Mercurial > repos > ucsb-phylogenetics > osiris_phylogenetics

annotate phylogenies/phytab_raxml.py @ 0:5b9a38ec4a39 draft default tip

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
First commit of old repositories
author osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
date Tue, 11 Mar 2014 12:19:13 -0700
parents
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
0
5b9a38ec4a39 First commit of old repositories
osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
parents:
diff changeset
1 #!/usr/bin/env python
5b9a38ec4a39 First commit of old repositories
osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
parents:
diff changeset
2
5b9a38ec4a39 First commit of old repositories
osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
parents:
diff changeset
3 ##
5b9a38ec4a39 First commit of old repositories
osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
parents:
diff changeset
4 ## This tool runs RAxML on each partition/gene in a PHYTAB file.
5b9a38ec4a39 First commit of old repositories
osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
parents:
diff changeset
5 ## If N = # of nodes requested in job runner, then N RAxML jobs will run simultaneously. Make sure that the
5b9a38ec4a39 First commit of old repositories
osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
parents:
diff changeset
6 ## number of processors ('ppn') in the job runner matches the 'numthreads' value set in command line arguement.
5b9a38ec4a39 First commit of old repositories
osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
parents:
diff changeset
7 ##
5b9a38ec4a39 First commit of old repositories
osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
parents:
diff changeset
8 ## Usage: ./phytab_raxml.py -i <phytabinput> -e <model> -f <modelfile> -T 4
5b9a38ec4a39 First commit of old repositories
osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
parents:
diff changeset
9 ## example: ./phytab_raxml.py -i myphytab.txt -e PROTGAMMAWAG -f None -T 4
5b9a38ec4a39 First commit of old repositories
osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
parents:
diff changeset
10 ## or: ./phytab_raxml.py -i myphtab.txt -e None -f modelsforeachpartition.txt -T 4
5b9a38ec4a39 First commit of old repositories
osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
parents:
diff changeset
11
5b9a38ec4a39 First commit of old repositories
osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
parents:
diff changeset
12 import optparse
5b9a38ec4a39 First commit of old repositories
osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
parents:
diff changeset
13 import os
5b9a38ec4a39 First commit of old repositories
osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
parents:
diff changeset
14 import subprocess
5b9a38ec4a39 First commit of old repositories
osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
parents:
diff changeset
15 import multiprocessing
5b9a38ec4a39 First commit of old repositories
osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
parents:
diff changeset
16
5b9a38ec4a39 First commit of old repositories
osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
parents:
diff changeset
17 RESULTS_DIR = 'results'
5b9a38ec4a39 First commit of old repositories
osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
parents:
diff changeset
18 RESULTS_FILE = 'results.phy'
5b9a38ec4a39 First commit of old repositories
osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
parents:
diff changeset
19 RAXML_PREFIX = 'RAxML_result.'
5b9a38ec4a39 First commit of old repositories
osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
parents:
diff changeset
20
5b9a38ec4a39 First commit of old repositories
osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
parents:
diff changeset
21 def unescape(string):
5b9a38ec4a39 First commit of old repositories
osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
parents:
diff changeset
22 mapped_chars = {
5b9a38ec4a39 First commit of old repositories
osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
parents:
diff changeset
23 '>': '__gt__',
5b9a38ec4a39 First commit of old repositories
osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
parents:
diff changeset
24 '<': '__lt__',
5b9a38ec4a39 First commit of old repositories
osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
parents:
diff changeset
25 "'": '__sq__',
5b9a38ec4a39 First commit of old repositories
osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
parents:
diff changeset
26 '"': '__dq__',
5b9a38ec4a39 First commit of old repositories
osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
parents:
diff changeset
27 '[': '__ob__',
5b9a38ec4a39 First commit of old repositories
osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
parents:
diff changeset
28 ']': '__cb__',
5b9a38ec4a39 First commit of old repositories
osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
parents:
diff changeset
29 '{': '__oc__',
5b9a38ec4a39 First commit of old repositories
osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
parents:
diff changeset
30 '}': '__cc__',
5b9a38ec4a39 First commit of old repositories
osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
parents:
diff changeset
31 '@': '__at__',
5b9a38ec4a39 First commit of old repositories
osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
parents:
diff changeset
32 '\n': '__cn__',
