Mercurial > repos > bgruening > htseq_clip

annotate htsc_create_sliding_windows.py @ 0:94a987a7da69 draft default tip

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/htseq-clip commit 4879439f0df3386b97d8507c5991051fbdda053a
author bgruening
date Tue, 11 Oct 2022 16:09:23 +0000
parents
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
0
94a987a7da69 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/htseq-clip commit 4879439f0df3386b97d8507c5991051fbdda053a
bgruening
parents:
diff changeset
1 #!/usr/bin/env python3
94a987a7da69 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/htseq-clip commit 4879439f0df3386b97d8507c5991051fbdda053a
bgruening
parents:
diff changeset
2
94a987a7da69 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/htseq-clip commit 4879439f0df3386b97d8507c5991051fbdda053a
bgruening
parents:
diff changeset
3 import argparse
94a987a7da69 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/htseq-clip commit 4879439f0df3386b97d8507c5991051fbdda053a
bgruening
parents:
diff changeset
4 import os
94a987a7da69 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/htseq-clip commit 4879439f0df3386b97d8507c5991051fbdda053a
bgruening
parents:
diff changeset
5 import subprocess
94a987a7da69 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/htseq-clip commit 4879439f0df3386b97d8507c5991051fbdda053a
bgruening
parents:
diff changeset
6
94a987a7da69 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/htseq-clip commit 4879439f0df3386b97d8507c5991051fbdda053a
bgruening
parents:
diff changeset
7 """
94a987a7da69 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/htseq-clip commit 4879439f0df3386b97d8507c5991051fbdda053a
bgruening
parents:
diff changeset
8
94a987a7da69 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/htseq-clip commit 4879439f0df3386b97d8507c5991051fbdda053a
bgruening
parents:
diff changeset
9 Install deseq-clip
94a987a7da69 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/htseq-clip commit 4879439f0df3386b97d8507c5991051fbdda053a
bgruening
parents:
diff changeset
10 ==================
94a987a7da69 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/htseq-clip commit 4879439f0df3386b97d8507c5991051fbdda053a
bgruening
parents:
diff changeset
11
94a987a7da69 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/htseq-clip commit 4879439f0df3386b97d8507c5991051fbdda053a
bgruening
parents:
diff changeset
12 conda install -c bioconda pysam
94a987a7da69 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/htseq-clip commit 4879439f0df3386b97d8507c5991051fbdda053a
bgruening
parents:
diff changeset
13 conda install -c bioconda htseq
94a987a7da69 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/htseq-clip commit 4879439f0df3386b97d8507c5991051fbdda053a
bgruening
parents:
diff changeset
14 pip install htseq-clip
94a987a7da69 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/htseq-clip commit 4879439f0df3386b97d8507c5991051fbdda053a
bgruening
parents:
diff changeset
15
94a987a7da69 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/htseq-clip commit 4879439f0df3386b97d8507c5991051fbdda053a
bgruening
parents:
diff changeset
16 Or directly by:
94a987a7da69 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/htseq-clip commit 4879439f0df3386b97d8507c5991051fbdda053a
bgruening
parents:
diff changeset
17 conda install -c bioconda htseq-clip
94a987a7da69 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/htseq-clip commit 4879439f0df3386b97d8507c5991051fbdda053a
bgruening
parents:
diff changeset
18
94a987a7da69 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/htseq-clip commit 4879439f0df3386b97d8507c5991051fbdda053a
bgruening
parents:
diff changeset
19
94a987a7da69 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/htseq-clip commit 4879439f0df3386b97d8507c5991051fbdda053a
bgruening
parents:
diff changeset
20 Test call
94a987a7da69 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/htseq-clip commit 4879439f0df3386b97d8507c5991051fbdda053a
bgruening
parents:
diff changeset
21 =========
94a987a7da69 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/htseq-clip commit 4879439f0df3386b97d8507c5991051fbdda053a
bgruening
parents:
diff changeset
22
94a987a7da69 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/htseq-clip commit 4879439f0df3386b97d8507c5991051fbdda053a
bgruening
parents:
diff changeset
23 python htsc_create_sliding_windows.py --gff test-data/paper_tus.Synechocystis_pSYSM.gff3 --out test_compare_out --hcw-w 50 --hcw-s 20 --no-zipper
94a987a7da69 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/htseq-clip commit 4879439f0df3386b97d8507c5991051fbdda053a
bgruening
parents:
diff changeset
24
94a987a7da69 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/htseq-clip commit 4879439f0df3386b97d8507c5991051fbdda053a
bgruening
parents:
diff changeset
25 Compare:
94a987a7da69 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/htseq-clip commit 4879439f0df3386b97d8507c5991051fbdda053a
bgruening
parents:
diff changeset
26 diff test_compare_out/windows_mapped_to_ids.txt test-data/windows.exp.txt
94a987a7da69 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/htseq-clip commit 4879439f0df3386b97d8507c5991051fbdda053a
bgruening
parents:
diff changeset
27 diff test_compare_out/windows.bed test-data/windows.exp.bed
94a987a7da69 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/htseq-clip commit 4879439f0df3386b97d8507c5991051fbdda053a
bgruening
parents:
diff changeset
28 diff test_compare_out/annotation.bed test-data/annotation.exp.bed
94a987a7da69 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/htseq-clip commit 4879439f0df3386b97d8507c5991051fbdda053a
bgruening
parents:
diff changeset
29
94a987a7da69 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/htseq-clip commit 4879439f0df3386b97d8507c5991051fbdda053a
