Mercurial > repos > iuc > raxml

annotate raxml.py @ 1:ba29b5e2a4be draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raxml commit b23553a3d29d50e05d8b37a5c5780e3ffc937069
author iuc
date Tue, 27 Jun 2017 16:27:39 -0400
parents 6805e85573b8
children a4b71be30c3c
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0
6805e85573b8 planemo upload for repository https://github.com/stamatak/standard-RAxML commit 174be06d7c7e7789df16ea5d5068f20b21257a2f
iuc
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diff changeset
1 #!/usr/bin/env python
6805e85573b8 planemo upload for repository https://github.com/stamatak/standard-RAxML commit 174be06d7c7e7789df16ea5d5068f20b21257a2f
iuc
parents:
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2 """
6805e85573b8 planemo upload for repository https://github.com/stamatak/standard-RAxML commit 174be06d7c7e7789df16ea5d5068f20b21257a2f
iuc
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3 Runs RAxML on a sequence file.
6805e85573b8 planemo upload for repository https://github.com/stamatak/standard-RAxML commit 174be06d7c7e7789df16ea5d5068f20b21257a2f
iuc
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4 For use with RAxML version 8.2.4
6805e85573b8 planemo upload for repository https://github.com/stamatak/standard-RAxML commit 174be06d7c7e7789df16ea5d5068f20b21257a2f
iuc
parents:
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5 """
6805e85573b8 planemo upload for repository https://github.com/stamatak/standard-RAxML commit 174be06d7c7e7789df16ea5d5068f20b21257a2f
iuc
parents:
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6 import fnmatch
6805e85573b8 planemo upload for repository https://github.com/stamatak/standard-RAxML commit 174be06d7c7e7789df16ea5d5068f20b21257a2f
iuc
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7 import glob
6805e85573b8 planemo upload for repository https://github.com/stamatak/standard-RAxML commit 174be06d7c7e7789df16ea5d5068f20b21257a2f
iuc
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8 import optparse
6805e85573b8 planemo upload for repository https://github.com/stamatak/standard-RAxML commit 174be06d7c7e7789df16ea5d5068f20b21257a2f
iuc
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9
6805e85573b8 planemo upload for repository https://github.com/stamatak/standard-RAxML commit 174be06d7c7e7789df16ea5d5068f20b21257a2f
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10
6805e85573b8 planemo upload for repository https://github.com/stamatak/standard-RAxML commit 174be06d7c7e7789df16ea5d5068f20b21257a2f
iuc
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11 def getint(name):
6805e85573b8 planemo upload for repository https://github.com/stamatak/standard-RAxML commit 174be06d7c7e7789df16ea5d5068f20b21257a2f
iuc
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12 basename = name.partition('RUN.')
6805e85573b8 planemo upload for repository https://github.com/stamatak/standard-RAxML commit 174be06d7c7e7789df16ea5d5068f20b21257a2f
iuc
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13 if basename[2] != '':
6805e85573b8 planemo upload for repository https://github.com/stamatak/standard-RAxML commit 174be06d7c7e7789df16ea5d5068f20b21257a2f
iuc
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14 num = basename[2]
6805e85573b8 planemo upload for repository https://github.com/stamatak/standard-RAxML commit 174be06d7c7e7789df16ea5d5068f20b21257a2f
iuc
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15 return int(num)
6805e85573b8 planemo upload for repository https://github.com/stamatak/standard-RAxML commit 174be06d7c7e7789df16ea5d5068f20b21257a2f
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16
6805e85573b8 planemo upload for repository https://github.com/stamatak/standard-RAxML commit 174be06d7c7e7789df16ea5d5068f20b21257a2f
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17
6805e85573b8 planemo upload for repository https://github.com/stamatak/standard-RAxML commit 174be06d7c7e7789df16ea5d5068f20b21257a2f
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18 def __main__():
6805e85573b8 planemo upload for repository https://github.com/stamatak/standard-RAxML commit 174be06d7c7e7789df16ea5d5068f20b21257a2f
iuc
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19 # Parse the primary wrapper's command line options
1
ba29b5e2a4be planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raxml commit b23553a3d29d50e05d8b37a5c5780e3ffc937069
iuc
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20 parser = optparse.OptionParser()
0
6805e85573b8 planemo upload for repository https://github.com/stamatak/standard-RAxML commit 174be06d7c7e7789df16ea5d5068f20b21257a2f