5b9a38ec4a39 First commit of old repositories
osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
parents:
diff changeset
33 '\r': '__cr__',
5b9a38ec4a39 First commit of old repositories
osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
parents:
diff changeset
34 '\t': '__tc__',
5b9a38ec4a39 First commit of old repositories
osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
parents:
diff changeset
35 '#': '__pd__'
5b9a38ec4a39 First commit of old repositories
osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
parents:
diff changeset
36 }
5b9a38ec4a39 First commit of old repositories
osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
parents:
diff changeset
37
5b9a38ec4a39 First commit of old repositories
osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
parents:
diff changeset
38 for key, value in mapped_chars.iteritems():
5b9a38ec4a39 First commit of old repositories
osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
parents:
diff changeset
39 string = string.replace(value, key)
5b9a38ec4a39 First commit of old repositories
osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
parents:
diff changeset
40
5b9a38ec4a39 First commit of old repositories
osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
parents:
diff changeset
41 return string
5b9a38ec4a39 First commit of old repositories
osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
parents:
diff changeset
42
5b9a38ec4a39 First commit of old repositories
osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
parents:
diff changeset
43
5b9a38ec4a39 First commit of old repositories
osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
parents:
diff changeset
44 class Species:
5b9a38ec4a39 First commit of old repositories
osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
parents:
diff changeset
45 def __init__(self, string):
5b9a38ec4a39 First commit of old repositories
osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
parents:
diff changeset
46 lis = string.split('\t')
5b9a38ec4a39 First commit of old repositories
osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
parents:
diff changeset
47 # print lis
5b9a38ec4a39 First commit of old repositories
osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
parents:
diff changeset
48 self.species = lis[0]
5b9a38ec4a39 First commit of old repositories
osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
parents:
diff changeset
49 self.gene = lis[1]
5b9a38ec4a39 First commit of old repositories
osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
parents:
diff changeset
50 self.name = lis[2]
5b9a38ec4a39 First commit of old repositories
osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
parents:
diff changeset
51 self.sequence = lis[3]
5b9a38ec4a39 First commit of old repositories
osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
parents:
diff changeset
52
5b9a38ec4a39 First commit of old repositories
osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
parents:
diff changeset
53 def toString(self):
5b9a38ec4a39 First commit of old repositories
osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
parents:
diff changeset
54 return self.species + '\t' + self.sequence
5b9a38ec4a39 First commit of old repositories
osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
parents:
diff changeset
55
5b9a38ec4a39 First commit of old repositories
osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
parents:
diff changeset
56
5b9a38ec4a39 First commit of old repositories
osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
parents:
diff changeset
57 class Gene:
5b9a38ec4a39 First commit of old repositories
osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
parents:
diff changeset
58 def __init__(self, name):
5b9a38ec4a39 First commit of old repositories
osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
parents:
diff changeset
59 self.name = name
5b9a38ec4a39 First commit of old repositories
osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
parents:
diff changeset
60 self.count = 0
5b9a38ec4a39 First commit of old repositories
osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
parents:
diff changeset
61 self.length = 0
5b9a38ec4a39 First commit of old repositories
osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
parents:
diff changeset
62 self.species = []
5b9a38ec4a39 First commit of old repositories
osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
parents:
diff changeset
63
5b9a38ec4a39 First commit of old repositories
osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
parents:
diff changeset
64 def output(self):
5b9a38ec4a39 First commit of old repositories
osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
parents:
diff changeset
65 file_name = self.name + ".phy"
5b9a38ec4a39 First commit of old repositories
osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
parents:
diff changeset
66 location = RESULTS_DIR + os.sep + file_name
5b9a38ec4a39 First commit of old repositories
osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
parents:
diff changeset
67 with open(location, 'w') as f:
5b9a38ec4a39 First commit of old repositories
osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
parents:
diff changeset
68 f.write(str(self.count) + '\t' + str(self.length) + '\n')
5b9a38ec4a39 First commit of old repositories
osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
