annotate NanocomporeDB_process.py @ 1:c43f4b80f5a9 draft

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanocompore commit 652a872061324ba1073bfa286777ffeefa352671"
author iuc
date Mon, 08 Jun 2020 14:36:18 -0400
parents
children 25abc2c72ff9
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
1
c43f4b80f5a9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanocompore commit 652a872061324ba1073bfa286777ffeefa352671"
iuc
parents:
diff changeset
1 #!/usr/bin/env python
c43f4b80f5a9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanocompore commit 652a872061324ba1073bfa286777ffeefa352671"
iuc
parents:
diff changeset
2
c43f4b80f5a9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanocompore commit 652a872061324ba1073bfa286777ffeefa352671"
iuc
parents:
diff changeset
3 import argparse
c43f4b80f5a9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanocompore commit 652a872061324ba1073bfa286777ffeefa352671"
iuc
parents:
diff changeset
4 import os
c43f4b80f5a9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanocompore commit 652a872061324ba1073bfa286777ffeefa352671"
iuc
parents:
diff changeset
5
c43f4b80f5a9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanocompore commit 652a872061324ba1073bfa286777ffeefa352671"
iuc
parents:
diff changeset
6 from nanocompore.SampCompDB import SampCompDB
c43f4b80f5a9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanocompore commit 652a872061324ba1073bfa286777ffeefa352671"
iuc
parents:
diff changeset
7
c43f4b80f5a9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanocompore commit 652a872061324ba1073bfa286777ffeefa352671"
iuc
parents:
diff changeset
8
c43f4b80f5a9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanocompore commit 652a872061324ba1073bfa286777ffeefa352671"
iuc
parents:
diff changeset
9 def is_valid_file(file_name):
c43f4b80f5a9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanocompore commit 652a872061324ba1073bfa286777ffeefa352671"
iuc
parents:
diff changeset
10 if os.path.isfile(file_name):
c43f4b80f5a9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanocompore commit 652a872061324ba1073bfa286777ffeefa352671"
iuc
parents:
diff changeset
11 return os.path.abspath(file_name)
c43f4b80f5a9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanocompore commit 652a872061324ba1073bfa286777ffeefa352671"
iuc
parents:
diff changeset
12 else:
c43f4b80f5a9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanocompore commit 652a872061324ba1073bfa286777ffeefa352671"
iuc
parents:
diff changeset
13 raise FileNotFoundError(os.path.abspath(file_name))
c43f4b80f5a9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanocompore commit 652a872061324ba1073bfa286777ffeefa352671"
iuc
parents:
diff changeset
14
c43f4b80f5a9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanocompore commit 652a872061324ba1073bfa286777ffeefa352671"
iuc
parents:
diff changeset
15
c43f4b80f5a9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanocompore commit 652a872061324ba1073bfa286777ffeefa352671"
iuc
parents:
diff changeset
16 def is_valid_directory(dir_name):
c43f4b80f5a9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanocompore commit 652a872061324ba1073bfa286777ffeefa352671"
iuc
parents:
diff changeset
17 if os.path.isdir(dir_name):
c43f4b80f5a9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanocompore commit 652a872061324ba1073bfa286777ffeefa352671"
iuc
parents:
diff changeset
18 return os.path.abspath(dir_name)
c43f4b80f5a9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanocompore commit 652a872061324ba1073bfa286777ffeefa352671"
iuc
parents:
diff changeset
19 else:
c43f4b80f5a9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanocompore commit 652a872061324ba1073bfa286777ffeefa352671"
iuc
parents:
diff changeset
20 raise NotADirectoryError(os.path.abspath(dir_name))
c43f4b80f5a9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanocompore commit 652a872061324ba1073bfa286777ffeefa352671"
iuc
parents:
diff changeset
21
c43f4b80f5a9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanocompore commit 652a872061324ba1073bfa286777ffeefa352671"
iuc
parents:
diff changeset
22
c43f4b80f5a9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanocompore commit 652a872061324ba1073bfa286777ffeefa352671"
iuc
parents:
diff changeset
23 if __name__ == '__main__':
c43f4b80f5a9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanocompore commit 652a872061324ba1073bfa286777ffeefa352671"
iuc
parents:
diff changeset
24
c43f4b80f5a9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanocompore commit 652a872061324ba1073bfa286777ffeefa352671"
iuc
parents:
diff changeset
25 parser = argparse.ArgumentParser(
c43f4b80f5a9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanocompore commit 652a872061324ba1073bfa286777ffeefa352671"
iuc
parents:
diff changeset
26 description='save nanocompre sampcomp \
c43f4b80f5a9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanocompore commit 652a872061324ba1073bfa286777ffeefa352671"
iuc
parents:
diff changeset
27 results as interval outputs \
c43f4b80f5a9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanocompore commit 652a872061324ba1073bfa286777ffeefa352671"
iuc
parents:
diff changeset
28 \nSample call: \"python Nannocompore-plot.py --db-path \
c43f4b80f5a9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanocompore commit 652a872061324ba1073bfa286777ffeefa352671"
iuc
parents:
diff changeset
29 ./out_SampComp.db --ref-fasta ref.fa --annotation-bed annot.bed \
c43f4b80f5a9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanocompore commit 652a872061324ba1073bfa286777ffeefa352671"
iuc
parents:
diff changeset
30 --out-dir ./plots/')
c43f4b80f5a9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanocompore commit 652a872061324ba1073bfa286777ffeefa352671"
iuc
parents:
diff changeset
31
c43f4b80f5a9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanocompore commit 652a872061324ba1073bfa286777ffeefa352671"
iuc
parents:
diff changeset
32 parser.add_argument('--ref-fasta', required=True, type=is_valid_file,
c43f4b80f5a9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanocompore commit 652a872061324ba1073bfa286777ffeefa352671"
iuc
parents:
diff changeset
33 help='The reference genome used for read alignment.')