bgruening
parents:
diff changeset
30 This corresponds to:
94a987a7da69 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/htseq-clip commit 4879439f0df3386b97d8507c5991051fbdda053a
bgruening
parents:
diff changeset
31 htseq-clip annotation -g test-data/paper_tus.Synechocystis_pSYSM.gff3 -o test-data/annotation.exp.bed
94a987a7da69 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/htseq-clip commit 4879439f0df3386b97d8507c5991051fbdda053a
bgruening
parents:
diff changeset
32 htseq-clip createSlidingWindows -i test-data/annotation.exp.bed -w 50 -s 20 -o test-data/windows.exp.bed
94a987a7da69 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/htseq-clip commit 4879439f0df3386b97d8507c5991051fbdda053a
bgruening
parents:
diff changeset
33 htseq-clip mapToId -a test-data/windows.exp.bed -o test-data/windows.exp.txt
94a987a7da69 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/htseq-clip commit 4879439f0df3386b97d8507c5991051fbdda053a
bgruening
parents:
diff changeset
34
94a987a7da69 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/htseq-clip commit 4879439f0df3386b97d8507c5991051fbdda053a
bgruening
parents:
diff changeset
35 More tests:
94a987a7da69 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/htseq-clip commit 4879439f0df3386b97d8507c5991051fbdda053a
bgruening
parents:
diff changeset
36 python htsc_create_sliding_windows.py --gff test-data/paper_tus.Synechocystis_pSYSM.gff3 --out test_compare_out --hcw-w 50 --hcw-s 20 --no-zipper --hca-unsorted
94a987a7da69 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/htseq-clip commit 4879439f0df3386b97d8507c5991051fbdda053a
bgruening
parents:
diff changeset
37
94a987a7da69 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/htseq-clip commit 4879439f0df3386b97d8507c5991051fbdda053a
bgruening
parents:
diff changeset
38 DEWSeq input files:
94a987a7da69 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/htseq-clip commit 4879439f0df3386b97d8507c5991051fbdda053a
bgruening
parents:
diff changeset
39 test_compare_out/windows_mapped_to_ids.txt
94a987a7da69 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/htseq-clip commit 4879439f0df3386b97d8507c5991051fbdda053a
bgruening
parents:
diff changeset
40
94a987a7da69 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/htseq-clip commit 4879439f0df3386b97d8507c5991051fbdda053a
bgruening
parents:
diff changeset
41 """
94a987a7da69 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/htseq-clip commit 4879439f0df3386b97d8507c5991051fbdda053a
bgruening
parents:
diff changeset
42
94a987a7da69 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/htseq-clip commit 4879439f0df3386b97d8507c5991051fbdda053a
bgruening
parents:
diff changeset
43
94a987a7da69 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/htseq-clip commit 4879439f0df3386b97d8507c5991051fbdda053a
bgruening
parents:
diff changeset
44 ################################################################################
94a987a7da69 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/htseq-clip commit 4879439f0df3386b97d8507c5991051fbdda053a
bgruening
parents:
diff changeset
45
94a987a7da69 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/htseq-clip commit 4879439f0df3386b97d8507c5991051fbdda053a
bgruening
parents:
diff changeset
46 def setup_argument_parser():
94a987a7da69 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/htseq-clip commit 4879439f0df3386b97d8507c5991051fbdda053a
bgruening
parents:
diff changeset
47 """Setup argparse parser."""
94a987a7da69 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/htseq-clip commit 4879439f0df3386b97d8507c5991051fbdda053a
bgruening
parents:
diff changeset
48 help_description = """
94a987a7da69 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/htseq-clip commit 4879439f0df3386b97d8507c5991051fbdda053a
bgruening
parents:
diff changeset
49 Based on genomic annotations GFF file (--gff), create sliding window
94a987a7da69 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/htseq-clip commit 4879439f0df3386b97d8507c5991051fbdda053a
bgruening
parents:
diff changeset
50 annotations with htseq-clip.
94a987a7da69 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/htseq-clip commit 4879439f0df3386b97d8507c5991051fbdda053a
bgruening
parents:
diff changeset
51
94a987a7da69 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/htseq-clip commit 4879439f0df3386b97d8507c5991051fbdda053a
bgruening
parents:
diff changeset
52 """
94a987a7da69 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/htseq-clip commit 4879439f0df3386b97d8507c5991051fbdda053a
bgruening
parents:
diff changeset
53 # Define argument parser.
94a987a7da69 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/htseq-clip commit 4879439f0df3386b97d8507c5991051fbdda053a
bgruening
parents:
diff changeset
54 p = argparse.ArgumentParser(add_help=False,
94a987a7da69 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/htseq-clip commit 4879439f0df3386b97d8507c5991051fbdda053a
bgruening
parents:
diff changeset
55 prog="htsc_create_sliding_windows.py",
94a987a7da69 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/htseq-clip commit 4879439f0df3386b97d8507c5991051fbdda053a
bgruening
parents:
diff changeset
56 description=help_description,
94a987a7da69 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/htseq-clip commit 4879439f0df3386b97d8507c5991051fbdda053a
bgruening
parents:
diff changeset
57 formatter_class=argparse.MetavarTypeHelpFormatter)
94a987a7da69 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/htseq-clip commit 4879439f0df3386b97d8507c5991051fbdda053a
bgruening
parents:
diff changeset
58
94a987a7da69 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/htseq-clip commit 4879439f0df3386b97d8507c5991051fbdda053a
bgruening
parents:
diff changeset
59 # Required arguments.