parents:
diff changeset
69 for s in self.species:
5b9a38ec4a39 First commit of old repositories
osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
parents:
diff changeset
70 f.write(s.toString())
5b9a38ec4a39 First commit of old repositories
osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
parents:
diff changeset
71 return file_name
5b9a38ec4a39 First commit of old repositories
osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
parents:
diff changeset
72
5b9a38ec4a39 First commit of old repositories
osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
parents:
diff changeset
73 def add(self, species):
5b9a38ec4a39 First commit of old repositories
osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
parents:
diff changeset
74 if species.name == "":
5b9a38ec4a39 First commit of old repositories
osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
parents:
diff changeset
75 return
5b9a38ec4a39 First commit of old repositories
osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
parents:
diff changeset
76 self.species.append(species)
5b9a38ec4a39 First commit of old repositories
osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
parents:
diff changeset
77 self.count += 1
5b9a38ec4a39 First commit of old repositories
osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
parents:
diff changeset
78 if self.length == 0:
5b9a38ec4a39 First commit of old repositories
osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
parents:
diff changeset
79 self.length = len(species.sequence) - 1
5b9a38ec4a39 First commit of old repositories
osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
parents:
diff changeset
80
5b9a38ec4a39 First commit of old repositories
osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
parents:
diff changeset
81
5b9a38ec4a39 First commit of old repositories
osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
parents:
diff changeset
82 def output_species(species):
5b9a38ec4a39 First commit of old repositories
osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
parents:
diff changeset
83 file_name = species.gene + ".phy"
5b9a38ec4a39 First commit of old repositories
osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
parents:
diff changeset
84 location = RESULTS_DIR + os.sep + file_name
5b9a38ec4a39 First commit of old repositories
osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
parents:
diff changeset
85 with open(location, 'a') as f:
5b9a38ec4a39 First commit of old repositories
osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
parents:
diff changeset
86 f.write(species.toString())
5b9a38ec4a39 First commit of old repositories
osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
parents:
diff changeset
87 return file_name
5b9a38ec4a39 First commit of old repositories
osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
parents:
diff changeset
88
5b9a38ec4a39 First commit of old repositories
osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
parents:
diff changeset
89
5b9a38ec4a39 First commit of old repositories
osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
parents:
diff changeset
90 def process_phytab(input):
5b9a38ec4a39 First commit of old repositories
osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
parents:
diff changeset
91 files = set()
5b9a38ec4a39 First commit of old repositories
osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
parents:
diff changeset
92 genes = dict()
5b9a38ec4a39 First commit of old repositories
osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
parents:
diff changeset
93 with open(input) as f:
5b9a38ec4a39 First commit of old repositories
osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
parents:
diff changeset
94 for line in f:
5b9a38ec4a39 First commit of old repositories
osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
parents:
diff changeset
95 if len(line) < 4:
5b9a38ec4a39 First commit of old repositories
osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
parents:
diff changeset
96 continue
5b9a38ec4a39 First commit of old repositories
osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
parents:
diff changeset
97 species = Species(line)
5b9a38ec4a39 First commit of old repositories
osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
parents:
diff changeset
98 if species.gene in genes:
5b9a38ec4a39 First commit of old repositories
osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
parents:
diff changeset
99 genes[species.gene].add(species)
5b9a38ec4a39 First commit of old repositories
osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
parents:
diff changeset
100 else:
5b9a38ec4a39 First commit of old repositories
osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
parents:
diff changeset
101 gene = Gene(species.gene)
5b9a38ec4a39 First commit of old repositories
osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
parents:
diff changeset
102 gene.add(species)
5b9a38ec4a39 First commit of old repositories
osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
parents:
diff changeset
103 genes[gene.name] = gene
5b9a38ec4a39 First commit of old repositories
osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
parents:
diff changeset
104 for k, gene in genes.iteritems():
5b9a38ec4a39 First commit of old repositories
osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
parents:
diff changeset
