<=^ ).+?(?=^//$)',re.MULTILINE+re.DOTALL)
_emblParseTX = re.compile('(?<= /db_xref="taxon:)[0-9]+(?=")')
def emblEntryParser(entry):
Id = _emblParseID.findall(entry)[0]
De = ' '.join(cleanDef(_emblParseDE.findall(entry)[0]).split())
Sq = cleanSeq(_emblParseSQ.findall(entry)[0].upper())
try:
Tx = int(_emblParseTX.findall(entry)[0])
except IndexError:
Tx = None
return {'id':Id,'taxid':Tx,'definition':De,'sequence':Sq}
######################
_fastaParseID = re.compile('(?<=^>)[^ ]+') _fastaParseID = re.compile('(?<=^>)[^ ]+')
_fastaParseDE = re.compile('(?<=^>).+',) _fastaParseDE = re.compile('(?<=^>).+',)
_fastaParseSQ = re.compile('^[^>].+',re.MULTILINE+re.DOTALL) _fastaParseSQ = re.compile('^[^>].+',re.MULTILINE+re.DOTALL)
@ -464,32 +488,53 @@ def ecoParseOptions(arguments):
} }
o,filenames = getopt.getopt(arguments, o,filenames = getopt.getopt(arguments,
'ht:n:gf', 'ht:n:gfe',
['help', ['help',
'taxonomy=', 'taxonomy=',
'name=', 'name=',
'genbank', 'genbank',
'fasta']) 'fasta',
'embl'])
for name,value in o: for name,value in o:
if name in ('-h','--help'): if name in ('-h','--help'):
pass printHelp()
exit()
elif name in ('-t','--taxonomy'): elif name in ('-t','--taxonomy'):
opt['taxdir']=value opt['taxdir']=value
elif name in ('-n','--name'): elif name in ('-n','--name'):
opt['prefix']=value opt['prefix']=value
elif name in ('-g','--genbank'): elif name in ('-g','--genbank'):
opt['parser']=sequenceIteratorFactory(genbankEntryParser, opt['parser']=sequenceIteratorFactory(genbankEntryParser,
entryIterator entryIterator)
)
elif name in ('-f','--fasta'): elif name in ('-f','--fasta'):
opt['parser']=sequenceIteratorFactory(fastaEntryParser, opt['parser']=sequenceIteratorFactory(fastaEntryParser,
fastaEntryIterator) fastaEntryIterator)
elif name in ('-e','--embl'):
opt['parser']=sequenceIteratorFactory(emblEntryParser,
entryIterator)
else: else:
raise ValueError,'Unknown option %s' % name raise ValueError,'Unknown option %s' % name
return opt,filenames return opt,filenames
def printHelp():
print "-----------------------------------"
print " ecoPCRFormat.py"
print "-----------------------------------"
print "ecoPCRFormat.py [option] <argument>"
print "-----------------------------------"
print "-e --embl :[E]mbl format file name"
print "-f --fasta :[F]asta format file name"
print "-g --genbank :[G]enbank format file name"
print "-h --help :[H]elp - print this help"
print "-n --name :[N]ame of the new database created"
print "-t --taxonomy :[T]axonomy - path to the taxonomy database"
print " :bcp-like dump from GenBank taxonomy database."
print "-----------------------------------"
if __name__ == '__main__': if __name__ == '__main__':
opt,filenames = ecoParseOptions(sys.argv[1:]) opt,filenames = ecoParseOptions(sys.argv[1:])