Mercurial > repos > iuc > raxml

comparison raxml.py @ 2:a4b71be30c3c draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raxml commit 9f9e37b75ae2e5735289eeec1c74ff49e6e388e0"
author iuc
date Mon, 02 Dec 2019 07:52:10 -0500
parents ba29b5e2a4be
children b1e68bbe4cef
comparison
equal deleted inserted replaced
1:ba29b5e2a4be 2:a4b71be30c3c
37 # Logs 37 # Logs
38 with open('RAxML_log.galaxy', 'w') as outfile: 38 with open('RAxML_log.galaxy', 'w') as outfile:
39 for filename in runfiles: 39 for filename in runfiles:
40 if fnmatch.fnmatch(filename, 'RAxML_log.galaxy.RUN.*'): 40 if fnmatch.fnmatch(filename, 'RAxML_log.galaxy.RUN.*'):
41 with open(filename, 'r') as infile: 41 with open(filename, 'r') as infile:
42 filename_line = "%s\n" % filename
43 outfile.write(filename_line)
44 for line in infile: 42 for line in infile:
45 outfile.write(line) 43 outfile.write(line)
46 # Parsimony Trees 44 # Parsimony Trees
47 with open('RAxML_parsimonyTree.galaxy', 'w') as outfile: 45 with open('RAxML_parsimonyTree.galaxy', 'w') as outfile:
48 for filename in runfiles: 46 for filename in runfiles:
49 if fnmatch.fnmatch(filename, 'RAxML_parsimonyTree.galaxy.RUN.*'): 47 if fnmatch.fnmatch(filename, 'RAxML_parsimonyTree.galaxy.RUN.*'):
50 with open(filename, 'r') as infile: 48 with open(filename, 'r') as infile:
51 filename_line = "%s\n" % filename
52 outfile.write(filename_line)
53 for line in infile: 49 for line in infile:
54 outfile.write(line) 50 outfile.write(line)
55 # Results 51 # Results
56 with open('RAxML_result.galaxy', 'w') as outfile: 52 with open('RAxML_result.galaxy', 'w') as outfile:
57 for filename in runfiles: 53 for filename in runfiles:
58 if fnmatch.fnmatch(filename, 'RAxML_result.galaxy.RUN.*'): 54 if fnmatch.fnmatch(filename, 'RAxML_result.galaxy.RUN.*'):
59 with open(filename, 'r') as infile: 55 with open(filename, 'r') as infile:
60 filename_line = "%s\n" % filename
61 outfile.write(filename_line)
62 for line in infile: 56 for line in infile:
63 outfile.write(line) 57 outfile.write(line)
64 # Multiple Model Partition Files 58 # Multiple Model Partition Files
65 if options.multiple_model: 59 if options.multiple_model:
66 files = glob.glob('RAxML_bestTree.galaxy.PARTITION.*') 60 files = glob.glob('RAxML_bestTree.galaxy.PARTITION.*')
69 # Best Tree Partitions 63 # Best Tree Partitions
70 with open('RAxML_bestTreePartitions.galaxy', 'w') as outfile: 64 with open('RAxML_bestTreePartitions.galaxy', 'w') as outfile:
71 for filename in files: 65 for filename in files:
72 if fnmatch.fnmatch(filename, 'RAxML_bestTree.galaxy.PARTITION.*'): 66 if fnmatch.fnmatch(filename, 'RAxML_bestTree.galaxy.PARTITION.*'):
73 with open(filename, 'r') as infile: 67 with open(filename, 'r') as infile:
74 filename_line = "%s\n" % filename
75 outfile.write(filename_line)
76 for line in infile: 68 for line in infile:
77 outfile.write(line) 69 outfile.write(line)
78 else: 70 else:
79 with open('RAxML_bestTreePartitions.galaxy', 'w') as outfile: 71 with open('RAxML_bestTreePartitions.galaxy', 'w') as outfile:
80 outfile.write("No partition files were produced.\n") 72 outfile.write("No partition files were produced.\n")
85 files.sort(key=getint) 77 files.sort(key=getint)
86 with open('RAxML_resultPartitions.galaxy', 'w') as outfile: 78 with open('RAxML_resultPartitions.galaxy', 'w') as outfile:
87 for filename in files: 79 for filename in files:
88 if fnmatch.fnmatch(filename, 'RAxML_result.galaxy.PARTITION.*'): 80 if fnmatch.fnmatch(filename, 'RAxML_result.galaxy.PARTITION.*'):
89 with open(filename, 'r') as infile: 81 with open(filename, 'r') as infile:
90 filename_line = "%s\n" % filename
91 outfile.write(filename_line)
92 for line in infile: 82 for line in infile:
93 outfile.write(line) 83 outfile.write(line)
94 else: 84 else:
95 with open('RAxML_resultPartitions.galaxy', 'w') as outfile: 85 with open('RAxML_resultPartitions.galaxy', 'w') as outfile:
96 outfile.write("No partition files were produced.\n") 86 outfile.write("No partition files were produced.\n")