def main(): usage = "usage: %prog [options] file.fa " parser = argparse.ArgumentParser(description='concatenate records from seperate fasta files into a single fasta record ') parser.add_argument('fastafile', metavar='fastafile', type=str, nargs='+', help='sample names to remove') parser.add_argument('-header', type=str,help='header of new concatenated fasta record (header will also serve as the newfilename') args = parser.parse_args() print args fastafilehandles=list(itertools.imap(open, args.fastafile)) #list of filehandles for fastq files concatenateseq='' for fh in fastafilehandles: for (header, sequence) in yieldFastaRecord(fh): concatenateseq+=sequence writefasta(concatenateseq,args.header, args.header+".fa")
def main(): usage = "usage: %prog [options] file.fa " parser = argparse.ArgumentParser(description='filter records based on genotypes') parser.add_argument('-start', type=int, help='zero based start index') parser.add_argument('-end', type=int, help='one-based end index') parser.add_argument('fasta', type=str,help='file.fa file') args = parser.parse_args() fh=open(args.fasta,'r') for (header, sequence) in yieldFastaRecord(fh): writefasta_stdout(sequence[args.start:args.end], header+":"+str(args.start)+"-"+str(args.end))