Mercurial > repos > iuc > circos
comparison alignments-to-links.py @ 2:014a21767ac4 draft
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 076837a2e9c2b6ececcea4aa286ea7a412387a96"
| author | iuc |
|---|---|
| date | Tue, 17 Sep 2019 16:54:57 -0400 |
| parents | |
| children |
comparison
equal
deleted
inserted
replaced
| 1:ae9994cf526f | 2:014a21767ac4 |
|---|---|
| 1 import itertools | |
| 2 import sys | |
| 3 | |
| 4 from Bio import AlignIO | |
| 5 | |
| 6 | |
| 7 format_mapping = { | |
| 8 "xmfa": "mauve", | |
| 9 "maf": "maf", | |
| 10 "nex": "nexus", | |
| 11 # 'phylip': 'phylip-relaxed', | |
| 12 "stockholm": "stockholm", | |
| 13 } | |
| 14 | |
| 15 for aln in AlignIO.parse(sys.argv[1], format_mapping.get(sys.argv[2], "maf")): | |
| 16 | |
| 17 for (a, b) in itertools.combinations(aln, 2): | |
| 18 a_s = a.annotations["start"] | |
| 19 b_s = b.annotations["start"] | |
| 20 | |
| 21 if "size" in a.annotations: | |
| 22 a_l = a.annotations["size"] | |
| 23 b_l = b.annotations["size"] | |
| 24 a_e = a_l + a_s | |
| 25 b_e = b_l + b_s | |
| 26 else: | |
| 27 a_e = a.annotations["end"] | |
| 28 b_e = b.annotations["end"] | |
| 29 | |
| 30 sys.stdout.write("%s\t%s\t%s\t%s\t%s\t%s\n" % (a.id, a_s, a_e, b.id, b_s, b_e)) |