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comparison tools/samtools_idxstats/samtools_idxstats.py @ 2:71afa65f444a draft default tip

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v0.0.5 Internal changes to command line handling
author peterjc
date Tue, 16 May 2017 09:24:18 -0400
parents 8945bad80f4a
children
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1:8945bad80f4a 2:71afa65f444a
8 8
9 This messes about with the filenames to make samtools happy, then 9 This messes about with the filenames to make samtools happy, then
10 runs "samtools idxstats" and captures the output to the desired 10 runs "samtools idxstats" and captures the output to the desired
11 tabular file. 11 tabular file.
12 """ 12 """
13
14 import os
13 import sys 15 import sys
14 import os
15 import subprocess
16 import tempfile 16 import tempfile
17 17
18 if "-v" in sys.argv or "--version" in sys.argv: 18 if "-v" in sys.argv or "--version" in sys.argv:
19 #Galaxy seems to invert the order of the two lines 19 # Galaxy seems to invert the order of the two lines
20 print "(Galaxy wrapper v0.0.2)" 20 print "(Galaxy wrapper v0.0.2)"
21 cmd = "samtools 2>&1 | grep -i ^Version" 21 cmd = "samtools 2>&1 | grep -i ^Version"
22 sys.exit(os.system(cmd)) 22 sys.exit(os.system(cmd))
23 23
24 def sys_exit(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: 24 if len(sys.argv) != 4:
30 sys_exit("Require three arguments: BAM, BAI, tabular filenames") 25 sys.exit("Require three arguments: BAM, BAI, tabular filenames")
31 26
32 bam_filename, bai_filename, tabular_filename = sys.argv[1:] 27 bam_filename, bai_filename, tabular_filename = sys.argv[1:]
33 28
34 if not os.path.isfile(bam_filename): 29 if not os.path.isfile(bam_filename):
35 sys_exit("Input BAM file not found: %s" % bam_filename) 30 sys.exit("Input BAM file not found: %s" % bam_filename)
36 if not os.path.isfile(bai_filename): 31 if not os.path.isfile(bai_filename):
37 if bai_filename == "None": 32 if bai_filename == "None":
38 sys_exit("Error: Galaxy did not index your BAM file") 33 sys.exit("Error: Galaxy did not index your BAM file")
39 sys_exit("Input BAI file not found: %s" % bai_filename) 34 sys.exit("Input BAI file not found: %s" % bai_filename)
40 35
41 #Assign sensible names with real extensions, and setup symlinks: 36 # Assign sensible names with real extensions, and setup symlinks:
42 tmp_dir = tempfile.mkdtemp() 37 tmp_dir = tempfile.mkdtemp()
43 bam_file = os.path.join(tmp_dir, "temp.bam") 38 bam_file = os.path.join(tmp_dir, "temp.bam")
44 bai_file = os.path.join(tmp_dir, "temp.bam.bai") 39 bai_file = os.path.join(tmp_dir, "temp.bam.bai")
45 os.symlink(os.path.abspath(bam_filename), bam_file) 40 os.symlink(os.path.abspath(bam_filename), bam_file)
46 os.symlink(os.path.abspath(bai_filename), bai_file) 41 os.symlink(os.path.abspath(bai_filename), bai_file)
47 assert os.path.isfile(bam_file), bam_file 42 assert os.path.isfile(bam_file), bam_file
48 assert os.path.isfile(bai_file), bai_file 43 assert os.path.isfile(bai_file), bai_file
49 assert os.path.isfile(bam_file + ".bai"), bam_file 44 assert os.path.isfile(bam_file + ".bai"), bam_file
50 45
51 #Run samtools idxstats: 46 # Run samtools idxstats:
52 cmd = 'samtools idxstats "%s" > "%s"' % (bam_file, tabular_filename) 47 cmd = 'samtools idxstats "%s" > "%s"' % (bam_file, tabular_filename)
53 return_code = os.system(cmd) 48 return_code = os.system(cmd)
54 49
55 #Remove the temp symlinks: 50 # Remove the temp symlinks:
56 os.remove(bam_file) 51 os.remove(bam_file)
57 os.remove(bai_file) 52 os.remove(bai_file)
58 os.rmdir(tmp_dir) 53 os.rmdir(tmp_dir)
59 54
60 if return_code: 55 if return_code:
61 sys_exit("Return code %i from command:\n%s" % (return_code, cmd)) 56 sys.exit("Return code %i from command:\n%s" % (return_code, cmd))