def main():
argc = len(sys.argv)
argv = sys.argv
if argc == 1:
print "Usage: bin-seq.py input-sequences bin-results-filename"
return
# load default settings
pre.default_settings()
pre.seqs_file = argv[1]
pre.bin_file = argv[2]
bindistri_file = pre.bin_file + 'distri'
if len(pre.seqs_file) == 0:
print 'The sequence file is not defined.'
return
if not os.path.exists(pre.seqs_file):
print 'The sequence file %s is not correctly defined.' % pre.seqs_file
return
print ' Input sequence file:', pre.seqs_file
print_section_title('Sequence Binning')
print ' Sequence binning model:', pre.binmodel
print ' Taxonomy map file:', pre.taxonomy
cmd = '%s -m %s -s %s -t %s -b %s -d %s' % \
(pre.bin_seqs, pre.binmodel, pre.seqs_file, pre.taxonomy, pre.bin_file, bindistri_file)
call(cmd, shell = True, stdout = PIPE)
print ' Binning result file:', pre.bin_file
return
def program_prepair(): # define program used in this script programs = pre.default_settings() global svmscale, svmtrain global subset_py, grid_py, is_win32 is_win32 = (sys.platform == 'win32') svmscale = pre.svm_scale svmtrain = pre.svm_train subset_py = pre.subset_py grid_py = pre.grid_py
def main():
argc = len(sys.argv)
argv = sys.argv
if argc == 1:
print "Usage: domain-search.py input-sequences search-results-filename"
return
# load default settings
pre.default_settings()
pre.seqs_file = argv[1]
pre.hit_file = argv[2]
if len(pre.seqs_file) == 0:
print 'The sequence file is not defined.'
return
if not os.path.exists(pre.seqs_file):
print 'The sequence file %s is not correctly defined.' % pre.seqs_file
return
print_section_title('Novel predict')
print ' Blast searches against known database:', pre.blast_db
alc_file = pre.seqs_file + '.alc'
csqa_file = pre.seqs_file + '.csqa'
pre.project_name = pre.seqs_file
pre.hit_file = argv[2]
cmd = '%s -p -n %s -a -s %s' % (pre.get_data, pre.project_name, pre.seqs_file)
call(cmd, shell = True, stdout = PIPE)
cmd = '%s -n %s -s %s -c %s -q 1' % (pre.get_data, pre.project_name, pre.seqs_file, alc_file)
call(cmd, shell = True, stdout = PIPE)
cmd = '%s -i %s -d %s -m 8 -v 1 -b 1 -e 1 -o %s' % (pre.rpsblast, csqa_file, pre.blast_db, pre.hit_file)
call(cmd, shell = True, stdout = PIPE)
rm_files([alc_file, csqa_file])
print ' Blast search results save in:', pre.hit_file
return
def main():
argc = len(sys.argv)
argv = sys.argv
if argc == 1:
print parse_command.__doc__
return
if command_line_parser(argv, '-h', '--help', False)[0]:
print detail_help.__doc__
return
# load default settings
pre.default_settings()
# parse settings from command line
parse_command(argv)
if len(pre.seqs_file) == 0:
print 'The sequence file is not defined.'
return
if not os.path.exists(pre.seqs_file):
print 'The sequence file %s is not correctly defined.' % pre.seqs_file
return
print_section_title('Start MetaGUN Prediction')
print ' Input sequence file:', pre.seqs_file
print ' Project name:', pre.project_name
print_section_title('Sequence Binning')
if pre.exists_bin_file == False:
pre.bin_file = pre.project_name + '.bin'
bindistri_file = pre.project_name + '.bindistri'
print ' Sequence binning model:', pre.binmodel
print ' Taxonomy map file:', pre.taxonomy
cmd = '%s -m %s -s %s -t %s -b %s -d %s' % \
(pre.bin_seqs, pre.binmodel, pre.seqs_file, pre.taxonomy, pre.bin_file, bindistri_file)
call(cmd, shell = True, stdout = PIPE)
print ' Binning result file:', pre.bin_file
else:
print ' Use given binning result:', pre.bin_file
uni_pred_file = pre.project_name + '.uni-pred'
novel_pred_file = pre.project_name + '.novel-pred'
if pre.run_uni_pred:
uni_pred(uni_pred_file)
if pre.run_novel_pred:
novel_pred(novel_pred_file)
metagun_file = pre.project_name + '.metagun'
if pre.run_uni_pred and pre.run_novel_pred:
cmd = '%s -a %s -b %s --a+b -o %s' % (pre.metalocs_operate, novel_pred_file, uni_pred_file, metagun_file)
call(cmd, shell=True, stdout=PIPE)
rm_files([uni_pred_file, novel_pred_file])
elif pre.run_uni_pred and not pre.run_novel_pred:
os.rename(uni_pred_file, metagun_file)
elif not pre.run_uni_pred and pre.run_novel_pred:
os.rename(novel_pred_file, metagun_file)
if not pre.run_metatisa:
print_section_title('MetaGUN Prediction Over')
print ' Final predictions output', metagun_file
return
print_section_title('TIS Refinement')
metatisa_file = metagun_file + '.metatisa'
cmd = '%s -s %s -l %s -b %s -p %s -f MED -o %s -c %s -w %i' % \
(pre.metatisa, pre.seqs_file, metagun_file, pre.bin_file, pre.tismodel, metatisa_file, pre.metatisa_settings, is_win)
call(cmd, shell=True, stdout=PIPE)
if os.path.exists(metagun_file):
os.remove(metagun_file)
os.rename(metatisa_file, metagun_file)
print_section_title('MetaGUN Prediction Over')
print ' Final predictions output', metagun_file
return