94a987a7da69 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/htseq-clip commit 4879439f0df3386b97d8507c5991051fbdda053a
bgruening
parents:
diff changeset
60 p.add_argument("-h", "--help",
94a987a7da69 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/htseq-clip commit 4879439f0df3386b97d8507c5991051fbdda053a
bgruening
parents:
diff changeset
61 action="help",
94a987a7da69 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/htseq-clip commit 4879439f0df3386b97d8507c5991051fbdda053a
bgruening
parents:
diff changeset
62 help="Print help message")
94a987a7da69 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/htseq-clip commit 4879439f0df3386b97d8507c5991051fbdda053a
bgruening
parents:
diff changeset
63 p.add_argument("--gff",
94a987a7da69 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/htseq-clip commit 4879439f0df3386b97d8507c5991051fbdda053a
bgruening
parents:
diff changeset
64 dest="in_gff",
94a987a7da69 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/htseq-clip commit 4879439f0df3386b97d8507c5991051fbdda053a
bgruening
parents:
diff changeset
65 type=str,
94a987a7da69 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/htseq-clip commit 4879439f0df3386b97d8507c5991051fbdda053a
bgruening
parents:
diff changeset
66 metavar='str',
94a987a7da69 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/htseq-clip commit 4879439f0df3386b97d8507c5991051fbdda053a
bgruening
parents:
diff changeset
67 required=True,
94a987a7da69 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/htseq-clip commit 4879439f0df3386b97d8507c5991051fbdda053a
bgruening
parents:
diff changeset
68 help="Annotation file GFF (so far tested with hg38 GENCODE format). Also accepts gff.gz as well")
94a987a7da69 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/htseq-clip commit 4879439f0df3386b97d8507c5991051fbdda053a
bgruening
parents:
diff changeset
69 p.add_argument("--out",
94a987a7da69 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/htseq-clip commit 4879439f0df3386b97d8507c5991051fbdda053a
bgruening
parents:
diff changeset
70 dest="out_folder",
94a987a7da69 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/htseq-clip commit 4879439f0df3386b97d8507c5991051fbdda053a
bgruening
parents:
diff changeset
71 type=str,
94a987a7da69 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/htseq-clip commit 4879439f0df3386b97d8507c5991051fbdda053a
bgruening
parents:
diff changeset
72 metavar='str',
94a987a7da69 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/htseq-clip commit 4879439f0df3386b97d8507c5991051fbdda053a
bgruening
parents:
diff changeset
73 required=True,
94a987a7da69 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/htseq-clip commit 4879439f0df3386b97d8507c5991051fbdda053a
bgruening
parents:
diff changeset
74 help="Results output folder")
94a987a7da69 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/htseq-clip commit 4879439f0df3386b97d8507c5991051fbdda053a
bgruening
parents:
diff changeset
75 # htseq-clip annotation.
94a987a7da69 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/htseq-clip commit 4879439f0df3386b97d8507c5991051fbdda053a
bgruening
parents:
diff changeset
76 p.add_argument("--hca-unsorted",
94a987a7da69 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/htseq-clip commit 4879439f0df3386b97d8507c5991051fbdda053a
bgruening
parents:
diff changeset
77 dest="hca_unsorted",
94a987a7da69 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/htseq-clip commit 4879439f0df3386b97d8507c5991051fbdda053a
bgruening
parents:
diff changeset
78 default=False,
94a987a7da69 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/htseq-clip commit 4879439f0df3386b97d8507c5991051fbdda053a
bgruening
parents:
diff changeset
79 action="store_true",
94a987a7da69 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/htseq-clip commit 4879439f0df3386b97d8507c5991051fbdda053a
bgruening
parents:
diff changeset
80 help="htseq-clip annotation --unsorted parameter. Use this flag if the GFF file is unsorted (default: False)")
94a987a7da69 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/htseq-clip commit 4879439f0df3386b97d8507c5991051fbdda053a
bgruening
parents:
diff changeset
81 # htseq-clip createSlidingWindows.
