Mercurial > repos > peterjc > samtools_idxstats
comparison tools/samtools_idxstats/samtools_idxstats.py @ 0:d4412c04d7b1 draft
Uploaded v0.0.1 (as tested previously on the Test Tool Shed)
| author | peterjc |
|---|---|
| date | Wed, 20 Nov 2013 12:27:33 -0500 |
| parents | |
| children | 8945bad80f4a |
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| -1:000000000000 | 0:d4412c04d7b1 |
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| 1 #!/usr/bin/env python | |
| 2 """Wrapper for "samtools idxstats" for use in Galaxy. | |
| 3 | |
| 4 This script takes exactly three command line arguments: | |
| 5 * Input BAM filename | |
| 6 * Input BAI filename (via Galaxy metadata) | |
| 7 * Output tabular filename | |
| 8 | |
| 9 This messes about with the filenames to make samtools happy, then | |
| 10 runs "samtools idxstats" and captures the output to the desired | |
| 11 tabular file. | |
| 12 """ | |
| 13 import sys | |
| 14 import os | |
| 15 import subprocess | |
| 16 import tempfile | |
| 17 | |
| 18 if "-v" in sys.argv or "--version" in sys.argv: | |
| 19 #Galaxy seems to invert the order of the two lines | |
| 20 print "(Galaxy wrapper v0.0.1)" | |
| 21 cmd = "samtools 2>&1 | grep -i ^Version" | |
| 22 sys.exit(os.system(cmd)) | |
| 23 | |
| 24 def stop_err(msg, error_level=1): | |
| 25 """Print error message to stdout and quit with given error level.""" | |
| 26 sys.stderr.write("%s\n" % msg) | |
| 27 sys.exit(error_level) | |
| 28 | |
| 29 if len(sys.argv) != 4: | |
| 30 stop_err("Require three arguments: BAM, BAI, tabular filenames") | |
| 31 | |
| 32 bam_filename, bai_filename, tabular_filename = sys.argv[1:] | |
| 33 | |
| 34 if not os.path.isfile(bam_filename): | |
| 35 stop_err("Input BAM file not found: %s" % bam_filename) | |
| 36 if not os.path.isfile(bai_filename): | |
| 37 if bai_filename == "None": | |
| 38 stop_err("Error: Galaxy did not index your BAM file") | |
| 39 stop_err("Input BAI file not found: %s" % bai_filename) | |
| 40 | |
| 41 #Assign sensible names with real extensions, and setup symlinks: | |
| 42 tmp_dir = tempfile.mkdtemp() | |
| 43 bam_file = os.path.join(tmp_dir, "temp.bam") | |
| 44 bai_file = os.path.join(tmp_dir, "temp.bam.bai") | |
| 45 os.symlink(os.path.abspath(bam_filename), bam_file) | |
| 46 os.symlink(os.path.abspath(bai_filename), bai_file) | |
| 47 assert os.path.isfile(bam_file), bam_file | |
| 48 assert os.path.isfile(bai_file), bai_file | |
| 49 assert os.path.isfile(bam_file + ".bai"), bam_file | |
| 50 | |
| 51 #Run samtools idxstats: | |
| 52 cmd = "samtools idxstats %s > %s" % (bam_file, tabular_filename) | |
| 53 return_code = os.system(cmd) | |
| 54 | |
| 55 #Remove the temp symlinks: | |
| 56 os.remove(bam_file) | |
| 57 os.remove(bai_file) | |
| 58 os.rmdir(tmp_dir) | |
| 59 | |
| 60 if return_code: | |
| 61 stop_err("Return code %i from command:\n%s" % (return_code, cmd)) |