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split_fasta.py
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81 lines (65 loc) · 2.39 KB
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"""
Split a multiple-sequence FASTA file into many single-sequence FASTA files
"""
from __future__ import division
from __future__ import print_function
from __future__ import unicode_literals
import argparse
import os
import utils
def parseArgs():
description = ("Split a multiple-sequence FASTA file into many "
"single-sequence FASTA files")
parser = argparse.ArgumentParser(
description=description)
parser.add_argument("fastaFile", help="the FASTA file to split")
args = parser.parse_args()
return args
def decompressFasta(args):
fastaFileName = args.fastaFile
filename, extension = os.path.splitext(fastaFileName)
if extension == '.gz':
utils.log("Decompressing {}".format(fastaFileName))
cmd = "gunzip {}".format(fastaFileName)
utils.runCommand(cmd)
fastaFileName = filename
return fastaFileName
def splitFasta(fastaFileName):
splitFileNames = []
with open(fastaFileName) as fastaFile:
currentFile = None
currentFileName = None
for line in fastaFile:
if line[0] == '>':
if currentFile is not None:
currentFile.close()
currentFileName = line[1:].split()[0].strip() + '.fa'
utils.log("Creating {}".format(currentFileName))
splitFileNames.append(currentFileName)
currentFile = open(currentFileName, 'w')
currentFile.write(line)
currentFile.close()
return splitFileNames
def compressSplits(splitFileNames):
compressedFileNames = []
for splitFileName in splitFileNames:
utils.log("Compressing {}".format(splitFileName))
cmd = "bgzip {}".format(splitFileName)
utils.runCommand(cmd)
compressedFileName = "{}.gz".format(splitFileName)
compressedFileNames.append(compressedFileName)
return compressedFileNames
def indexSplits(compressedFileNames):
for compressedFileName in compressedFileNames:
utils.log("Indexing {}".format(compressedFileName))
cmd = "samtools faidx {}".format(compressedFileName)
utils.runCommand(cmd)
@utils.Timed()
def main():
args = parseArgs()
fastaFileName = decompressFasta(args)
splitFileNames = splitFasta(fastaFileName)
compressedFileNames = compressSplits(splitFileNames)
indexSplits(compressedFileNames)
if __name__ == '__main__':
main()