94a987a7da69 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/htseq-clip commit 4879439f0df3386b97d8507c5991051fbdda053a
bgruening
parents:
diff changeset
82 p.add_argument("--hcw-w",
94a987a7da69 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/htseq-clip commit 4879439f0df3386b97d8507c5991051fbdda053a
bgruening
parents:
diff changeset
83 dest="hcw_w",
94a987a7da69 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/htseq-clip commit 4879439f0df3386b97d8507c5991051fbdda053a
bgruening
parents:
diff changeset
84 type=int,
94a987a7da69 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/htseq-clip commit 4879439f0df3386b97d8507c5991051fbdda053a
bgruening
parents:
diff changeset
85 metavar='int',
94a987a7da69 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/htseq-clip commit 4879439f0df3386b97d8507c5991051fbdda053a
bgruening
parents:
diff changeset
86 default=50,
94a987a7da69 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/htseq-clip commit 4879439f0df3386b97d8507c5991051fbdda053a
bgruening
parents:
diff changeset
87 help="htseq-clip createSlidingWindows -w parameter. Sliding window size. If unsure, try 75-100 (default: 50)")
94a987a7da69 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/htseq-clip commit 4879439f0df3386b97d8507c5991051fbdda053a
bgruening
parents:
diff changeset
88 p.add_argument("--hcw-s",
94a987a7da69 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/htseq-clip commit 4879439f0df3386b97d8507c5991051fbdda053a
bgruening
parents:
diff changeset
89 dest="hcw_s",
94a987a7da69 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/htseq-clip commit 4879439f0df3386b97d8507c5991051fbdda053a
bgruening
parents:
diff changeset
90 type=int,
94a987a7da69 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/htseq-clip commit 4879439f0df3386b97d8507c5991051fbdda053a
bgruening
parents:
diff changeset
91 metavar='int',
94a987a7da69 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/htseq-clip commit 4879439f0df3386b97d8507c5991051fbdda053a
bgruening
parents:
diff changeset
92 default=20,
94a987a7da69 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/htseq-clip commit 4879439f0df3386b97d8507c5991051fbdda053a
bgruening
parents:
diff changeset
93 help="htseq-clip createSlidingWindows -s parameter. Step size for sliding window (default: 20)")
94a987a7da69 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/htseq-clip commit 4879439f0df3386b97d8507c5991051fbdda053a
bgruening
parents:
diff changeset
94 # More.
94a987a7da69 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/htseq-clip commit 4879439f0df3386b97d8507c5991051fbdda053a
bgruening
parents:
diff changeset
95 p.add_argument("--no-zipper",
94a987a7da69 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/htseq-clip commit 4879439f0df3386b97d8507c5991051fbdda053a
bgruening
parents:
diff changeset
96 dest="no_zipper",
94a987a7da69 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/htseq-clip commit 4879439f0df3386b97d8507c5991051fbdda053a
bgruening
parents:
diff changeset
97 default=False,
94a987a7da69 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/htseq-clip commit 4879439f0df3386b97d8507c5991051fbdda053a
bgruening
parents:
diff changeset
98 action="store_true",
94a987a7da69 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/htseq-clip commit 4879439f0df3386b97d8507c5991051fbdda053a
bgruening
parents:
diff changeset
99 help="Do not gzip output files (default: False)")
94a987a7da69 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/htseq-clip commit 4879439f0df3386b97d8507c5991051fbdda053a
bgruening
parents:
diff changeset
100 return p
94a987a7da69 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/htseq-clip commit 4879439f0df3386b97d8507c5991051fbdda053a
bgruening
parents:
diff changeset
101
94a987a7da69 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/htseq-clip commit 4879439f0df3386b97d8507c5991051fbdda053a
bgruening
parents:
diff changeset
102
94a987a7da69 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/htseq-clip commit 4879439f0df3386b97d8507c5991051fbdda053a
bgruening
parents:
diff changeset
103 ################################################################################
94a987a7da69 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/htseq-clip commit 4879439f0df3386b97d8507c5991051fbdda053a
bgruening
parents:
diff changeset
104
94a987a7da69 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/htseq-clip commit 4879439f0df3386b97d8507c5991051fbdda053a
bgruening
parents:
diff changeset
105 if __name__ == '__main__':
94a987a7da69 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/htseq-clip commit 4879439f0df3386b97d8507c5991051fbdda053a
bgruening
parents:
diff changeset
106
94a987a7da69 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/htseq-clip commit 4879439f0df3386b97d8507c5991051fbdda053a
bgruening
parents:
diff changeset
107 parser = setup_argument_parser()
94a987a7da69 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/htseq-clip commit 4879439f0df3386b97d8507c5991051fbdda053a
bgruening
parents:
diff changeset
108 args = parser.parse_args()
94a987a7da69 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/htseq-clip commit 4879439f0df3386b97d8507c5991051fbdda053a
bgruening
parents:
diff changeset
109
94a987a7da69 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/htseq-clip commit 4879439f0df3386b97d8507c5991051fbdda053a
bgruening
parents:
diff changeset
110 assert os.path.exists(args.in_gff), "--gff file \"%s\" not found" % (args.in_gff)
94a987a7da69 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/htseq-clip commit 4879439f0df3386b97d8507c5991051fbdda053a
bgruening
parents:
diff changeset
111
94a987a7da69 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/htseq-clip commit 4879439f0df3386b97d8507c5991051fbdda053a
bgruening
parents:
diff changeset
112 # Output folder.
94a987a7da69 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/htseq-clip commit 4879439f0df3386b97d8507c5991051fbdda053a
bgruening
parents:
diff changeset
113 if not os.path.exists(args.out_folder):
94a987a7da69 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/htseq-clip commit 4879439f0df3386b97d8507c5991051fbdda053a
bgruening
parents:
diff changeset
114 os.makedirs(args.out_folder)
94a987a7da69 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/htseq-clip commit 4879439f0df3386b97d8507c5991051fbdda053a
bgruening
parents:
diff changeset
115
94a987a7da69 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/htseq-clip commit 4879439f0df3386b97d8507c5991051fbdda053a
bgruening
parents:
diff changeset
116 """
94a987a7da69 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/htseq-clip commit 4879439f0df3386b97d8507c5991051fbdda053a
bgruening
parents:
diff changeset
117 1) Flatten annotation.
