Mercurial > repos > xuebing > sharplab_seq_motif
view mytools/revcompl.py @ 4:797cb854c805
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author | xuebing |
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date | Fri, 16 Mar 2012 14:00:54 -0400 |
parents | 39217fa39ff2 |
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import sys compldna = {'A':'T', 'C':'G', 'G':'C', 'T':'A', 'U':'A', 'M':'K', 'K':'M', 'W':'W', 'S':'S', 'R':'Y', 'Y':'R', 'N':'N'} complrna = {'A':'U', 'C':'G', 'G':'C', 'T':'A', 'U':'A', 'M':'K', 'K':'M', 'W':'W', 'S':'S', 'R':'Y', 'Y':'R', 'N':'N'} def complement(seq,compl): complseq = [compl[base] for base in seq] return complseq def reverse_complement(seq,compl): seq = list(seq) seq.reverse() return ''.join(complement(seq,compl)) def readFastaFile(infile,outfile,compl): fin = open(infile) out = open(outfile,'w') currSeq='' currSeqname=None for line in fin: if '>' in line: if currSeqname !=None: out.write(currSeqname+reverse_complement(currSeq,compl)+'\n') currSeqname=None currSeq='' currSeqname=line else: currSeq=currSeq+line.strip().upper() if currSeqname!=None: out.write(currSeqname+reverse_complement(currSeq,compl)+'\n') fin.close() out.close() def readrawseq(infile,outfile,compl): ''' each line is a sequence ''' fin = open(infile) out = open(outfile,'w') for line in fin: out.write(reverse_complement(line.strip().upper(),compl)+'\n') fin.close() out.close() def main(): seqfile = sys.argv[1] outfile = sys.argv[2] fasta = sys.argv[3] rna = sys.argv[4] if rna == 'rna': compl = complrna else: compl = compldna if fasta == 'fasta': readFastaFile(seqfile,outfile,compl) else: readrawseq(seqfile,outfile,compl) main()