Mercurial > repos > fcaramia > contra
comparison Contra/scripts/get_chr_length.py @ 0:7564f3b1e675
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| author | fcaramia |
|---|---|
| date | Thu, 13 Sep 2012 02:31:43 -0400 |
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| -1:000000000000 | 0:7564f3b1e675 |
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| 1 # ----------------------------------------------------------------------# | |
| 2 # Copyright (c) 2011, Richard Lupat & Jason Li. | |
| 3 # | |
| 4 # > Source License < | |
| 5 # This file is part of CONTRA. | |
| 6 # | |
| 7 # CONTRA is free software: you can redistribute it and/or modify | |
| 8 # it under the terms of the GNU General Public License as published by | |
| 9 # the Free Software Foundation, either version 3 of the License, or | |
| 10 # (at your option) any later version. | |
| 11 # | |
| 12 # CONTRA is distributed in the hope that it will be useful, | |
| 13 # but WITHOUT ANY WARRANTY; without even the implied warranty of | |
| 14 # MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the | |
| 15 # GNU General Public License for more details. | |
| 16 # | |
| 17 # You should have received a copy of the GNU General Public License | |
| 18 # along with CONTRA. If not, see <http://www.gnu.org/licenses/>. | |
| 19 # | |
| 20 # | |
| 21 #-----------------------------------------------------------------------# | |
| 22 # Last Updated : 05 October 2011 16:43PM | |
| 23 | |
| 24 | |
| 25 import subprocess, shlex | |
| 26 | |
| 27 def get_genome(srcFile, genomeOut): | |
| 28 genome = open(genomeOut, "w") | |
| 29 | |
| 30 args = shlex.split("samtools view -H %s" %(srcFile)) | |
| 31 raw_header = subprocess.Popen(args, stdout = subprocess.PIPE).communicate()[0] | |
| 32 headers = raw_header.split("\n") | |
| 33 | |
| 34 for header in headers: | |
| 35 header = header.split("\t") | |
| 36 if header[0][1:] != "SQ": | |
| 37 continue | |
| 38 | |
| 39 genome.write(header[1].strip("SN:") + "\t" + header[2].strip("LN:") + "\n") | |
| 40 | |
| 41 genome.close() | |
| 42 | |
| 43 |