| #! /usr/bin/env python | |
| # -*- coding: UTF8 -*- | |
| from Bio import SeqIO | |
| from optparse import OptionParser | |
| from random import shuffle | |
| parser = OptionParser() | |
| parser.add_option("-i", "--input", dest="inp", help ="") | |
| parser.add_option("-o", "--output", dest="out", help ="") | |
| parser.add_option("-n", "--number", dest="num", help ="") | |
| (options, args) = parser.parse_args() | |
| inp = options.inp | |
| out = options.out | |
| num = int(options.num) | |
| fasta = str(out) | |
| fastaw = open(fasta, "a+b") | |
| nbrtotal = 0 | |
| count = -1 | |
| for record in SeqIO.parse(inp, "fastq"): | |
| nbrtotal += 1 | |
| # print nbrtotal | |
| # print num | |
| if num > nbrtotal: | |
| num = nbrtotal | |
| # print num | |
| listseq = list(xrange(nbrtotal)) | |
| shuffle(listseq) | |
| listprelev = listseq[0:num] | |
| listprelev = sorted(listprelev) | |
| for record in SeqIO.parse(inp, "fastq"): | |
| count += 1 | |
| if count == listprelev[0]: | |
| listprelev.pop(0) | |
| sqname = record.description | |
| sq = str(record.seq) | |
| writeoupt = ">" + sqname + "\n" + sq + "\n" | |
| fastaw.write(writeoupt) | |
| if len(listprelev) == 0: | |
| break | |
| fastaw.close() | |