def main(iFileHandle, oFileHandle): iFile = fasta.load_mfa_iter(iFileHandle) oFile = smartopen(oFileHandle) for h,s in iFile: s = s.replace('-','') s = s.replace('.','') fasta.pretty(h, s, stream=oFile)
#!/usr/bin/env python """ fastaCleanHeader.py <input file> """ import sys from optparse import OptionParser import mungo.old.fasta as fasta from mungo.useful import * usage = "%prog [options] <input file>" parser = OptionParser(usage=usage, version="%prog - Version 1") options, args = parser.parse_args(sys.argv) faFile = fasta.load_mfa_iter(args[1]) for h,s in faFile: h = h.split()[0] if '|' in h: h = h.split('|')[1] print '>%s' % h print s