105 files.add(gene.output())
5b9a38ec4a39 First commit of old repositories
osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
parents:
diff changeset
106 return files
5b9a38ec4a39 First commit of old repositories
osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
parents:
diff changeset
107
5b9a38ec4a39 First commit of old repositories
osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
parents:
diff changeset
108
5b9a38ec4a39 First commit of old repositories
osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
parents:
diff changeset
109 def runRaxml(list_of_files, evo, evoDict, NUMTHREADS):
5b9a38ec4a39 First commit of old repositories
osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
parents:
diff changeset
110 count = 0
5b9a38ec4a39 First commit of old repositories
osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
parents:
diff changeset
111 list_of_files = sorted(list_of_files)
5b9a38ec4a39 First commit of old repositories
osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
parents:
diff changeset
112 for gene_file in list_of_files:
5b9a38ec4a39 First commit of old repositories
osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
parents:
diff changeset
113 count+=1
5b9a38ec4a39 First commit of old repositories
osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
parents:
diff changeset
114 if gene_file.split(".")[0] in evoDict:
5b9a38ec4a39 First commit of old repositories
osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
parents:
diff changeset
115 newEvo = evoDict[gene_file.split(".")[0]]
5b9a38ec4a39 First commit of old repositories
osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
parents:
diff changeset
116 else:
5b9a38ec4a39 First commit of old repositories
osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
parents:
diff changeset
117 newEvo = evo
5b9a38ec4a39 First commit of old repositories
osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
parents:
diff changeset
118 file_name = RESULTS_DIR + os.sep + gene_file
5b9a38ec4a39 First commit of old repositories
osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
parents:
diff changeset
119 ## RAxML notes: ##
5b9a38ec4a39 First commit of old repositories
osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
parents:
diff changeset
120 # to run parsimony trees:
5b9a38ec4a39 First commit of old repositories
osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
parents:
diff changeset
121 # popen = subprocess.Popen(['raxmlHPC-PTHREADS', '-T', cpu_count,'-f', 'd', '-s', file_name,'-y', '-m', newEvo, '-n', gene_file[:-4]+'.tre', '-p', '34'])
5b9a38ec4a39 First commit of old repositories
osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
parents:
diff changeset
122 # to run likelihood trees:
5b9a38ec4a39 First commit of old repositories
osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
parents:
diff changeset
123 # popen = subprocess.Popen(['raxmlHPC-PTHREADS', "-T", cpu_count, "-s", file_name, '-m', newEvo, '-n', gene_file[:-4], '-p', '34'])
5b9a38ec4a39 First commit of old repositories
osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
parents:
diff changeset
124 # to run likelihood trees using starting tree:
5b9a38ec4a39 First commit of old repositories
osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
parents:
diff changeset
125 # popen = subprocess.Popen(['raxmlHPC-PTHREADS', '-T', cpu_count, '-f', 'e','-s', file_name, '-m', newEvo, '-n', gene_file[:-4], '-t', ptre])
5b9a38ec4a39 First commit of old repositories
osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
parents:
diff changeset
126
5b9a38ec4a39 First commit of old repositories
osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
parents:
diff changeset
127 ## run trees as simultaneously as possible--but wait until last tree completes to resume script
5b9a38ec4a39 First commit of old repositories
osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
parents:
diff changeset
128 raxml_cmd = ['raxmlHPC-PTHREADS', '-T', NUMTHREADS, '-s', file_name, '-m', newEvo, '-n', gene_file[:-4], '-p', '34']
5b9a38ec4a39 First commit of old repositories
osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
parents:
diff changeset
129 if count == len(list_of_files):
5b9a38ec4a39 First commit of old repositories
osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
parents:
diff changeset
130 run = subprocess.Popen(raxml_cmd)
5b9a38ec4a39 First commit of old repositories
osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
parents:
diff changeset
131 run.wait()
5b9a38ec4a39 First commit of old repositories
osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
parents:
diff changeset
132 else:
5b9a38ec4a39 First commit of old repositories
osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
parents:
diff changeset
133 run = subprocess.Popen(raxml_cmd)
5b9a38ec4a39 First commit of old repositories
osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
parents:
diff changeset
134 run.communicate()[0]
5b9a38ec4a39 First commit of old repositories
osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
parents:
diff changeset
135
5b9a38ec4a39 First commit of old repositories
osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
parents:
diff changeset
136
5b9a38ec4a39 First commit of old repositories
osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
parents:
diff changeset