iuc
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21 # (-b)
1
ba29b5e2a4be planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raxml commit b23553a3d29d50e05d8b37a5c5780e3ffc937069
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22 parser.add_option("--bootseed", action="store", type="int", dest="bootseed", help="Random number for non-parametric bootstrapping")
0
6805e85573b8 planemo upload for repository https://github.com/stamatak/standard-RAxML commit 174be06d7c7e7789df16ea5d5068f20b21257a2f
iuc
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23 # (-N/#)
1
ba29b5e2a4be planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raxml commit b23553a3d29d50e05d8b37a5c5780e3ffc937069
iuc
parents: 0
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24 parser.add_option("--number_of_runs", action="store", type="int", dest="number_of_runs", default=1, help="Number of alternative runs")
0
6805e85573b8 planemo upload for repository https://github.com/stamatak/standard-RAxML commit 174be06d7c7e7789df16ea5d5068f20b21257a2f
iuc
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25 # (-q)
6805e85573b8 planemo upload for repository https://github.com/stamatak/standard-RAxML commit 174be06d7c7e7789df16ea5d5068f20b21257a2f
iuc
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26 parser.add_option("--multiple_model", action="store", type="string", dest="multiple_model", help="Multiple Model File")
6805e85573b8 planemo upload for repository https://github.com/stamatak/standard-RAxML commit 174be06d7c7e7789df16ea5d5068f20b21257a2f
iuc
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27 # (-x)
6805e85573b8 planemo upload for repository https://github.com/stamatak/standard-RAxML commit 174be06d7c7e7789df16ea5d5068f20b21257a2f
iuc
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28 parser.add_option("--rapid_bootstrap_random_seed", action="store", type="int", dest="rapid_bootstrap_random_seed", help="Rapid Boostrap Random Seed")
6805e85573b8 planemo upload for repository https://github.com/stamatak/standard-RAxML commit 174be06d7c7e7789df16ea5d5068f20b21257a2f
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29
6805e85573b8 planemo upload for repository https://github.com/stamatak/standard-RAxML commit 174be06d7c7e7789df16ea5d5068f20b21257a2f
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30 (options, args) = parser.parse_args()
6805e85573b8 planemo upload for repository https://github.com/stamatak/standard-RAxML commit 174be06d7c7e7789df16ea5d5068f20b21257a2f
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31
6805e85573b8 planemo upload for repository https://github.com/stamatak/standard-RAxML commit 174be06d7c7e7789df16ea5d5068f20b21257a2f
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32 # Multiple runs - concatenate
1
ba29b5e2a4be planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raxml commit b23553a3d29d50e05d8b37a5c5780e3ffc937069
iuc
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33 if options.number_of_runs > 1:
ba29b5e2a4be planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raxml commit b23553a3d29d50e05d8b37a5c5780e3ffc937069
iuc
parents: 0
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34 if options.bootseed is None and options.rapid_bootstrap_random_seed is None:
0
6805e85573b8 planemo upload for repository https://github.com/stamatak/standard-RAxML commit 174be06d7c7e7789df16ea5d5068f20b21257a2f
iuc
parents:
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35 runfiles = glob.glob('RAxML*RUN*')
6805e85573b8 planemo upload for repository https://github.com/stamatak/standard-RAxML commit 174be06d7c7e7789df16ea5d5068f20b21257a2f
iuc
parents:
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36 runfiles.sort(key=getint)
1
ba29b5e2a4be planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raxml commit b23553a3d29d50e05d8b37a5c5780e3ffc937069
iuc
parents: 0
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37 # Logs
ba29b5e2a4be planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raxml commit b23553a3d29d50e05d8b37a5c5780e3ffc937069
iuc
parents: 0
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38 with open('RAxML_log.galaxy', 'w') as outfile:
ba29b5e2a4be planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raxml commit b23553a3d29d50e05d8b37a5c5780e3ffc937069
iuc
parents: 0
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39 for filename in runfiles:
ba29b5e2a4be planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raxml commit b23553a3d29d50e05d8b37a5c5780e3ffc937069
iuc
