Mercurial > repos > weilong-guo > bs_seeker2

comparison BSseeker2/bs_utils/utils.py @ 1:8b26adf64adc draft default tip

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V2.0.5
author weilong-guo
date Tue, 05 Nov 2013 01:55:39 -0500
parents e6df770c0e58
children
comparison
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0:e6df770c0e58 1:8b26adf64adc
21 21
22 22
23 23
24 def show_version() : 24 def show_version() :
25 print "" 25 print ""
26 print " BS-Seeker2 v2.0.3 - May 19, 2013 " 26 print " BS-Seeker2 v2.0.5 - Nov 5, 2013 "
27 print "" 27 print ""
28 28
29 29
30 30
31 """ 31 """
133 aligner_options_prefixes = { BOWTIE : '--bt-', 133 aligner_options_prefixes = { BOWTIE : '--bt-',
134 BOWTIE2 : '--bt2-', 134 BOWTIE2 : '--bt2-',
135 SOAP : '--soap-', 135 SOAP : '--soap-',
136 RMAP : '--rmap-' } 136 RMAP : '--rmap-' }
137 137
138 aligner_path = dict((aligner, os.path.expanduser(find_location(aligner) or default_path)) 138 #aligner_path = dict((aligner, os.path.expanduser(find_location(aligner) or default_path))
139 for aligner, default_path in 139 # for aligner, default_path in
140 [(BOWTIE,'~/bowtie-0.12.7/'), 140 # [(BOWTIE,'~/bowtie/'),
141 (BOWTIE2, '~/bowtie-0.12.7/'), 141 # (BOWTIE2, '~/bowtie2/'),
142 (SOAP, '~/soap2.21release/'), 142 # (SOAP, '~/soap/'),
143 (RMAP, '~/rmap_v2.05/bin') 143 # (RMAP, '~/rmap/bin')
144 ]) 144 # ])
145 145 aligner_path = dict((aligner, os.path.expanduser(find_location(aligner) or "None"))
146 for aligner in [(BOWTIE), (BOWTIE2), (SOAP), (RMAP)])
146 147
147 reference_genome_path = os.path.join(os.path.split(globals()['__file__'])[0],'reference_genomes') 148 reference_genome_path = os.path.join(os.path.split(globals()['__file__'])[0],'reference_genomes')
148 149
149 150
150 151
212 213
213 def split_file(filename, output_prefix, nlines): 214 def split_file(filename, output_prefix, nlines):
214 """ Splits a file (equivalend to UNIX split -l ) """ 215 """ Splits a file (equivalend to UNIX split -l ) """
215 fno = 0 216 fno = 0
216 lno = 0 217 lno = 0
217 INPUT = open(filename, 'r') 218 if filename.endswith(".gz") :
219 INPUT = gzip.open(filename, 'rb')
220 else :
221 INPUT = open(filename, 'r')
218 output = None 222 output = None
219 for l in INPUT: 223 for l in INPUT:
220 if lno == 0: 224 if lno == 0:
221 fno += 1 225 fno += 1
222 if output is not None: output.close() 226 if output is not None: output.close()
319 323
320 def run_in_parallel(commands): 324 def run_in_parallel(commands):
321 325
322 commands = [(cmd[0], open(cmd[1], 'w')) if type(cmd) is tuple else (cmd, None) for cmd in commands] 326 commands = [(cmd[0], open(cmd[1], 'w')) if type(cmd) is tuple else (cmd, None) for cmd in commands]
323 327
324 logm('Starting commands:\n' + '\n'.join([cmd for cmd, stdout in commands])) 328 #logm('Starting commands:\n' + '\n'.join([cmd for cmd, stdout in commands]))
329 logm('Starting commands:')
330 for cmd, stdout in commands :
331 logm("Launched: "+cmd)
325 for i, proc in enumerate([subprocess.Popen(args = shlex.split(cmd), stdout = stdout) for cmd, stdout in commands]): 332 for i, proc in enumerate([subprocess.Popen(args = shlex.split(cmd), stdout = stdout) for cmd, stdout in commands]):
326 return_code = proc.wait() 333 return_code = proc.wait()
327 logm('Finished: ' + commands[i][0]) 334 logm('Finished: ' + commands[i][0])
328 if return_code != 0: 335 if return_code != 0:
329 error('%s \nexit with an error code: %d. Please, check the log files.' % (commands[i], return_code)) 336 error('%s \nexit with an error code: %d. Please, check the log files.' % (commands[i], return_code))