Mercurial > repos > estrain > metaspades

annotate write_tsv_script.py @ 0:292d633441ad draft default tip

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload commit c251e9b174b5370300a209b2b4c5e2052976eb2d
author estrain
date Fri, 13 Mar 2026 12:07:47 +0000
parents
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
0
292d633441ad planemo upload commit c251e9b174b5370300a209b2b4c5e2052976eb2d
estrain
parents:
diff changeset
1 #!/usr/bin/env python
292d633441ad planemo upload commit c251e9b174b5370300a209b2b4c5e2052976eb2d
estrain
parents:
diff changeset
2
292d633441ad planemo upload commit c251e9b174b5370300a209b2b4c5e2052976eb2d
estrain
parents:
diff changeset
3 import re
292d633441ad planemo upload commit c251e9b174b5370300a209b2b4c5e2052976eb2d
estrain
parents:
diff changeset
4 import sys
292d633441ad planemo upload commit c251e9b174b5370300a209b2b4c5e2052976eb2d
estrain
parents:
diff changeset
5
292d633441ad planemo upload commit c251e9b174b5370300a209b2b4c5e2052976eb2d
estrain
parents:
diff changeset
6 search_str = r"^>(NODE|\S+)_(\d+)(?:_|\s)length_(\d+)_cov_(\d+\.*\d*)(.*\$)?"
292d633441ad planemo upload commit c251e9b174b5370300a209b2b4c5e2052976eb2d
estrain
parents:
diff changeset
7
292d633441ad planemo upload commit c251e9b174b5370300a209b2b4c5e2052976eb2d
estrain
parents:
diff changeset
8 replace_str = r"\1_\2\t\3\t\4"
292d633441ad planemo upload commit c251e9b174b5370300a209b2b4c5e2052976eb2d
estrain
parents:
diff changeset
9
292d633441ad planemo upload commit c251e9b174b5370300a209b2b4c5e2052976eb2d
estrain
parents:
diff changeset
10 cmd = re.compile(search_str)
292d633441ad planemo upload commit c251e9b174b5370300a209b2b4c5e2052976eb2d
estrain
parents:
diff changeset
11
292d633441ad planemo upload commit c251e9b174b5370300a209b2b4c5e2052976eb2d
estrain
parents:
diff changeset
12 sys.stdout.write("#name\tlength\tcoverage\n")
292d633441ad planemo upload commit c251e9b174b5370300a209b2b4c5e2052976eb2d
estrain
parents:
diff changeset
13
292d633441ad planemo upload commit c251e9b174b5370300a209b2b4c5e2052976eb2d
estrain
parents:
diff changeset
14 for i, line in enumerate(sys.stdin):
292d633441ad planemo upload commit c251e9b174b5370300a209b2b4c5e2052976eb2d
estrain
parents:
diff changeset
15 if cmd.match(line):
292d633441ad planemo upload commit c251e9b174b5370300a209b2b4c5e2052976eb2d
estrain
parents:
diff changeset
16 sys.stdout.write(cmd.sub(replace_str, line))