Mercurial > repos > iuc > spades_metaviralspades

annotate write_tsv_script.py @ 2:f1532cb33c75 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 2609367ebbce7e0c3f5b4b2d7c60a82d4bd03246"
author iuc
date Tue, 25 Jan 2022 07:56:43 +0000
parents
children 86f66ab58e14
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
2
f1532cb33c75 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 2609367ebbce7e0c3f5b4b2d7c60a82d4bd03246"
iuc
parents:
diff changeset
1 #!/usr/bin/env python
f1532cb33c75 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 2609367ebbce7e0c3f5b4b2d7c60a82d4bd03246"
iuc
parents:
diff changeset
2
f1532cb33c75 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 2609367ebbce7e0c3f5b4b2d7c60a82d4bd03246"
iuc
parents:
diff changeset
3 import re
f1532cb33c75 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 2609367ebbce7e0c3f5b4b2d7c60a82d4bd03246"
iuc
parents:
diff changeset
4 import sys
f1532cb33c75 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 2609367ebbce7e0c3f5b4b2d7c60a82d4bd03246"
iuc
parents:
diff changeset
5
f1532cb33c75 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 2609367ebbce7e0c3f5b4b2d7c60a82d4bd03246"
iuc
parents:
diff changeset
6 search_str = r"^>(NODE|\S+)_(\d+)(?:_|\s)length_(\d+)_cov_(\d+\.*\d*).*\$"
f1532cb33c75 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 2609367ebbce7e0c3f5b4b2d7c60a82d4bd03246"
iuc
parents:
diff changeset
7
f1532cb33c75 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 2609367ebbce7e0c3f5b4b2d7c60a82d4bd03246"
iuc
parents:
diff changeset
8 replace_str = r"\1_\2\t\3\t\4"
f1532cb33c75 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 2609367ebbce7e0c3f5b4b2d7c60a82d4bd03246"
iuc
parents:
diff changeset
9
f1532cb33c75 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 2609367ebbce7e0c3f5b4b2d7c60a82d4bd03246"
iuc
parents:
diff changeset
10 cmd = re.compile(search_str)
f1532cb33c75 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 2609367ebbce7e0c3f5b4b2d7c60a82d4bd03246"
iuc
parents:
diff changeset
11
f1532cb33c75 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 2609367ebbce7e0c3f5b4b2d7c60a82d4bd03246"
iuc
parents:
diff changeset
12 sys.stdout.write("#name\tlength\tcoverage\n")
f1532cb33c75 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 2609367ebbce7e0c3f5b4b2d7c60a82d4bd03246"
iuc
parents:
diff changeset
13
f1532cb33c75 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 2609367ebbce7e0c3f5b4b2d7c60a82d4bd03246"
iuc
parents:
diff changeset
14 for i, line in enumerate(sys.stdin):
f1532cb33c75 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 2609367ebbce7e0c3f5b4b2d7c60a82d4bd03246"
iuc
parents:
diff changeset
15 if cmd.match(line):
f1532cb33c75 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 2609367ebbce7e0c3f5b4b2d7c60a82d4bd03246"
iuc
parents:
diff changeset
16 sys.stdout.write(cmd.sub(replace_str, line))