parents: 0
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40 if fnmatch.fnmatch(filename, 'RAxML_log.galaxy.RUN.*'):
ba29b5e2a4be planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raxml commit b23553a3d29d50e05d8b37a5c5780e3ffc937069
iuc
parents: 0
diff changeset
41 with open(filename, 'r') as infile:
ba29b5e2a4be planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raxml commit b23553a3d29d50e05d8b37a5c5780e3ffc937069
iuc
parents: 0
diff changeset
42 filename_line = "%s\n" % filename
ba29b5e2a4be planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raxml commit b23553a3d29d50e05d8b37a5c5780e3ffc937069
iuc
parents: 0
diff changeset
43 outfile.write(filename_line)
ba29b5e2a4be planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raxml commit b23553a3d29d50e05d8b37a5c5780e3ffc937069
iuc
parents: 0
diff changeset
44 for line in infile:
ba29b5e2a4be planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raxml commit b23553a3d29d50e05d8b37a5c5780e3ffc937069
iuc
parents: 0
diff changeset
45 outfile.write(line)
ba29b5e2a4be planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raxml commit b23553a3d29d50e05d8b37a5c5780e3ffc937069
iuc
parents: 0
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46 # Parsimony Trees
ba29b5e2a4be planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raxml commit b23553a3d29d50e05d8b37a5c5780e3ffc937069
iuc
parents: 0
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47 with open('RAxML_parsimonyTree.galaxy', 'w') as outfile:
ba29b5e2a4be planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raxml commit b23553a3d29d50e05d8b37a5c5780e3ffc937069
iuc
parents: 0
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48 for filename in runfiles:
ba29b5e2a4be planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raxml commit b23553a3d29d50e05d8b37a5c5780e3ffc937069
iuc
parents: 0
diff changeset
49 if fnmatch.fnmatch(filename, 'RAxML_parsimonyTree.galaxy.RUN.*'):
ba29b5e2a4be planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raxml commit b23553a3d29d50e05d8b37a5c5780e3ffc937069
iuc
parents: 0
diff changeset
50 with open(filename, 'r') as infile:
ba29b5e2a4be planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raxml commit b23553a3d29d50e05d8b37a5c5780e3ffc937069
iuc
parents: 0
diff changeset
51 filename_line = "%s\n" % filename
ba29b5e2a4be planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raxml commit b23553a3d29d50e05d8b37a5c5780e3ffc937069
iuc
parents: 0
diff changeset
52 outfile.write(filename_line)
ba29b5e2a4be planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raxml commit b23553a3d29d50e05d8b37a5c5780e3ffc937069
iuc
parents: 0
diff changeset
53 for line in infile:
ba29b5e2a4be planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raxml commit b23553a3d29d50e05d8b37a5c5780e3ffc937069
iuc
parents: 0
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54 outfile.write(line)
ba29b5e2a4be planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raxml commit b23553a3d29d50e05d8b37a5c5780e3ffc937069
iuc
parents: 0
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55 # Results
ba29b5e2a4be planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raxml commit b23553a3d29d50e05d8b37a5c5780e3ffc937069
iuc
parents: 0
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56 with open('RAxML_result.galaxy', 'w') as outfile:
ba29b5e2a4be planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raxml commit b23553a3d29d50e05d8b37a5c5780e3ffc937069
iuc
parents: 0
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57 for filename in runfiles:
ba29b5e2a4be planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raxml commit b23553a3d29d50e05d8b37a5c5780e3ffc937069
iuc
parents: 0
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58 if fnmatch.fnmatch(filename, 'RAxML_result.galaxy.RUN.*'):
ba29b5e2a4be planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raxml commit b23553a3d29d50e05d8b37a5c5780e3ffc937069
iuc
parents: 0
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59 with open(filename, 'r') as infile:
ba29b5e2a4be planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raxml commit b23553a3d29d50e05d8b37a5c5780e3ffc937069
iuc
parents: 0
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60 filename_line = "%s\n" % filename
ba29b5e2a4be planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raxml commit b23553a3d29d50e05d8b37a5c5780e3ffc937069
iuc
parents: 0
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61 outfile.write(filename_line)
ba29b5e2a4be planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raxml commit b23553a3d29d50e05d8b37a5c5780e3ffc937069
