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"planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/hcluster_sg_parser commit e015ac3e0d8c1bc62b1301527241ee5e377b91db"
author earlhaminst
date Fri, 10 Sep 2021 15:08:06 +0000
parents 02d73e6ca869
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17aa68582a05 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/hcluster_sg_parser commit a79c8f1799189754eae80aede6fbe5428570f36b
earlhaminst
parents:
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1 """
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f9e418125021 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/hcluster_sg_parser commit 66af14bc1642c1ca6ceb21f6018c8d665da890e8
earlhaminst
parents: 1
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2 A simple parser to convert the hcluster_sg output into lists of IDs, one list for each cluster.
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17aa68582a05 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/hcluster_sg_parser commit a79c8f1799189754eae80aede6fbe5428570f36b
earlhaminst
parents:
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17aa68582a05 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/hcluster_sg_parser commit a79c8f1799189754eae80aede6fbe5428570f36b
earlhaminst
parents:
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4 When a minimum and/or maximum number of cluster elements are specified, the IDs contained in the filtered-out clusters are collected in the "discarded IDS" output dataset.
17aa68582a05 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/hcluster_sg_parser commit a79c8f1799189754eae80aede6fbe5428570f36b
earlhaminst
parents:
diff changeset
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17aa68582a05 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/hcluster_sg_parser commit a79c8f1799189754eae80aede6fbe5428570f36b
earlhaminst
parents:
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6 Usage:
17aa68582a05 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/hcluster_sg_parser commit a79c8f1799189754eae80aede6fbe5428570f36b
earlhaminst
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07f5b2c5ac10 "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/hcluster_sg_parser commit e015ac3e0d8c1bc62b1301527241ee5e377b91db"
earlhaminst
parents: 4
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8 python hcluster_sg_parser.py [-m <N>] [-M <N>] <file> <discarded_min_out> <discarded_max_out>
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17aa68582a05 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/hcluster_sg_parser commit a79c8f1799189754eae80aede6fbe5428570f36b
earlhaminst
parents:
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9 """
17aa68582a05 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/hcluster_sg_parser commit a79c8f1799189754eae80aede6fbe5428570f36b
earlhaminst
parents:
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10 import optparse
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07f5b2c5ac10 "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/hcluster_sg_parser commit e015ac3e0d8c1bc62b1301527241ee5e377b91db"
earlhaminst
parents: 4
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11 import os
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17aa68582a05 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/hcluster_sg_parser commit a79c8f1799189754eae80aede6fbe5428570f36b
earlhaminst
parents:
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12 import sys
17aa68582a05 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/hcluster_sg_parser commit a79c8f1799189754eae80aede6fbe5428570f36b
earlhaminst
parents:
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17aa68582a05 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/hcluster_sg_parser commit a79c8f1799189754eae80aede6fbe5428570f36b
earlhaminst
parents:
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17aa68582a05 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/hcluster_sg_parser commit a79c8f1799189754eae80aede6fbe5428570f36b
earlhaminst
parents:
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15 def main():
17aa68582a05 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/hcluster_sg_parser commit a79c8f1799189754eae80aede6fbe5428570f36b
earlhaminst
parents:
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16 parser = optparse.OptionParser()
17aa68582a05 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/hcluster_sg_parser commit a79c8f1799189754eae80aede6fbe5428570f36b
earlhaminst
parents:
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17 parser.add_option('-m', '--min', type='int', default=0, help='Minimum number of cluster elements')
17aa68582a05 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/hcluster_sg_parser commit a79c8f1799189754eae80aede6fbe5428570f36b
earlhaminst
parents:
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18 parser.add_option('-M', '--max', type='int', default=sys.maxsize, help='Maximum number of cluster elements')
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07f5b2c5ac10 "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/hcluster_sg_parser commit e015ac3e0d8c1bc62b1301527241ee5e377b91db"
earlhaminst
parents: 4
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19 parser.add_option('-d', '--dir', type='string', help="Absolute or relative path to output directory. If the directory does not exist, it will be created")
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17aa68582a05 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/hcluster_sg_parser commit a79c8f1799189754eae80aede6fbe5428570f36b
earlhaminst
parents:
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20 options, args = parser.parse_args()
17aa68582a05 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/hcluster_sg_parser commit a79c8f1799189754eae80aede6fbe5428570f36b
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parents:
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07f5b2c5ac10 "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/hcluster_sg_parser commit e015ac3e0d8c1bc62b1301527241ee5e377b91db"
