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#!/usr/bin/env python
'''
Created on Jan. 26, 2015
@author: Tung Nguyen <nltung@gmail.com>
'''
import sys, os, time, multiprocessing, optparse
import subprocess, logging, datetime
def parse_config(config_file):
singleAln, partitionAln, partOpts, genericOpts = [], [], [], []
with open(config_file) as f:
#lines = f.readlines()
lines = [line.strip() for line in f if line.strip()]
readSingleAln = False
readPartAln = False
partOpt = False
genericOpt = False
for line in lines:
#print line
if line == 'START_SINGLE_ALN':
readSingleAln = True
continue
if line == 'END_SINGLE_ALN':
readSingleAln = False
continue
if readSingleAln:
singleAln.append(line)
if line == 'START_PARTITION_ALN':
readPartAln = True
continue
if line == 'END_PARTITION_ALN':
readPartAln = False
continue
if readPartAln:
partitionAln.append(line.split())
if line == 'START_PARTITION_OPTIONS':
partOpt = True
continue
if line == 'END_PARTITION_OPTIONS':
partOpt = False
continue
if line == 'START_GENERIC_OPTIONS':
genericOpt = True
continue
if line == 'END_GENERIC_OPTIONS':
genericOpt = False
continue
if partOpt:
partOpts.append(line)
if genericOpt:
genericOpts.append(line)
return (singleAln, partitionAln, genericOpts, partOpts)
if __name__ == '__main__':
usage = "USAGE: %prog [options]"
parser = optparse.OptionParser(usage=usage)
parser.add_option('-b','--binary', dest="iqtree_bin", help='Path to your IQ-TREE binary')
parser.add_option('-c','--config', dest="config_file", help='Path to test configuration file')
parser.add_option('-o', '--output', dest="outFile", help='Output file for test cases')
parser.add_option('-f', '--flags', dest="flags", help='Additional flags for IQ-TREE')
(options, args) = parser.parse_args()
if not options.iqtree_bin or not options.config_file:
parser.print_help()
exit(0)
(singleAln, partitionAln, genericOpts, partOpts) = parse_config(options.config_file)
testCmds = []
# Generate test commands for single model
for aln in singleAln:
for opt in genericOpts:
cmd = '-s ' + aln + ' -redo ' + opt
if options.flags:
cmd = cmd + ' ' + options.flags
testCmds.append(cmd)
# Generate test commands for partition model
for aln in partitionAln:
for opt in genericOpts:
for partOpt in partOpts:
cmd = '-s ' + aln[0] + ' -redo ' + opt + ' ' + partOpt + ' ' + aln[1]
if options.flags:
cmd = cmd + ' ' + options.flags
testCmds.append(cmd)
testNr = 1
jobs = []
for cmd in testCmds:
testIDRel = os.path.basename(options.iqtree_bin) + "_TEST_" + str(testNr)
testCMD = testIDRel + " " + os.path.abspath(options.iqtree_bin) + " -pre " + testIDRel + " " + cmd
testNr = testNr + 1
jobs.append(testCMD)
# print "\n".join(jobs)
outfile = open(options.outFile, "wb")
for job in jobs:
print >> outfile, job
outfile.close()
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