iuc
parents: 0
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62 for line in infile:
ba29b5e2a4be planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raxml commit b23553a3d29d50e05d8b37a5c5780e3ffc937069
iuc
parents: 0
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63 outfile.write(line)
0
6805e85573b8 planemo upload for repository https://github.com/stamatak/standard-RAxML commit 174be06d7c7e7789df16ea5d5068f20b21257a2f
iuc
parents:
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64 # Multiple Model Partition Files
1
ba29b5e2a4be planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raxml commit b23553a3d29d50e05d8b37a5c5780e3ffc937069
iuc
parents: 0
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65 if options.multiple_model:
0
6805e85573b8 planemo upload for repository https://github.com/stamatak/standard-RAxML commit 174be06d7c7e7789df16ea5d5068f20b21257a2f
iuc
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66 files = glob.glob('RAxML_bestTree.galaxy.PARTITION.*')
6805e85573b8 planemo upload for repository https://github.com/stamatak/standard-RAxML commit 174be06d7c7e7789df16ea5d5068f20b21257a2f
iuc
parents:
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67 if len(files) > 0:
6805e85573b8 planemo upload for repository https://github.com/stamatak/standard-RAxML commit 174be06d7c7e7789df16ea5d5068f20b21257a2f
iuc
parents:
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68 files.sort(key=getint)
6805e85573b8 planemo upload for repository https://github.com/stamatak/standard-RAxML commit 174be06d7c7e7789df16ea5d5068f20b21257a2f
iuc
parents:
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69 # Best Tree Partitions
1
ba29b5e2a4be planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raxml commit b23553a3d29d50e05d8b37a5c5780e3ffc937069
iuc
parents: 0
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70 with open('RAxML_bestTreePartitions.galaxy', 'w') as outfile:
ba29b5e2a4be planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raxml commit b23553a3d29d50e05d8b37a5c5780e3ffc937069
iuc
parents: 0
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71 for filename in files:
ba29b5e2a4be planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raxml commit b23553a3d29d50e05d8b37a5c5780e3ffc937069
iuc
parents: 0
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72 if fnmatch.fnmatch(filename, 'RAxML_bestTree.galaxy.PARTITION.*'):
ba29b5e2a4be planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raxml commit b23553a3d29d50e05d8b37a5c5780e3ffc937069
iuc
parents: 0
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73 with open(filename, 'r') as infile:
ba29b5e2a4be planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raxml commit b23553a3d29d50e05d8b37a5c5780e3ffc937069
iuc
parents: 0
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74 filename_line = "%s\n" % filename
ba29b5e2a4be planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raxml commit b23553a3d29d50e05d8b37a5c5780e3ffc937069
iuc
parents: 0
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75 outfile.write(filename_line)
ba29b5e2a4be planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raxml commit b23553a3d29d50e05d8b37a5c5780e3ffc937069
iuc
parents: 0
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76 for line in infile:
ba29b5e2a4be planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raxml commit b23553a3d29d50e05d8b37a5c5780e3ffc937069
iuc
parents: 0
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77 outfile.write(line)
0
6805e85573b8 planemo upload for repository https://github.com/stamatak/standard-RAxML commit 174be06d7c7e7789df16ea5d5068f20b21257a2f
iuc
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78 else:
1
ba29b5e2a4be planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raxml commit b23553a3d29d50e05d8b37a5c5780e3ffc937069
iuc
parents: 0
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79 with open('RAxML_bestTreePartitions.galaxy', 'w') as outfile:
ba29b5e2a4be planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raxml commit b23553a3d29d50e05d8b37a5c5780e3ffc937069
iuc
parents: 0
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80 outfile.write("No partition files were produced.\n")
0
6805e85573b8 planemo upload for repository https://github.com/stamatak/standard-RAxML commit 174be06d7c7e7789df16ea5d5068f20b21257a2f
iuc
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81
6805e85573b8 planemo upload for repository https://github.com/stamatak/standard-RAxML commit 174be06d7c7e7789df16ea5d5068f20b21257a2f
