diff maf2bed.py @ 61:e7a6f7a7148d draft

planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 6dde5ad41d63730085116ab2c9a9d3e500a760e4-dirty

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/maf2bed.py	Tue Mar 26 00:52:34 2024 +0000
@@ -0,0 +1,44 @@
+#!/usr/bin/env python
+# painfully converted from b0rken perl from
+# https://unpkg.com/browse/jbrowse-plugin-mafviewer@1.0.6/dist/
+# license is Apache2_license.txt included here
+
+import sys
+
+id = 0
+buffer = ''
+start = 0
+end = 0
+score = 0
+chrom = ''
+
+db = "%s." % sys.argv[1]
+# Read input from stdin
+for line in sys.stdin:
+    line = line.strip()
+    if not line:
+        continue
+
+    line = line.split()
+    if line[0] == 's' and line[1].startswith(db):
+        chrom = line[1]
+        chrom = chrom.replace(db, '')
+        start = int(line[2])
+        end = int(line[2]) + int(line[3])
+        line = line[1:]
+        line = ':'.join(line)
+        temp = line
+        buffer = temp if buffer == '' else f"{buffer},{temp}"
+    elif line[0] == 'a':
+        score = int(line[1].split('=')[1])
+        if id > 0:
+            sys.stdout.write('\t'.join([chrom, '%d' % start, '%d' % end, f"{sys.argv[1]}_{id}", '%d' % score, buffer])+ '\n')
+        id += 1
+        buffer = ''
+    elif line[0] == 's':
+        line = line[1:]
+        line = ':'.join(line)
+        temp = line
+        buffer = temp if buffer == '' else f"{buffer},{temp}"
+
+sys.stdout.write('\t'.join([chrom, '%d' % start, '%d' % end, f"{sys.argv[1]}_{id}", '%d' % score, buffer]) + '\n')