94a987a7da69 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/htseq-clip commit 4879439f0df3386b97d8507c5991051fbdda053a
bgruening
parents:
diff changeset
118 htseq-clip annotation -g args.in_gff -o annotation.bed
94a987a7da69 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/htseq-clip commit 4879439f0df3386b97d8507c5991051fbdda053a
bgruening
parents:
diff changeset
119
94a987a7da69 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/htseq-clip commit 4879439f0df3386b97d8507c5991051fbdda053a
bgruening
parents:
diff changeset
120 -o content example:
94a987a7da69 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/htseq-clip commit 4879439f0df3386b97d8507c5991051fbdda053a
bgruening
parents:
diff changeset
121 Synechocystis 5 105 TU1@TU1@protein_coding@exon@1/1@TU1:exon0001 2 -
94a987a7da69 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/htseq-clip commit 4879439f0df3386b97d8507c5991051fbdda053a
bgruening
parents:
diff changeset
122 Synechocystis 576 990 TU2@TU2@protein_coding@exon@1/1@TU2:exon0001 2 +
94a987a7da69 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/htseq-clip commit 4879439f0df3386b97d8507c5991051fbdda053a
bgruening
parents:
diff changeset
123 Synechocystis 809 909 TU3@TU3@protein_coding@exon@1/1@TU3:exon0001 2 -
94a987a7da69 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/htseq-clip commit 4879439f0df3386b97d8507c5991051fbdda053a
bgruening
parents:
diff changeset
124 Synechocystis 1531 2150 TU4@TU4@protein_coding@exon@1/1@TU4:exon0001 2 +
94a987a7da69 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/htseq-clip commit 4879439f0df3386b97d8507c5991051fbdda053a
bgruening
parents:
diff changeset
125 Synechocystis 2150 2701 TU6@TU6@protein_coding@exon@1/1@TU6:exon0001 2 +
94a987a7da69 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/htseq-clip commit 4879439f0df3386b97d8507c5991051fbdda053a
bgruening
parents:
diff changeset
126 ...
94a987a7da69 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/htseq-clip commit 4879439f0df3386b97d8507c5991051fbdda053a
bgruening
parents:
diff changeset
127
94a987a7da69 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/htseq-clip commit 4879439f0df3386b97d8507c5991051fbdda053a
bgruening
parents:
diff changeset
128 """
94a987a7da69 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/htseq-clip commit 4879439f0df3386b97d8507c5991051fbdda053a
bgruening
parents:
diff changeset
129
94a987a7da69 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/htseq-clip commit 4879439f0df3386b97d8507c5991051fbdda053a
bgruening
parents:
diff changeset
130 annot_bed = args.out_folder + "/annotation.bed.gz"
94a987a7da69 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/htseq-clip commit 4879439f0df3386b97d8507c5991051fbdda053a
bgruening
parents:
diff changeset
131 if args.no_zipper:
94a987a7da69 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/htseq-clip commit 4879439f0df3386b97d8507c5991051fbdda053a
bgruening
parents:
diff changeset
132 annot_bed = args.out_folder + "/annotation.bed"
94a987a7da69 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/htseq-clip commit 4879439f0df3386b97d8507c5991051fbdda053a
bgruening
parents:
diff changeset
133
94a987a7da69 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/htseq-clip commit 4879439f0df3386b97d8507c5991051fbdda053a
bgruening
parents:
diff changeset
134 print("Convert --gff to BED ... ")
94a987a7da69 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/htseq-clip commit 4879439f0df3386b97d8507c5991051fbdda053a
bgruening
parents:
diff changeset
135 check_cmd = "htseq-clip annotation -g " + args.in_gff + " -o " + annot_bed
94a987a7da69 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/htseq-clip commit 4879439f0df3386b97d8507c5991051fbdda053a
bgruening
parents:
diff changeset
136 if args.hca_unsorted:
94a987a7da69 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/htseq-clip commit 4879439f0df3386b97d8507c5991051fbdda053a
bgruening
parents:
diff changeset
137 check_cmd += " --unsorted"
94a987a7da69 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/htseq-clip commit 4879439f0df3386b97d8507c5991051fbdda053a
bgruening
parents:
diff changeset
138 output = subprocess.getoutput(check_cmd)
94a987a7da69 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/htseq-clip commit 4879439f0df3386b97d8507c5991051fbdda053a
bgruening
parents:
diff changeset
139
94a987a7da69 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/htseq-clip commit 4879439f0df3386b97d8507c5991051fbdda053a
bgruening
parents:
diff changeset
140 print(check_cmd)
94a987a7da69 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/htseq-clip commit 4879439f0df3386b97d8507c5991051fbdda053a
bgruening
parents:
diff changeset
141 print(output)
94a987a7da69 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/htseq-clip commit 4879439f0df3386b97d8507c5991051fbdda053a
bgruening
parents:
diff changeset
142
94a987a7da69 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/htseq-clip commit 4879439f0df3386b97d8507c5991051fbdda053a
bgruening
parents:
diff changeset
143 assert os.path.exists(annot_bed), "htseq-clip annotation -o file \"%s\" not found" % (annot_bed)
94a987a7da69 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/htseq-clip commit 4879439f0df3386b97d8507c5991051fbdda053a
bgruening
parents:
diff changeset
144
94a987a7da69 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/htseq-clip commit 4879439f0df3386b97d8507c5991051fbdda053a
bgruening
parents:
diff changeset
145 """
94a987a7da69 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/htseq-clip commit 4879439f0df3386b97d8507c5991051fbdda053a
bgruening
parents:
diff changeset
146 2) Create sliding windows.
