Mercurial > repos > scottx611x > qualimap2_bamqc

annotate qualimap_bamqc.py @ 34:7e359370b5a2 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload for repository https://github.com/scottx611x/qualimap2 commit dc78b7c4b1780b316ca4aba2be247969ac1100ec-dirty
author scottx611x
date Thu, 26 Jul 2018 16:52:28 -0400
parents 0ea51e29a0ce
children a3e9c80894dd
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
1
716e406ce6ea planemo upload for repository https://github.com/scottx611x/qualimap2 commit 2e9620ea29d3a146e8669ec0037932d9a2135c79-dirty
scottx611x
parents:
diff changeset
1 #!/usr/bin/env python
716e406ce6ea planemo upload for repository https://github.com/scottx611x/qualimap2 commit 2e9620ea29d3a146e8669ec0037932d9a2135c79-dirty
scottx611x
parents:
diff changeset
2 from __future__ import print_function
716e406ce6ea planemo upload for repository https://github.com/scottx611x/qualimap2 commit 2e9620ea29d3a146e8669ec0037932d9a2135c79-dirty
scottx611x
parents:
diff changeset
3 import argparse
32
90170eb47bd1 planemo upload for repository https://github.com/scottx611x/qualimap2 commit dc78b7c4b1780b316ca4aba2be247969ac1100ec-dirty
scottx611x
parents: 31
diff changeset
4 import os
1
716e406ce6ea planemo upload for repository https://github.com/scottx611x/qualimap2 commit 2e9620ea29d3a146e8669ec0037932d9a2135c79-dirty
scottx611x
parents:
diff changeset
5 from subprocess import check_call, CalledProcessError
23
cefa83db3ebf planemo upload for repository https://github.com/scottx611x/qualimap2 commit dc78b7c4b1780b316ca4aba2be247969ac1100ec-dirty
scottx611x
parents: 10
diff changeset
6 import shutil
1
716e406ce6ea planemo upload for repository https://github.com/scottx611x/qualimap2 commit 2e9620ea29d3a146e8669ec0037932d9a2135c79-dirty
scottx611x
parents:
diff changeset
7 import sys
716e406ce6ea planemo upload for repository https://github.com/scottx611x/qualimap2 commit 2e9620ea29d3a146e8669ec0037932d9a2135c79-dirty
scottx611x
parents:
diff changeset
8
30
418ee04dd1b2 planemo upload for repository https://github.com/scottx611x/qualimap2 commit dc78b7c4b1780b316ca4aba2be247969ac1100ec-dirty
scottx611x
parents: 29
diff changeset
9 OUTPUT_DIR = "qualimap_results"
418ee04dd1b2 planemo upload for repository https://github.com/scottx611x/qualimap2 commit dc78b7c4b1780b316ca4aba2be247969ac1100ec-dirty
scottx611x
parents: 29
diff changeset
10
1
716e406ce6ea planemo upload for repository https://github.com/scottx611x/qualimap2 commit 2e9620ea29d3a146e8669ec0037932d9a2135c79-dirty
scottx611x
parents:
diff changeset
11
34
7e359370b5a2 planemo upload for repository https://github.com/scottx611x/qualimap2 commit dc78b7c4b1780b316ca4aba2be247969ac1100ec-dirty
scottx611x
parents: 33
diff changeset
12 def qualimap_bamqc(bam_filename, genomecov_file, out_dir, jv_mem_size):
1
716e406ce6ea planemo upload for repository https://github.com/scottx611x/qualimap2 commit 2e9620ea29d3a146e8669ec0037932d9a2135c79-dirty
scottx611x
parents:
diff changeset
13 qualimap_command = [
716e406ce6ea planemo upload for repository https://github.com/scottx611x/qualimap2 commit 2e9620ea29d3a146e8669ec0037932d9a2135c79-dirty
scottx611x
parents:
diff changeset
14 "qualimap", "bamqc",
716e406ce6ea planemo upload for repository https://github.com/scottx611x/qualimap2 commit 2e9620ea29d3a146e8669ec0037932d9a2135c79-dirty
scottx611x
parents:
diff changeset
15 "-bam " + bam_filename,
716e406ce6ea planemo upload for repository https://github.com/scottx611x/qualimap2 commit 2e9620ea29d3a146e8669ec0037932d9a2135c79-dirty
scottx611x
parents:
diff changeset
16 "-oc " + genomecov_file,
34
7e359370b5a2 planemo upload for repository https://github.com/scottx611x/qualimap2 commit dc78b7c4b1780b316ca4aba2be247969ac1100ec-dirty
scottx611x
parents: 33
diff changeset
17 "-outdir " + out_dir,
1
716e406ce6ea planemo upload for repository https://github.com/scottx611x/qualimap2 commit 2e9620ea29d3a146e8669ec0037932d9a2135c79-dirty