137 def readEfile(efile):
5b9a38ec4a39 First commit of old repositories
osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
parents:
diff changeset
138 evoDict = {}
5b9a38ec4a39 First commit of old repositories
osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
parents:
diff changeset
139 with open(efile, "r") as f:
5b9a38ec4a39 First commit of old repositories
osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
parents:
diff changeset
140 for line in f:
5b9a38ec4a39 First commit of old repositories
osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
parents:
diff changeset
141 pair = line.split("\t")
5b9a38ec4a39 First commit of old repositories
osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
parents:
diff changeset
142 evoDict[pair[0].strip()] = pair[1].strip()
5b9a38ec4a39 First commit of old repositories
osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
parents:
diff changeset
143 return evoDict
5b9a38ec4a39 First commit of old repositories
osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
parents:
diff changeset
144
5b9a38ec4a39 First commit of old repositories
osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
parents:
diff changeset
145 def main():
5b9a38ec4a39 First commit of old repositories
osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
parents:
diff changeset
146 usage = """%prog [options]
5b9a38ec4a39 First commit of old repositories
osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
parents:
diff changeset
147 options (listed below) default to 'None' if omitted
5b9a38ec4a39 First commit of old repositories
osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
parents:
diff changeset
148 """
5b9a38ec4a39 First commit of old repositories
osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
parents:
diff changeset
149 parser = optparse.OptionParser(usage=usage)
5b9a38ec4a39 First commit of old repositories
osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
parents:
diff changeset
150
5b9a38ec4a39 First commit of old repositories
osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
parents:
diff changeset
151 parser.add_option(
5b9a38ec4a39 First commit of old repositories
osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
parents:
diff changeset
152 '-i', '--in',
5b9a38ec4a39 First commit of old repositories
osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
parents:
diff changeset
153 dest='input',
5b9a38ec4a39 First commit of old repositories
osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
parents:
diff changeset
154 action='store',
5b9a38ec4a39 First commit of old repositories
osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
parents:
diff changeset
155 type='string',
5b9a38ec4a39 First commit of old repositories
osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
parents:
diff changeset
156 metavar="FILE",
5b9a38ec4a39 First commit of old repositories
osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
parents:
diff changeset
157 help='Name of input data.')
5b9a38ec4a39 First commit of old repositories
osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
parents:
diff changeset
158
5b9a38ec4a39 First commit of old repositories
osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
parents:
diff changeset
159 parser.add_option(
5b9a38ec4a39 First commit of old repositories
osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
parents:
diff changeset
160 '-e', '--evo',
5b9a38ec4a39 First commit of old repositories
osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
parents:
diff changeset
161 dest='evo',
5b9a38ec4a39 First commit of old repositories
osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
parents:
diff changeset
162 action='store',
5b9a38ec4a39 First commit of old repositories
osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
parents:
diff changeset
163 type='string',
5b9a38ec4a39 First commit of old repositories
osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
parents:
diff changeset
164 metavar="EVO",
5b9a38ec4a39 First commit of old repositories
osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
parents:
diff changeset
165 help='Evolution model.')
5b9a38ec4a39 First commit of old repositories
osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
parents:
diff changeset
166
5b9a38ec4a39 First commit of old repositories
osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
parents:
diff changeset
167 parser.add_option(
5b9a38ec4a39 First commit of old repositories
osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
parents:
diff changeset
168 '-f', '--evo-file',
5b9a38ec4a39 First commit of old repositories
osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
parents:
diff changeset
169 dest='efile',
5b9a38ec4a39 First commit of old repositories
osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
parents:
diff changeset
170 action='store',
5b9a38ec4a39 First commit of old repositories
osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
parents:
diff changeset
171 type='string',
5b9a38ec4a39 First commit of old repositories
osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
parents:
diff changeset
172 metavar="EVO_FILE",
5b9a38ec4a39 First commit of old repositories
osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
parents:
diff changeset
173 help='Evolution model file. Format is gene_name [tab] evolution_model.')