94a987a7da69 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/htseq-clip commit 4879439f0df3386b97d8507c5991051fbdda053a
bgruening
parents:
diff changeset
147 htseq-clip createSlidingWindows -i annotation.bed -w hcw_w -s hcw_s -o windows.bed.gz
94a987a7da69 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/htseq-clip commit 4879439f0df3386b97d8507c5991051fbdda053a
bgruening
parents:
diff changeset
148
94a987a7da69 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/htseq-clip commit 4879439f0df3386b97d8507c5991051fbdda053a
bgruening
parents:
diff changeset
149 -o content example:
94a987a7da69 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/htseq-clip commit 4879439f0df3386b97d8507c5991051fbdda053a
bgruening
parents:
diff changeset
150 Synechocystis 5 80 TU1@TU1@protein_coding@exon@1/1@TU1:exon0001W00001@1 2 -
94a987a7da69 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/htseq-clip commit 4879439f0df3386b97d8507c5991051fbdda053a
bgruening
parents:
diff changeset
151 Synechocystis 15 90 TU1@TU1@protein_coding@exon@1/1@TU1:exon0001W00002@2 2 -
94a987a7da69 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/htseq-clip commit 4879439f0df3386b97d8507c5991051fbdda053a
bgruening
parents:
diff changeset
152 Synechocystis 25 100 TU1@TU1@protein_coding@exon@1/1@TU1:exon0001W00003@3 2 -
94a987a7da69 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/htseq-clip commit 4879439f0df3386b97d8507c5991051fbdda053a
bgruening
parents:
diff changeset
153 Synechocystis 35 105 TU1@TU1@protein_coding@exon@1/1@TU1:exon0001W00004@4 2 -
94a987a7da69 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/htseq-clip commit 4879439f0df3386b97d8507c5991051fbdda053a
bgruening
parents:
diff changeset
154 Synechocystis 576 651 TU2@TU2@protein_coding@exon@1/1@TU2:exon0001W00001@1 2 +
94a987a7da69 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/htseq-clip commit 4879439f0df3386b97d8507c5991051fbdda053a
bgruening
parents:
diff changeset
155 Synechocystis 586 661 TU2@TU2@protein_coding@exon@1/1@TU2:exon0001W00002@2 2 +
94a987a7da69 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/htseq-clip commit 4879439f0df3386b97d8507c5991051fbdda053a
bgruening
parents:
diff changeset
156 Synechocystis 596 671 TU2@TU2@protein_coding@exon@1/1@TU2:exon0001W00003@3 2 +
94a987a7da69 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/htseq-clip commit 4879439f0df3386b97d8507c5991051fbdda053a
bgruening
parents:
diff changeset
157 Synechocystis 606 681 TU2@TU2@protein_coding@exon@1/1@TU2:exon0001W00004@4 2 +
94a987a7da69 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/htseq-clip commit 4879439f0df3386b97d8507c5991051fbdda053a
bgruening
parents:
diff changeset
158 Synechocystis 616 691 TU2@TU2@protein_coding@exon@1/1@TU2:exon0001W00005@5 2 +
94a987a7da69 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/htseq-clip commit 4879439f0df3386b97d8507c5991051fbdda053a
bgruening
parents:
diff changeset
159 ...
94a987a7da69 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/htseq-clip commit 4879439f0df3386b97d8507c5991051fbdda053a
bgruening
parents:
diff changeset
160
94a987a7da69 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/htseq-clip commit 4879439f0df3386b97d8507c5991051fbdda053a
bgruening
parents:
diff changeset
161 """
94a987a7da69 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/htseq-clip commit 4879439f0df3386b97d8507c5991051fbdda053a
bgruening
parents:
diff changeset
162
94a987a7da69 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/htseq-clip commit 4879439f0df3386b97d8507c5991051fbdda053a
bgruening
parents:
diff changeset
163 win_bed = args.out_folder + "/windows.bed.gz"
94a987a7da69 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/htseq-clip commit 4879439f0df3386b97d8507c5991051fbdda053a
bgruening
parents:
diff changeset
164 if args.no_zipper:
94a987a7da69 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/htseq-clip commit 4879439f0df3386b97d8507c5991051fbdda053a
bgruening
parents:
diff changeset
165 win_bed = args.out_folder + "/windows.bed"
94a987a7da69 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/htseq-clip commit 4879439f0df3386b97d8507c5991051fbdda053a
bgruening
parents:
diff changeset
166
94a987a7da69 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/htseq-clip commit 4879439f0df3386b97d8507c5991051fbdda053a
bgruening
parents:
diff changeset
167 print("Create sliding windows BED ... ")
94a987a7da69 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/htseq-clip commit 4879439f0df3386b97d8507c5991051fbdda053a
bgruening
parents:
diff changeset
168 win_params = " -w %i -s %i " % (args.hcw_w, args.hcw_s)
94a987a7da69 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/htseq-clip commit 4879439f0df3386b97d8507c5991051fbdda053a
bgruening
parents:
diff changeset
169 check_cmd = "htseq-clip createSlidingWindows -i " + annot_bed + win_params + " -o " + win_bed
94a987a7da69 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/htseq-clip commit 4879439f0df3386b97d8507c5991051fbdda053a
bgruening
parents:
diff changeset
170 output = subprocess.getoutput(check_cmd)
94a987a7da69 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/htseq-clip commit 4879439f0df3386b97d8507c5991051fbdda053a
bgruening
parents:
diff changeset
171
94a987a7da69 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/htseq-clip commit 4879439f0df3386b97d8507c5991051fbdda053a
bgruening
parents:
diff changeset
172 print(check_cmd)
94a987a7da69 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/htseq-clip commit 4879439f0df3386b97d8507c5991051fbdda053a
bgruening
parents:
diff changeset
173 print(output)
94a987a7da69 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/htseq-clip commit 4879439f0df3386b97d8507c5991051fbdda053a
bgruening
parents:
diff changeset
174
94a987a7da69 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/htseq-clip commit 4879439f0df3386b97d8507c5991051fbdda053a
bgruening
parents:
diff changeset
175 assert os.path.exists(annot_bed), "htseq-clip createSlidingWindows -o file \"%s\" not found" % (win_bed)
94a987a7da69 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/htseq-clip commit 4879439f0df3386b97d8507c5991051fbdda053a
bgruening
parents:
diff changeset
176
94a987a7da69 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/htseq-clip commit 4879439f0df3386b97d8507c5991051fbdda053a
bgruening
parents:
diff changeset
177 """
94a987a7da69 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/htseq-clip commit 4879439f0df3386b97d8507c5991051fbdda053a
bgruening
parents:
diff changeset
178 3) Create mapping file for DEWSeq.