scottx611x
parents:
diff changeset
18 "--java-mem-size=" + jv_mem_size
716e406ce6ea planemo upload for repository https://github.com/scottx611x/qualimap2 commit 2e9620ea29d3a146e8669ec0037932d9a2135c79-dirty
scottx611x
parents:
diff changeset
19 ]
716e406ce6ea planemo upload for repository https://github.com/scottx611x/qualimap2 commit 2e9620ea29d3a146e8669ec0037932d9a2135c79-dirty
scottx611x
parents:
diff changeset
20
716e406ce6ea planemo upload for repository https://github.com/scottx611x/qualimap2 commit 2e9620ea29d3a146e8669ec0037932d9a2135c79-dirty
scottx611x
parents:
diff changeset
21 try:
716e406ce6ea planemo upload for repository https://github.com/scottx611x/qualimap2 commit 2e9620ea29d3a146e8669ec0037932d9a2135c79-dirty
scottx611x
parents:
diff changeset
22 check_call(qualimap_command)
716e406ce6ea planemo upload for repository https://github.com/scottx611x/qualimap2 commit 2e9620ea29d3a146e8669ec0037932d9a2135c79-dirty
scottx611x
parents:
diff changeset
23 except CalledProcessError:
716e406ce6ea planemo upload for repository https://github.com/scottx611x/qualimap2 commit 2e9620ea29d3a146e8669ec0037932d9a2135c79-dirty
scottx611x
parents:
diff changeset
24 print("Error running the qualimap bamqc", file=sys.stderr)
716e406ce6ea planemo upload for repository https://github.com/scottx611x/qualimap2 commit 2e9620ea29d3a146e8669ec0037932d9a2135c79-dirty
scottx611x
parents:
diff changeset
25
716e406ce6ea planemo upload for repository https://github.com/scottx611x/qualimap2 commit 2e9620ea29d3a146e8669ec0037932d9a2135c79-dirty
scottx611x
parents:
diff changeset
26
716e406ce6ea planemo upload for repository https://github.com/scottx611x/qualimap2 commit 2e9620ea29d3a146e8669ec0037932d9a2135c79-dirty
scottx611x
parents:
diff changeset
27 def main():
716e406ce6ea planemo upload for repository https://github.com/scottx611x/qualimap2 commit 2e9620ea29d3a146e8669ec0037932d9a2135c79-dirty
scottx611x
parents:
diff changeset
28 parser = argparse.ArgumentParser(
716e406ce6ea planemo upload for repository https://github.com/scottx611x/qualimap2 commit 2e9620ea29d3a146e8669ec0037932d9a2135c79-dirty
scottx611x
parents:
diff changeset
29 description="Generate Bam Quality Statistics"
716e406ce6ea planemo upload for repository https://github.com/scottx611x/qualimap2 commit 2e9620ea29d3a146e8669ec0037932d9a2135c79-dirty
scottx611x
parents:
diff changeset
30 )
716e406ce6ea planemo upload for repository https://github.com/scottx611x/qualimap2 commit 2e9620ea29d3a146e8669ec0037932d9a2135c79-dirty
scottx611x
parents:
diff changeset
31 parser.add_argument('--input_file')
23
cefa83db3ebf planemo upload for repository https://github.com/scottx611x/qualimap2 commit dc78b7c4b1780b316ca4aba2be247969ac1100ec-dirty
scottx611x
parents: 10
diff changeset
32 parser.add_argument('--out_genome_file')
34
7e359370b5a2 planemo upload for repository https://github.com/scottx611x/qualimap2 commit dc78b7c4b1780b316ca4aba2be247969ac1100ec-dirty
scottx611x
parents: 33
diff changeset
33 parser.add_argument('--out_dir')
23
cefa83db3ebf planemo upload for repository https://github.com/scottx611x/qualimap2 commit dc78b7c4b1780b316ca4aba2be247969ac1100ec-dirty
scottx611x
parents: 10
diff changeset
34 parser.add_argument('--java_mem_size')
1
716e406ce6ea planemo upload for repository https://github.com/scottx611x/qualimap2 commit 2e9620ea29d3a146e8669ec0037932d9a2135c79-dirty
scottx611x
parents:
diff changeset
35
716e406ce6ea planemo upload for repository https://github.com/scottx611x/qualimap2 commit 2e9620ea29d3a146e8669ec0037932d9a2135c79-dirty
scottx611x
parents:
diff changeset
36 args = parser.parse_args()
10
4e5e0a116434 planemo upload for repository https://github.com/scottx611x/qualimap2 commit dc78b7c4b1780b316ca4aba2be247969ac1100ec-dirty
scottx611x
parents: 2
diff changeset
37
34
