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))