94a987a7da69 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/htseq-clip commit 4879439f0df3386b97d8507c5991051fbdda053a
bgruening
parents:
diff changeset
179 mapToId: extract "name" column from the annotation file and map the entries
94a987a7da69 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/htseq-clip commit 4879439f0df3386b97d8507c5991051fbdda053a
bgruening
parents:
diff changeset
180 to unique id and print out in tab separated format.
94a987a7da69 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/htseq-clip commit 4879439f0df3386b97d8507c5991051fbdda053a
bgruening
parents:
diff changeset
181 htseq-clip mapToId -a windows.bed.gz -o windows.txt.gz
94a987a7da69 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/htseq-clip commit 4879439f0df3386b97d8507c5991051fbdda053a
bgruening
parents:
diff changeset
182
94a987a7da69 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/htseq-clip commit 4879439f0df3386b97d8507c5991051fbdda053a
bgruening
parents:
diff changeset
183 -o content example:
94a987a7da69 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/htseq-clip commit 4879439f0df3386b97d8507c5991051fbdda053a
bgruening
parents:
diff changeset
184 unique_id chromosome begin end strand gene_id gene_name gene_type gene_region Nr_of_region Total_nr_of_region window_number
94a987a7da69 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/htseq-clip commit 4879439f0df3386b97d8507c5991051fbdda053a
bgruening
parents:
diff changeset
185 TU1:exon0001W00001 Synechocystis 5 80 - TU1 TU1 protein_coding exon 1 1 1
94a987a7da69 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/htseq-clip commit 4879439f0df3386b97d8507c5991051fbdda053a
bgruening
parents:
diff changeset
186 TU1:exon0001W00002 Synechocystis 15 90 - TU1 TU1 protein_coding exon 1 1 2
94a987a7da69 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/htseq-clip commit 4879439f0df3386b97d8507c5991051fbdda053a
bgruening
parents:
diff changeset
187 TU1:exon0001W00003 Synechocystis 25 100 - TU1 TU1 protein_coding exon 1 1 3
94a987a7da69 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/htseq-clip commit 4879439f0df3386b97d8507c5991051fbdda053a
bgruening
parents:
diff changeset
188 TU1:exon0001W00004 Synechocystis 35 105 - TU1 TU1 protein_coding exon 1 1 4
94a987a7da69 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/htseq-clip commit 4879439f0df3386b97d8507c5991051fbdda053a
bgruening
parents:
diff changeset
189 TU2:exon0001W00001 Synechocystis 576 651 + TU2 TU2 protein_coding exon 1 1 1
94a987a7da69 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/htseq-clip commit 4879439f0df3386b97d8507c5991051fbdda053a
bgruening
parents:
diff changeset
190 TU2:exon0001W00002 Synechocystis 586 661 + TU2 TU2 protein_coding exon 1 1 2
94a987a7da69 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/htseq-clip commit 4879439f0df3386b97d8507c5991051fbdda053a
bgruening
parents:
diff changeset
191 TU2:exon0001W00003 Synechocystis 596 671 + TU2 TU2 protein_coding exon 1 1 3
94a987a7da69 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/htseq-clip commit 4879439f0df3386b97d8507c5991051fbdda053a
bgruening
parents:
diff changeset
192 TU2:exon0001W00004 Synechocystis 606 681 + TU2 TU2 protein_coding exon 1 1 4
94a987a7da69 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/htseq-clip commit 4879439f0df3386b97d8507c5991051fbdda053a
bgruening
parents:
diff changeset
193 TU2:exon0001W00005 Synechocystis 616 691 + TU2 TU2 protein_coding exon 1 1 5
94a987a7da69 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/htseq-clip commit 4879439f0df3386b97d8507c5991051fbdda053a
bgruening
parents:
diff changeset
194 ...