7e359370b5a2 planemo upload for repository https://github.com/scottx611x/qualimap2 commit dc78b7c4b1780b316ca4aba2be247969ac1100ec-dirty
scottx611x
parents: 33
diff changeset
38 print(os.listdir(args.out_dir))
32
90170eb47bd1 planemo upload for repository https://github.com/scottx611x/qualimap2 commit dc78b7c4b1780b316ca4aba2be247969ac1100ec-dirty
scottx611x
parents: 31
diff changeset
39
1
716e406ce6ea planemo upload for repository https://github.com/scottx611x/qualimap2 commit 2e9620ea29d3a146e8669ec0037932d9a2135c79-dirty
scottx611x
parents:
diff changeset
40 qualimap_bamqc(
716e406ce6ea planemo upload for repository https://github.com/scottx611x/qualimap2 commit 2e9620ea29d3a146e8669ec0037932d9a2135c79-dirty
scottx611x
parents:
diff changeset
41 args.input_file,
716e406ce6ea planemo upload for repository https://github.com/scottx611x/qualimap2 commit 2e9620ea29d3a146e8669ec0037932d9a2135c79-dirty
scottx611x
parents:
diff changeset
42 args.out_genome_file,
34
7e359370b5a2 planemo upload for repository https://github.com/scottx611x/qualimap2 commit dc78b7c4b1780b316ca4aba2be247969ac1100ec-dirty
scottx611x
parents: 33
diff changeset
43 args.out_dir,
1
716e406ce6ea planemo upload for repository https://github.com/scottx611x/qualimap2 commit 2e9620ea29d3a146e8669ec0037932d9a2135c79-dirty
scottx611x
parents:
diff changeset
44 args.java_mem_size
716e406ce6ea planemo upload for repository https://github.com/scottx611x/qualimap2 commit 2e9620ea29d3a146e8669ec0037932d9a2135c79-dirty
scottx611x
parents:
diff changeset
45 )
716e406ce6ea planemo upload for repository https://github.com/scottx611x/qualimap2 commit 2e9620ea29d3a146e8669ec0037932d9a2135c79-dirty
scottx611x
parents:
diff changeset
46
34
7e359370b5a2 planemo upload for repository https://github.com/scottx611x/qualimap2 commit dc78b7c4b1780b316ca4aba2be247969ac1100ec-dirty
scottx611x
parents: 33
diff changeset
47 shutil.move(args.out_dir + "/genome_results.txt", "./genome_results.txt")
7e359370b5a2 planemo upload for repository https://github.com/scottx611x/qualimap2 commit dc78b7c4b1780b316ca4aba2be247969ac1100ec-dirty
scottx611x
parents: 33
diff changeset
48 shutil.move(args.out_dir + "/qualimapReport.html", "./qualimapReport.html")
23
cefa83db3ebf planemo upload for repository https://github.com/scottx611x/qualimap2 commit dc78b7c4b1780b316ca4aba2be247969ac1100ec-dirty
scottx611x
parents: 10
diff changeset
49 shutil.make_archive(
31
a77bae54b1c7 planemo upload for repository https://github.com/scottx611x/qualimap2 commit dc78b7c4b1780b316ca4aba2be247969ac1100ec-dirty
scottx611x
parents: 30
diff changeset
50 './raw_data_qualimapReport',
23
cefa83db3ebf planemo upload for repository https://github.com/scottx611x/qualimap2 commit dc78b7c4b1780b316ca4aba2be247969ac1100ec-dirty
scottx611x
parents: 10
diff changeset
51 'zip',
34
7e359370b5a2 planemo upload for repository https://github.com/scottx611x/qualimap2 commit dc78b7c4b1780b316ca4aba2be247969ac1100ec-dirty
scottx611x
parents: 33
diff changeset
52 args.out_dir + '/raw_data_qualimapReport'
23
cefa83db3ebf planemo upload for repository https://github.com/scottx611x/qualimap2 commit dc78b7c4b1780b316ca4aba2be247969ac1100ec-dirty
scottx611x
parents: 10
diff changeset
53 )
cefa83db3ebf planemo upload for repository https://github.com/scottx611x/qualimap2 commit dc78b7c4b1780b316ca4aba2be247969ac1100ec-dirty
scottx611x
parents: 10
diff changeset
54
cefa83db3ebf planemo upload for repository https://github.com/scottx611x/qualimap2 commit dc78b7c4b1780b316ca4aba2be247969ac1100ec-dirty
scottx611x
parents: 10
diff changeset
55
1
716e406ce6ea planemo upload for repository https://github.com/scottx611x/qualimap2 commit 2e9620ea29d3a146e8669ec0037932d9a2135c79-dirty
scottx611x
parents:
diff changeset
56 if __name__ == "__main__":
716e406ce6ea planemo upload for repository https://github.com/scottx611x/qualimap2 commit 2e9620ea29d3a146e8669ec0037932d9a2135c79-dirty
scottx611x
parents:
diff changeset
57 main()