Mercurial > repos > bgruening > salmon

annotate vpolo_convert.py @ 17:c56d23a0a2a4 draft

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/salmon commit dee6a6f4aa8cbee9f81692fc6f3a2e4ad1f3abf6"
author bgruening
date Sat, 03 Oct 2020 18:20:44 +0000
parents dc35ae3a672e
children c6c81a918ae1
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
14
dc35ae3a672e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit c17bc974bf9bbaa1fc1e47ea72162fd244f0e612"
bgruening
parents:
diff changeset
1 #!/usr/bin/env python
17
c56d23a0a2a4 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit dee6a6f4aa8cbee9f81692fc6f3a2e4ad1f3abf6"
bgruening
parents: 14
diff changeset
2 import argparse
c56d23a0a2a4 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit dee6a6f4aa8cbee9f81692fc6f3a2e4ad1f3abf6"
bgruening
parents: 14
diff changeset
3 import os
14
dc35ae3a672e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit c17bc974bf9bbaa1fc1e47ea72162fd244f0e612"
bgruening
parents:
diff changeset
4
dc35ae3a672e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit c17bc974bf9bbaa1fc1e47ea72162fd244f0e612"
bgruening
parents:
diff changeset
5 from vpolo.alevin import parser as par
17
c56d23a0a2a4 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit dee6a6f4aa8cbee9f81692fc6f3a2e4ad1f3abf6"
bgruening
parents: 14
diff changeset
6
14
dc35ae3a672e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit c17bc974bf9bbaa1fc1e47ea72162fd244f0e612"
bgruening
parents:
diff changeset
7
dc35ae3a672e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit c17bc974bf9bbaa1fc1e47ea72162fd244f0e612"
bgruening
parents:
diff changeset
8 parser = argparse.ArgumentParser()
dc35ae3a672e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit c17bc974bf9bbaa1fc1e47ea72162fd244f0e612"
bgruening
parents:
diff changeset
9 parser.add_argument("--mtx", "-m", action="store_true", help="--dumpMtx flag set")
dc35ae3a672e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit c17bc974bf9bbaa1fc1e47ea72162fd244f0e612"
bgruening
parents:
diff changeset
10 parser.add_argument("--umi", "-u", action="store_true", help="--dumpUmiGraph flag set")
dc35ae3a672e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit c17bc974bf9bbaa1fc1e47ea72162fd244f0e612"
bgruening
parents:
diff changeset
11 args = parser.parse_args()
dc35ae3a672e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit c17bc974bf9bbaa1fc1e47ea72162fd244f0e612"
bgruening
parents:
diff changeset
12
dc35ae3a672e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit c17bc974bf9bbaa1fc1e47ea72162fd244f0e612"
bgruening
parents:
diff changeset
13 if args.mtx:
dc35ae3a672e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit c17bc974bf9bbaa1fc1e47ea72162fd244f0e612"
bgruening
parents:
diff changeset
14 alevin_df = par.read_quants_bin("output")
dc35ae3a672e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit c17bc974bf9bbaa1fc1e47ea72162fd244f0e612"
bgruening
parents:
diff changeset
15 with open("quants_mat.tsv", "w") as f:
dc35ae3a672e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit c17bc974bf9bbaa1fc1e47ea72162fd244f0e612"
bgruening
parents:
diff changeset
16 f.write(alevin_df.to_csv(sep="\t"))
dc35ae3a672e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit c17bc974bf9bbaa1fc1e47ea72162fd244f0e612"
bgruening
parents:
diff changeset
17
dc35ae3a672e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit c17bc974bf9bbaa1fc1e47ea72162fd244f0e612"
bgruening
parents:
diff changeset
18 if args.umi:
dc35ae3a672e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit c17bc974bf9bbaa1fc1e47ea72162fd244f0e612"
bgruening
parents:
diff changeset
19 os.mkdir("umiout")
dc35ae3a672e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit c17bc974bf9bbaa1fc1e47ea72162fd244f0e612"
bgruening
parents:
diff changeset
20 par.read_umi_graph("output", "umiout")