c43f4b80f5a9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanocompore commit 652a872061324ba1073bfa286777ffeefa352671"
iuc
parents:
diff changeset
34 parser.add_argument('--db-path', default="./out_SampComp.db", type=str,
c43f4b80f5a9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanocompore commit 652a872061324ba1073bfa286777ffeefa352671"
iuc
parents:
diff changeset
35 help='Path to the SampCompDB database path prefix.')
c43f4b80f5a9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanocompore commit 652a872061324ba1073bfa286777ffeefa352671"
iuc
parents:
diff changeset
36 parser.add_argument('--annotation-bed', required=False, type=is_valid_file,
c43f4b80f5a9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanocompore commit 652a872061324ba1073bfa286777ffeefa352671"
iuc
parents:
diff changeset
37 help='BED file containing the annotation of the transcriptome used as reference when mapping')
c43f4b80f5a9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanocompore commit 652a872061324ba1073bfa286777ffeefa352671"
iuc
parents:
diff changeset
38 parser.add_argument('--pvalue-types', type=str,
c43f4b80f5a9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanocompore commit 652a872061324ba1073bfa286777ffeefa352671"
iuc
parents:
diff changeset
39 default='GMM_logit_pvalue,KS_dwell_pvalue,KS_intensity_pvalue',
c43f4b80f5a9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanocompore commit 652a872061324ba1073bfa286777ffeefa352671"
iuc
parents:
diff changeset
40 help='path to the annotations')
c43f4b80f5a9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanocompore commit 652a872061324ba1073bfa286777ffeefa352671"
iuc
parents:
diff changeset
41 parser.add_argument('--bedgraph', default=False,
c43f4b80f5a9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanocompore commit 652a872061324ba1073bfa286777ffeefa352671"
iuc
parents:
diff changeset
42 help='write output in BEDGRAPH format instead of BED')
c43f4b80f5a9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanocompore commit 652a872061324ba1073bfa286777ffeefa352671"
iuc
parents:
diff changeset
43 parser.add_argument('--pvalue-threshold', default=1.0,
c43f4b80f5a9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanocompore commit 652a872061324ba1073bfa286777ffeefa352671"
iuc
parents:
diff changeset
44 help='Maximum reported p-value.')
c43f4b80f5a9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanocompore commit 652a872061324ba1073bfa286777ffeefa352671"
iuc
parents:
diff changeset
45 parser.add_argument('--out-dir', default="./", type=is_valid_directory,
c43f4b80f5a9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanocompore commit 652a872061324ba1073bfa286777ffeefa352671"
iuc
parents:
diff changeset
46 help='path the plotting output directory.')
c43f4b80f5a9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanocompore commit 652a872061324ba1073bfa286777ffeefa352671"
iuc
parents:
diff changeset
47
c43f4b80f5a9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanocompore commit 652a872061324ba1073bfa286777ffeefa352671"
iuc
parents:
diff changeset
48 args = parser.parse_args()
c43f4b80f5a9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanocompore commit 652a872061324ba1073bfa286777ffeefa352671"
iuc
parents:
diff changeset
49
c43f4b80f5a9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanocompore commit 652a872061324ba1073bfa286777ffeefa352671"
iuc
parents:
diff changeset
50 db = SampCompDB(args.db_path, fasta_fn=args.ref_fasta,
c43f4b80f5a9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanocompore commit 652a872061324ba1073bfa286777ffeefa352671"
iuc
parents:
diff changeset
51 bed_fn=args.annotation_bed)
c43f4b80f5a9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanocompore commit 652a872061324ba1073bfa286777ffeefa352671"
iuc
parents:
diff changeset
52 print(db)
c43f4b80f5a9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanocompore commit 652a872061324ba1073bfa286777ffeefa352671"
iuc
parents:
diff changeset
53 print("DB read ids:", db.ref_id_list)
c43f4b80f5a9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanocompore commit 652a872061324ba1073bfa286777ffeefa352671"
iuc
parents:
diff changeset
54
c43f4b80f5a9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanocompore commit 652a872061324ba1073bfa286777ffeefa352671"
iuc
parents:
diff changeset
55 if args.annotation_bed:
c43f4b80f5a9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanocompore commit 652a872061324ba1073bfa286777ffeefa352671"
iuc
parents:
diff changeset
56 for pt in args.pvalue_types.split(','):
c43f4b80f5a9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanocompore commit 652a872061324ba1073bfa286777ffeefa352671"
iuc
parents:
diff changeset
57 print("bedgraph output for p-value type:", pt)
c43f4b80f5a9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanocompore commit 652a872061324ba1073bfa286777ffeefa352671"
iuc
parents:
diff changeset
58 db.save_to_bed(output_fn='{}/{}.bedgraph'.format(args.out_dir, pt),
c43f4b80f5a9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanocompore commit 652a872061324ba1073bfa286777ffeefa352671"
iuc
parents:
diff changeset
59 pvalue_field=pt, pvalue_thr=args.pvalue_threshold,
c43f4b80f5a9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanocompore commit 652a872061324ba1073bfa286777ffeefa352671"
iuc
parents:
diff changeset
60 bedgraph=args.bedgraph)