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82 # Result Partitions
6805e85573b8 planemo upload for repository https://github.com/stamatak/standard-RAxML commit 174be06d7c7e7789df16ea5d5068f20b21257a2f
iuc
parents:
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83 files = glob.glob('RAxML_result.galaxy.PARTITION.*')
6805e85573b8 planemo upload for repository https://github.com/stamatak/standard-RAxML commit 174be06d7c7e7789df16ea5d5068f20b21257a2f
iuc
parents:
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84 if len(files) > 0:
6805e85573b8 planemo upload for repository https://github.com/stamatak/standard-RAxML commit 174be06d7c7e7789df16ea5d5068f20b21257a2f
iuc
parents:
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85 files.sort(key=getint)
1
ba29b5e2a4be planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raxml commit b23553a3d29d50e05d8b37a5c5780e3ffc937069
iuc
parents: 0
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86 with open('RAxML_resultPartitions.galaxy', 'w') as outfile:
ba29b5e2a4be planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raxml commit b23553a3d29d50e05d8b37a5c5780e3ffc937069
iuc
parents: 0
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87 for filename in files:
ba29b5e2a4be planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raxml commit b23553a3d29d50e05d8b37a5c5780e3ffc937069
iuc
parents: 0
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88 if fnmatch.fnmatch(filename, 'RAxML_result.galaxy.PARTITION.*'):
ba29b5e2a4be planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raxml commit b23553a3d29d50e05d8b37a5c5780e3ffc937069
iuc
parents: 0
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89 with open(filename, 'r') as infile:
ba29b5e2a4be planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raxml commit b23553a3d29d50e05d8b37a5c5780e3ffc937069
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90 filename_line = "%s\n" % filename
ba29b5e2a4be planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raxml commit b23553a3d29d50e05d8b37a5c5780e3ffc937069
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91 outfile.write(filename_line)
ba29b5e2a4be planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raxml commit b23553a3d29d50e05d8b37a5c5780e3ffc937069
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92 for line in infile:
ba29b5e2a4be planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raxml commit b23553a3d29d50e05d8b37a5c5780e3ffc937069
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93 outfile.write(line)
0
6805e85573b8 planemo upload for repository https://github.com/stamatak/standard-RAxML commit 174be06d7c7e7789df16ea5d5068f20b21257a2f
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94 else:
1
ba29b5e2a4be planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raxml commit b23553a3d29d50e05d8b37a5c5780e3ffc937069
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95 with open('RAxML_resultPartitions.galaxy', 'w') as outfile:
ba29b5e2a4be planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raxml commit b23553a3d29d50e05d8b37a5c5780e3ffc937069
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96 outfile.write("No partition files were produced.\n")
0
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97
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98 # DEBUG options
1
ba29b5e2a4be planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raxml commit b23553a3d29d50e05d8b37a5c5780e3ffc937069
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99 with open('RAxML_info.galaxy', 'a') as infof:
ba29b5e2a4be planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raxml commit b23553a3d29d50e05d8b37a5c5780e3ffc937069
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100 infof.write('\nOM: CLI options DEBUG START:\n')
ba29b5e2a4be planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raxml commit b23553a3d29d50e05d8b37a5c5780e3ffc937069
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101 infof.write(options.__repr__())
ba29b5e2a4be planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raxml commit b23553a3d29d50e05d8b37a5c5780e3ffc937069
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102 infof.write('\nOM: CLI options DEBUG END\n')
ba29b5e2a4be planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raxml commit b23553a3d29d50e05d8b37a5c5780e3ffc937069
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103
0
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104
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105 if __name__ == "__main__":
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106 __main__()