5b9a38ec4a39 First commit of old repositories
osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
parents:
diff changeset
174
5b9a38ec4a39 First commit of old repositories
osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
parents:
diff changeset
175 parser.add_option(
5b9a38ec4a39 First commit of old repositories
osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
parents:
diff changeset
176 '-T', '--numthreads',
5b9a38ec4a39 First commit of old repositories
osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
parents:
diff changeset
177 dest='numthreads',
5b9a38ec4a39 First commit of old repositories
osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
parents:
diff changeset
178 action='store',
5b9a38ec4a39 First commit of old repositories
osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
parents:
diff changeset
179 type='int',
5b9a38ec4a39 First commit of old repositories
osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
parents:
diff changeset
180 metavar="NUMT",
5b9a38ec4a39 First commit of old repositories
osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
parents:
diff changeset
181 help='Specify number of threads.')
5b9a38ec4a39 First commit of old repositories
osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
parents:
diff changeset
182
5b9a38ec4a39 First commit of old repositories
osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
parents:
diff changeset
183 options, args = parser.parse_args()
5b9a38ec4a39 First commit of old repositories
osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
parents:
diff changeset
184
5b9a38ec4a39 First commit of old repositories
osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
parents:
diff changeset
185 os.mkdir(RESULTS_DIR)
5b9a38ec4a39 First commit of old repositories
osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
parents:
diff changeset
186
5b9a38ec4a39 First commit of old repositories
osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
parents:
diff changeset
187 list_of_species_files = process_phytab(unescape(options.input))
5b9a38ec4a39 First commit of old repositories
osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
parents:
diff changeset
188
5b9a38ec4a39 First commit of old repositories
osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
parents:
diff changeset
189 try:
5b9a38ec4a39 First commit of old repositories
osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
parents:
diff changeset
190 evoDict = readEfile(unescape(options.efile))
5b9a38ec4a39 First commit of old repositories
osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
parents:
diff changeset
191 except IOError:
5b9a38ec4a39 First commit of old repositories
osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
parents:
diff changeset
192 print "No sequence model file provide...using", unescape(options.evo), "as the model"
5b9a38ec4a39 First commit of old repositories
osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
parents:
diff changeset
193 evoDict = {}
5b9a38ec4a39 First commit of old repositories
osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
parents:
diff changeset
194
5b9a38ec4a39 First commit of old repositories
osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
parents:
diff changeset
195 runRaxml(list_of_species_files, unescape(options.evo), evoDict, str(options.numthreads))
5b9a38ec4a39 First commit of old repositories
osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
parents:
diff changeset
196
5b9a38ec4a39 First commit of old repositories
osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
parents:
diff changeset
197 result = [file for file in os.listdir('./') if file.startswith(RAXML_PREFIX)]
5b9a38ec4a39 First commit of old repositories
osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
parents:
diff changeset
198 result = sorted(result)
5b9a38ec4a39 First commit of old repositories
osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
parents:
diff changeset
199 with open(RESULTS_DIR + os.sep + RESULTS_FILE, "w") as f:
5b9a38ec4a39 First commit of old repositories
osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
parents:
diff changeset
200 for file in result:
5b9a38ec4a39 First commit of old repositories
osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
parents:
diff changeset
201 with open(file, "r") as r:
5b9a38ec4a39 First commit of old repositories
osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
parents:
diff changeset
202 f.write(file[len(RAXML_PREFIX):] + '\t' + r.read())
5b9a38ec4a39 First commit of old repositories
osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
parents:
diff changeset
203
5b9a38ec4a39 First commit of old repositories
osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
parents:
diff changeset
204 if __name__ == '__main__':
5b9a38ec4a39 First commit of old repositories
osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
parents:
diff changeset
205 main()
5b9a38ec4a39 First commit of old repositories
osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
parents:
diff changeset
206