def search(init_param):
try:
Path.Check(init_param['output.path'])
if platform.system() == 'Linux':
bat_file = os.path.join(init_param['output.path'], 'normal.bash')
bat_fp = open(bat_file, 'w')
bat_fp.write('export PATH=%s:$PATH\n' % ClusterSetting.MPIPath) #modified 2012.6.11
bat_fp.write('export LD_LIBRARY_PATH=%s:$LD_LIBRARY_PATH\n' % ClusterSetting.pLinkBinPath)
elif platform.system() == 'Windows':
bat_file = os.path.join(init_param['output.path'], 'normal.bat')
bat_fp = open(bat_file, 'w')
bat_fp.write('@echo off\n')
bat_fp.write('%s\n' % init_param['bin.path'][0:2])
else:
raise Exception('search_and_filter', 'unknown platform, only support Windows and Linux')
bat_fp.write('cd "%s"\n' % init_param['bin.path'])
search_mode = string.atoi(init_param['search_mode'])
pfind_param = Search._ConstructpFindParam(init_param, search_mode, init_param['output.path'])
print 'Step : Search by Searcher'
spectra_list = init_param['spectra_list']
spectra_title = init_param['spectra.title']
bin_path = init_param['bin.path']
for i in range(0, len(init_param['spectra_list'])):
pfind_file = os.path.join(init_param['output.path'], '%s%d.pfind' % (init_param['spectra.title'], i+1))
pfind_result_file = os.path.join(init_param['output.path'], '%s%d_qry.proteins.txt' % (init_param['spectra.title'], i+1))
if os.path.isfile(pfind_result_file):
print os.path.split(pfind_result_file)[-1] + ' did exist, skip the step';
else:
print 'Searcher of '+ spectra_list[i];
spectrum = []
spectrum.append(('spec_title', spectra_title+'%d' %(i+1)))
spectrum.append(('spec_type', '%s' % init_param['spectra.format'].upper()))
spectrum.append(('spec_path', spectra_list[i]))
pfind_param['spectrum'] = spectrum
Search._WritepFind(pfind_param, pfind_file, search_mode)
if platform.system() == 'Windows':
bat_fp.write('"%s" "%s"\n' % (os.path.join(bin_path,'Searcher'), pfind_file))
else:
bat_fp.write('"%s" "%s"\n' % (os.path.join(bin_path,'Importer'), pfind_file))
if 'mpicores' in init_param:
mpicores = init_param['mpicores']
else:
mpicores = ClusterSetting.DefaultCores
if 'mpihosts' in init_param:
mpihosts = init_param['mpihosts']
else:
mpihosts = ClusterSetting.DefaultHosts
bat_fp.write('mpirun -np %s -host %s "%s" "%s"\n' %(mpicores, mpihosts, os.path.join(bin_path,'MPISearcher'), pfind_file))
bat_fp.close()
except Exception, e:
print Exception + ": " + e
def Run(initparam, spectra_list, search_mode, normal_dir_path):
Path.Check(normal_dir_path)
bin_path = initparam['bin.path']
spectra_title = initparam['spectra.title']
if platform.system() == 'Linux':
bat_file=os.path.join(normal_dir_path,'normal.bash')
bfile=open(bat_file, 'w')
bfile.write('export PATH=%s:$PATH\n' % ClusterSetting.MPIPath)#modified 2012.6.11
bfile.write('export LD_LIBRARY_PATH=%s:$LD_LIBRARY_PATH\n' % ClusterSetting.pLinkBinPath)
if platform.system() == 'Windows':
bat_file=os.path.join(normal_dir_path,'normal.bat')
bfile=open(bat_file, 'w')
bfile.write('%s\n' % bin_path[0:2])
bfile.write('cd "%s"\n' % bin_path)
pFind_Param = Search._ConstructpFindParam(initparam, search_mode, normal_dir_path)
print 'Step : Search by Searcher'
for i in range(0, len(spectra_list)):
pfind_file = os.path.join(normal_dir_path, spectra_title+'%d.pfind' %(i+1))
pfind_result_file = os.path.join(normal_dir_path, spectra_title+'%d_qry.proteins.txt' %(i+1));
if os.path.isfile(pfind_result_file):
print pfind_result_file + ' is existed , skip the step';
else:
print 'Searcher of '+ spectra_list[i];
spectrum = []
spectrum.append(('spec_title', spectra_title+'%d' %(i+1)))
spectrum.append(('spec_type', '%s' %initparam['spectra.format'].upper()))
spectrum.append(('spec_path', spectra_list[i]))
pFind_Param['spectrum'] = spectrum
Search._WritepFind(pFind_Param, pfind_file, search_mode)
if platform.system() == 'Windows':
bfile.write('"%s" "%s"\n' % (os.path.join(bin_path,'Searcher'), pfind_file))
else:
bfile.write('"%s" "%s"\n' % (os.path.join(bin_path,'Importer'), pfind_file))
if 'mpicores' in initparam:
mpicores = initparam['mpicores']
else:
mpicores = ClusterSetting.DefaultCores
if 'mpihosts' in initparam:
mpihosts = initparam['mpihosts']
else:
mpihosts = ClusterSetting.DefaultHosts
bfile.write('mpirun -np %s -host %s "%s" "%s"\n' %(mpicores, mpihosts, os.path.join(bin_path,'MPISearcher'), pfind_file))
if not "index_content" in initparam:
initparam["index_content"] = "PEPTIDE_PAIR"
if not 'noninterexport' in initparam:
initparam['noninterexport'] = 'false'
if 'evalue_max' in initparam and float(initparam['evalue_max']) < 1:#added at 2013.10.22, evalue cut, fan
bEvalueMax = True
else:
bEvalueMax = False
if initparam['index_content'] != "PEPTIDE_TRI_ALL":
Filter.RunForType(bfile, 'inter', initparam, spectra_list, normal_dir_path, bEvalueMax)
if initparam['noninterexport'] == 'true':
Filter.RunForType(bfile, 'loop', initparam, spectra_list, normal_dir_path, bEvalueMax)
Filter.RunForType(bfile, 'mono', initparam, spectra_list, normal_dir_path, bEvalueMax)
Filter.RunForType(bfile, 'common', initparam, spectra_list, normal_dir_path, bEvalueMax)
else:
Filter.RunForTri(bfile, initparam, spectra_list, normal_dir_path, bEvalueMax);
bfile.close()
if platform.system() == 'Linux':
os.system('chmod 766 %s' % bat_file)
os.system('"%s"' % bat_file)
search_time = os.stat(pfind_result_file).st_mtime
return search_time