Mercurial > repos > fubar > jbrowse2

annotate maf2bed.py @ 136:93fdd696c281 draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
author iuc
date Thu, 02 Oct 2025 10:20:29 +0000
parents b1260bca5fdc
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
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e7a6f7a7148d planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 6dde5ad41d63730085116ab2c9a9d3e500a760e4-dirty
fubar
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diff changeset
1 #!/usr/bin/env python
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93fdd696c281 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
iuc
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93fdd696c281 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
iuc
parents: 98
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3 # adapted from https://github.com/bgruening/galaxytools/blob/f96142ca5acea989b828d6c92940172355b7f125/tools/jbrowse2/maf2bed.py
93fdd696c281 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
iuc
parents: 98
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4 # which was "painfully converted from b0rken perl from:"
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e7a6f7a7148d planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 6dde5ad41d63730085116ab2c9a9d3e500a760e4-dirty
fubar
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5 # https://unpkg.com/browse/jbrowse-plugin-mafviewer@1.0.6/dist/
e7a6f7a7148d planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 6dde5ad41d63730085116ab2c9a9d3e500a760e4-dirty
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93fdd696c281 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
iuc
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7 import argparse
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e7a6f7a7148d planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 6dde5ad41d63730085116ab2c9a9d3e500a760e4-dirty
fubar
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8 import sys
e7a6f7a7148d planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 6dde5ad41d63730085116ab2c9a9d3e500a760e4-dirty
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e7a6f7a7148d planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 6dde5ad41d63730085116ab2c9a9d3e500a760e4-dirty
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93fdd696c281 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
iuc
parents: 98
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11 def maf2bed(assembly_name, input, output):
93fdd696c281 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
iuc
parents: 98
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12 id = 0
93fdd696c281 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
iuc
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13 buffer = ''
93fdd696c281 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
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14 start = 0
93fdd696c281 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
iuc
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15 end = 0
93fdd696c281 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
iuc
parents: 98
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16 score = 0
93fdd696c281 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
iuc
parents: 98
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17 chrom = ''
93fdd696c281 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
iuc
parents: 98
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93fdd696c281 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
iuc
parents: 98
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19 db = "%s." % assembly_name
93fdd696c281 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
iuc
parents: 98
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20 # Read input from stdin
93fdd696c281 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
iuc
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21 for line in input:
93fdd696c281 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
iuc
parents: 98
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22 line = line.strip()
93fdd696c281 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
iuc
parents: 98
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23 if not line:
93fdd696c281 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
iuc
parents: 98
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24 continue
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e7a6f7a7148d planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 6dde5ad41d63730085116ab2c9a9d3e500a760e4-dirty
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93fdd696c281 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
iuc
parents: 98
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26 line = line.split()
93fdd696c281 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
iuc
parents: 98
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27 if line[0] == 's' and line[1].startswith(db):
93fdd696c281 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
iuc
parents: 98
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28 chrom = line[1]
93fdd696c281 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
iuc
parents: 98
diff changeset
29 chrom = chrom.replace(db, '')
93fdd696c281 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
iuc
parents: 98
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30 start = int(line[2])
93fdd696c281 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
iuc
parents: 98
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31 end = int(line[2]) + int(line[3])
93fdd696c281 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
iuc
parents: 98
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32 line = line[1:]
93fdd696c281 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
iuc
parents: 98
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33 line = ':'.join(line)
93fdd696c281 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
iuc
parents: 98
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34 temp = line
93fdd696c281 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
iuc
parents: 98
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35 buffer = temp if buffer == '' else f"{buffer},{temp}"
93fdd696c281 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
iuc
parents: 98
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36 elif line[0] == 'a':
93fdd696c281 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
iuc
parents: 98
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37 score = int(line[1].split('=')[1])
93fdd696c281 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
iuc
parents: 98
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38 if id > 0:
93fdd696c281 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
iuc
parents: 98
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39 output.write('\t'.join([chrom, '%d' % start, '%d' % end, f"{assembly_name}_{id}", '%d' % score, buffer]) + '\n')
93fdd696c281 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
iuc
parents: 98
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40 id += 1
93fdd696c281 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
iuc
parents: 98
diff changeset
41 buffer = ''
93fdd696c281 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
iuc
parents: 98
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42 elif line[0] == 's':
93fdd696c281 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
iuc
parents: 98
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43 line = line[1:]
93fdd696c281 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
iuc
parents: 98
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44 line = ':'.join(line)
93fdd696c281 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
iuc
parents: 98
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45 temp = line
93fdd696c281 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
iuc
parents: 98
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46 buffer = temp if buffer == '' else f"{buffer},{temp}"
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e7a6f7a7148d planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 6dde5ad41d63730085116ab2c9a9d3e500a760e4-dirty
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47
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93fdd696c281 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
iuc
parents: 98
diff changeset
48 output.write('\t'.join([chrom, '%d' % start, '%d' % end, f"{assembly_name}_{id}", '%d' % score, buffer]) + '\n')
93fdd696c281 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
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parents: 98
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93fdd696c281 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
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93fdd696c281 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
iuc
parents: 98
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51 if __name__ == "__main__":
93fdd696c281 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
iuc
parents: 98
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52 parser = argparse.ArgumentParser(description="", epilog="")
93fdd696c281 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
iuc
parents: 98
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53 parser.add_argument("assembly_name", help="Assembly name")
93fdd696c281 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
iuc
parents: 98
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54 parser.add_argument('input', nargs='?', type=argparse.FileType('r'), default=sys.stdin)
93fdd696c281 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
iuc
parents: 98
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55 parser.add_argument('output', nargs='?', type=argparse.FileType('w'), default=sys.stdout)
93fdd696c281 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
iuc
parents: 98
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56 args = parser.parse_args()
93fdd696c281 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
iuc
parents: 98
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93fdd696c281 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
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parents: 98
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58 maf2bed(args.assembly_name, args.input, args.output)