earlhaminst
parents: 4
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22 if options.dir and not os.path.exists(options.dir):
07f5b2c5ac10 "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/hcluster_sg_parser commit e015ac3e0d8c1bc62b1301527241ee5e377b91db"
earlhaminst
parents: 4
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23 os.mkdir(options.dir)
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02d73e6ca869 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/hcluster_sg_parser commit e35f2ea026b79daaced9a2a50da02b4881d6154b
earlhaminst
parents: 3
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24 with open(args[2], 'w') as discarded_max_out:
02d73e6ca869 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/hcluster_sg_parser commit e35f2ea026b79daaced9a2a50da02b4881d6154b
earlhaminst
parents: 3
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25 with open(args[1], 'w') as discarded_min_out:
02d73e6ca869 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/hcluster_sg_parser commit e35f2ea026b79daaced9a2a50da02b4881d6154b
earlhaminst
parents: 3
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26 with open(args[0]) as fh:
02d73e6ca869 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/hcluster_sg_parser commit e35f2ea026b79daaced9a2a50da02b4881d6154b
earlhaminst
parents: 3
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27 for line in fh:
02d73e6ca869 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/hcluster_sg_parser commit e35f2ea026b79daaced9a2a50da02b4881d6154b
earlhaminst
parents: 3
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28 line = line.rstrip()
02d73e6ca869 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/hcluster_sg_parser commit e35f2ea026b79daaced9a2a50da02b4881d6154b
earlhaminst
parents: 3
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29 line_cols = line.split('\t')
02d73e6ca869 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/hcluster_sg_parser commit e35f2ea026b79daaced9a2a50da02b4881d6154b
earlhaminst
parents: 3
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30 cluster_id = line_cols[0]
02d73e6ca869 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/hcluster_sg_parser commit e35f2ea026b79daaced9a2a50da02b4881d6154b
earlhaminst
parents: 3
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31 n_ids = int(line_cols[-2])
02d73e6ca869 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/hcluster_sg_parser commit e35f2ea026b79daaced9a2a50da02b4881d6154b
earlhaminst
parents: 3
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32 id_list = line_cols[-1].replace(',', '\n')
02d73e6ca869 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/hcluster_sg_parser commit e35f2ea026b79daaced9a2a50da02b4881d6154b
earlhaminst
parents: 3
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33 if n_ids < options.min:
02d73e6ca869 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/hcluster_sg_parser commit e35f2ea026b79daaced9a2a50da02b4881d6154b
earlhaminst
parents: 3
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34 discarded_min_out.write(id_list)
02d73e6ca869 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/hcluster_sg_parser commit e35f2ea026b79daaced9a2a50da02b4881d6154b
earlhaminst
parents: 3
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35 elif n_ids > options.max:
02d73e6ca869 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/hcluster_sg_parser commit e35f2ea026b79daaced9a2a50da02b4881d6154b
earlhaminst
parents: 3
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36 discarded_max_out.write(id_list)
02d73e6ca869 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/hcluster_sg_parser commit e35f2ea026b79daaced9a2a50da02b4881d6154b
earlhaminst
parents: 3
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37 else:
02d73e6ca869 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/hcluster_sg_parser commit e35f2ea026b79daaced9a2a50da02b4881d6154b
earlhaminst
parents: 3
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38 outfile = cluster_id + '_output.txt'
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07f5b2c5ac10 "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/hcluster_sg_parser commit e015ac3e0d8c1bc62b1301527241ee5e377b91db"
earlhaminst
parents: 4
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39 if options.dir:
07f5b2c5ac10 "planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/hcluster_sg_parser commit e015ac3e0d8c1bc62b1301527241ee5e377b91db"
earlhaminst
parents: 4
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40 outfile = os.path.join(options.dir, outfile)
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02d73e6ca869 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/hcluster_sg_parser commit e35f2ea026b79daaced9a2a50da02b4881d6154b
earlhaminst
parents: 3
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41 with open(outfile, 'w') as f:
02d73e6ca869 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/hcluster_sg_parser commit e35f2ea026b79daaced9a2a50da02b4881d6154b
earlhaminst
parents: 3
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42 f.write(id_list)
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17aa68582a05 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/hcluster_sg_parser commit a79c8f1799189754eae80aede6fbe5428570f36b
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17aa68582a05 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/hcluster_sg_parser commit a79c8f1799189754eae80aede6fbe5428570f36b
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17aa68582a05 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/hcluster_sg_parser commit a79c8f1799189754eae80aede6fbe5428570f36b
earlhaminst
parents:
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45 if __name__ == "__main__":
17aa68582a05 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/hcluster_sg_parser commit a79c8f1799189754eae80aede6fbe5428570f36b
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46 main()