94a987a7da69 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/htseq-clip commit 4879439f0df3386b97d8507c5991051fbdda053a
bgruening
parents:
diff changeset
195
94a987a7da69 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/htseq-clip commit 4879439f0df3386b97d8507c5991051fbdda053a
bgruening
parents:
diff changeset
196 """
94a987a7da69 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/htseq-clip commit 4879439f0df3386b97d8507c5991051fbdda053a
bgruening
parents:
diff changeset
197
94a987a7da69 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/htseq-clip commit 4879439f0df3386b97d8507c5991051fbdda053a
bgruening
parents:
diff changeset
198 mapped2ids_txt = args.out_folder + "/windows_mapped_to_ids.txt.gz"
94a987a7da69 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/htseq-clip commit 4879439f0df3386b97d8507c5991051fbdda053a
bgruening
parents:
diff changeset
199 if args.no_zipper:
94a987a7da69 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/htseq-clip commit 4879439f0df3386b97d8507c5991051fbdda053a
bgruening
parents:
diff changeset
200 mapped2ids_txt = args.out_folder + "/windows_mapped_to_ids.txt"
94a987a7da69 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/htseq-clip commit 4879439f0df3386b97d8507c5991051fbdda053a
bgruening
parents:
diff changeset
201
94a987a7da69 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/htseq-clip commit 4879439f0df3386b97d8507c5991051fbdda053a
bgruening
parents:
diff changeset
202 print("Create DEWSeq input annotation file ... ")
94a987a7da69 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/htseq-clip commit 4879439f0df3386b97d8507c5991051fbdda053a
bgruening
parents:
diff changeset
203 win_params = " -w %i -s %i " % (args.hcw_w, args.hcw_s)
94a987a7da69 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/htseq-clip commit 4879439f0df3386b97d8507c5991051fbdda053a
bgruening
parents:
diff changeset
204 check_cmd = "htseq-clip mapToId -a " + win_bed + " -o " + mapped2ids_txt
94a987a7da69 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/htseq-clip commit 4879439f0df3386b97d8507c5991051fbdda053a
bgruening
parents:
diff changeset
205 output = subprocess.getoutput(check_cmd)
94a987a7da69 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/htseq-clip commit 4879439f0df3386b97d8507c5991051fbdda053a
bgruening
parents:
diff changeset
206
94a987a7da69 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/htseq-clip commit 4879439f0df3386b97d8507c5991051fbdda053a
bgruening
parents:
diff changeset
207 print(check_cmd)
94a987a7da69 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/htseq-clip commit 4879439f0df3386b97d8507c5991051fbdda053a
bgruening
parents:
diff changeset
208 print(output)
94a987a7da69 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/htseq-clip commit 4879439f0df3386b97d8507c5991051fbdda053a
bgruening
parents:
diff changeset
209
94a987a7da69 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/htseq-clip commit 4879439f0df3386b97d8507c5991051fbdda053a
bgruening
parents:
diff changeset
210 assert os.path.exists(mapped2ids_txt), "htseq-clip mapToId -o file \"%s\" not found" % (mapped2ids_txt)
94a987a7da69 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/htseq-clip commit 4879439f0df3386b97d8507c5991051fbdda053a
bgruening
parents:
diff changeset
211
94a987a7da69 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/htseq-clip commit 4879439f0df3386b97d8507c5991051fbdda053a
bgruening
parents:
diff changeset
212 """
94a987a7da69 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/htseq-clip commit 4879439f0df3386b97d8507c5991051fbdda053a
bgruening
parents:
diff changeset
213 Report.
94a987a7da69 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/htseq-clip commit 4879439f0df3386b97d8507c5991051fbdda053a
bgruening
parents:
diff changeset
214
94a987a7da69 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/htseq-clip commit 4879439f0df3386b97d8507c5991051fbdda053a
bgruening
parents:
diff changeset
215 """
94a987a7da69 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/htseq-clip commit 4879439f0df3386b97d8507c5991051fbdda053a
bgruening
parents:
diff changeset
216
94a987a7da69 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/htseq-clip commit 4879439f0df3386b97d8507c5991051fbdda053a
bgruening
parents:
diff changeset
217 print("")
94a987a7da69 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/htseq-clip commit 4879439f0df3386b97d8507c5991051fbdda053a
bgruening
parents:
diff changeset
218 print("OUTPUT FILES")
94a987a7da69 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/htseq-clip commit 4879439f0df3386b97d8507c5991051fbdda053a
bgruening
parents:
diff changeset
219 print("============")
94a987a7da69 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/htseq-clip commit 4879439f0df3386b97d8507c5991051fbdda053a
bgruening
parents:
diff changeset
220 print("Annotation BED:\n%s" % (annot_bed))
94a987a7da69 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/htseq-clip commit 4879439f0df3386b97d8507c5991051fbdda053a
bgruening
parents:
diff changeset
221 print("Windows BED:\n%s" % (win_bed))
94a987a7da69 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/htseq-clip commit 4879439f0df3386b97d8507c5991051fbdda053a
bgruening
parents:
diff changeset
222 print("Windows mapped to IDs TXT (DEWseq annotation file):\n%s" % (mapped2ids_txt))
94a987a7da69 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/htseq-clip commit 4879439f0df3386b97d8507c5991051fbdda053a
bgruening
parents:
diff changeset
223 print("")