usr/bin/python from __future__ import division from Bio import ... - PLOS
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usr/bin/python from __future__ import division from Bio import ... - PLOS
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#!/usr/bin/python from __future__ import division from Bio import SeqIO import sys import random import shlex import os ''' README author: romain blanc-mathieu, INRA sophia antipolis, FRANCE. aim1: get the genomics sequences corresponding to within genome syntenic blocks (as defined by MCScanX). aim2: Nucmer pairwise alignment of block genomic sequences and compute percent identity between the two. command: extractColBlock.py McScanX.collinearity genomeAssembly.fna genomeAnnotation.gff3 dependencies: SeqIO from Bio python and nucmer, delta-filter and dnadiff from the Mummer package. ''' if len(sys.argv)
