Mercurial > repos > iuc > bbgbigwig

annotate gff_to_bed_converter.py @ 0:65a296d558e7 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/galaxyproject/tools-iuc/tree/main/tools/bbgbigwig commit decf6daa4769664f779bc088b83b0f89ac1df147
author iuc
date Fri, 12 Dec 2025 21:28:28 +0000
parents
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
0
65a296d558e7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/bbgbigwig commit decf6daa4769664f779bc088b83b0f89ac1df147
iuc
parents:
diff changeset
1 #!/usr/bin/env python
65a296d558e7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/bbgbigwig commit decf6daa4769664f779bc088b83b0f89ac1df147
iuc
parents:
diff changeset
2
65a296d558e7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/bbgbigwig commit decf6daa4769664f779bc088b83b0f89ac1df147
iuc
parents:
diff changeset
3 import sys
65a296d558e7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/bbgbigwig commit decf6daa4769664f779bc088b83b0f89ac1df147
iuc
parents:
diff changeset
4
65a296d558e7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/bbgbigwig commit decf6daa4769664f779bc088b83b0f89ac1df147
iuc
parents:
diff changeset
5 assert sys.version_info[:2] >= (2, 6)
65a296d558e7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/bbgbigwig commit decf6daa4769664f779bc088b83b0f89ac1df147
iuc
parents:
diff changeset
6
65a296d558e7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/bbgbigwig commit decf6daa4769664f779bc088b83b0f89ac1df147
iuc
parents:
diff changeset
7
65a296d558e7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/bbgbigwig commit decf6daa4769664f779bc088b83b0f89ac1df147
iuc
parents:
diff changeset
8 def __main__():
65a296d558e7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/bbgbigwig commit decf6daa4769664f779bc088b83b0f89ac1df147
iuc
parents:
diff changeset
9 skipped_lines = 0
65a296d558e7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/bbgbigwig commit decf6daa4769664f779bc088b83b0f89ac1df147
iuc
parents:
diff changeset
10 first_skipped_line = None
65a296d558e7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/bbgbigwig commit decf6daa4769664f779bc088b83b0f89ac1df147
iuc
parents:
diff changeset
11 # was sys.argv[2] but we need stdout for a pipe in bam_bed_gff_to_bigwig.xml
65a296d558e7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/bbgbigwig commit decf6daa4769664f779bc088b83b0f89ac1df147
iuc
parents:
diff changeset
12 for i, line in enumerate(sys.stdin):
65a296d558e7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/bbgbigwig commit decf6daa4769664f779bc088b83b0f89ac1df147
iuc
parents:
diff changeset
13 line = line.rstrip("\r\n")
65a296d558e7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/bbgbigwig commit decf6daa4769664f779bc088b83b0f89ac1df147
iuc
parents:
diff changeset
14 if line and not line.startswith("#"):
65a296d558e7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/bbgbigwig commit decf6daa4769664f779bc088b83b0f89ac1df147
iuc
parents:
diff changeset
15 try:
65a296d558e7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/bbgbigwig commit decf6daa4769664f779bc088b83b0f89ac1df147
iuc
parents:
diff changeset
16 elems = line.split("\t")
65a296d558e7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/bbgbigwig commit decf6daa4769664f779bc088b83b0f89ac1df147
iuc
parents:
diff changeset
17 start = str(int(elems[3]) - 1)
65a296d558e7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/bbgbigwig commit decf6daa4769664f779bc088b83b0f89ac1df147
iuc
parents:
diff changeset
18 endoff = str(int(elems[4]) - 1)
65a296d558e7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/bbgbigwig commit decf6daa4769664f779bc088b83b0f89ac1df147
iuc
parents:
diff changeset
19 # GFF format: chrom, source, name, chromStart, chromEnd, score, strand
65a296d558e7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/bbgbigwig commit decf6daa4769664f779bc088b83b0f89ac1df147
iuc
parents:
diff changeset
20 # bedtools puts out only 4 fields: chrom, chromStart, chromEnd, score
65a296d558e7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/bbgbigwig commit decf6daa4769664f779bc088b83b0f89ac1df147
iuc
parents:
diff changeset
21 sys.stdout.write(f"{elems[0]}\t{start}\t{endoff}\t0\n")
65a296d558e7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/bbgbigwig commit decf6daa4769664f779bc088b83b0f89ac1df147
iuc
parents:
diff changeset
22 except Exception:
65a296d558e7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/bbgbigwig commit decf6daa4769664f779bc088b83b0f89ac1df147
iuc
parents:
diff changeset
23 skipped_lines += 1
65a296d558e7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/bbgbigwig commit decf6daa4769664f779bc088b83b0f89ac1df147
iuc
parents:
diff changeset
24 if not first_skipped_line:
65a296d558e7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/bbgbigwig commit decf6daa4769664f779bc088b83b0f89ac1df147
iuc
parents:
diff changeset
25 first_skipped_line = i + 1
65a296d558e7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/bbgbigwig commit decf6daa4769664f779bc088b83b0f89ac1df147
iuc
parents:
diff changeset
26 else:
65a296d558e7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/bbgbigwig commit decf6daa4769664f779bc088b83b0f89ac1df147
iuc
parents:
diff changeset
27 skipped_lines += 1
65a296d558e7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/bbgbigwig commit decf6daa4769664f779bc088b83b0f89ac1df147
iuc
parents:
diff changeset
28 if not first_skipped_line:
65a296d558e7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/bbgbigwig commit decf6daa4769664f779bc088b83b0f89ac1df147
iuc
parents:
diff changeset
29 first_skipped_line = i + 1
65a296d558e7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/bbgbigwig commit decf6daa4769664f779bc088b83b0f89ac1df147
iuc
parents:
diff changeset
30
65a296d558e7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/bbgbigwig commit decf6daa4769664f779bc088b83b0f89ac1df147
iuc
parents:
diff changeset
31
65a296d558e7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/bbgbigwig commit decf6daa4769664f779bc088b83b0f89ac1df147
iuc
parents:
diff changeset
32 if __name__ == "__main__":
65a296d558e7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/bbgbigwig commit decf6daa4769664f779bc088b83b0f89ac1df147
iuc
parents:
diff changeset
33 __main__()