Commit 2f66a775 by Eric Coissac

Patch the obicut program

parent ccd2e284
......@@ -27,26 +27,27 @@ computed using a python expression.
Trims the first and last 50 nucleotides of the sequence object.
'''
from obitools.fasta import fastaIterator,formatFasta
from obitools.format.options import addInOutputOption, sequenceWriterGenerator
from obitools.options import getOptionManager
from obitools.options.bioseqfilter import addSequenceFilteringOptions, sequenceFilterIteratorGenerator
from obitools.options.bioseqcutter import addSequenceCuttingOptions, cutterIteratorGenerator
if __name__=='__main__':
if __name__=='__main__': # @UndefinedVariable
optionParser = getOptionManager([addSequenceCuttingOptions,
addSequenceFilteringOptions
],
entryIterator=fastaIterator
)
addSequenceFilteringOptions,
addInOutputOption],
progdoc=__doc__) # @UndefinedVariable
(options, entries) = optionParser()
filter = sequenceFilterIteratorGenerator(options)
cutter = cutterIteratorGenerator(options)
writer = sequenceWriterGenerator(options)
for seq in cutter(filter(entries)):
print formatFasta(seq)
writer(seq)
\ No newline at end of file
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