import stat import mstb_helper as helper usage_mesg = 'Usage: prepare-omssa.py' dirname = 'omssa' MSTB_HOME = helper.get_mstb_home() CWD = helper.get_cwd() conf = helper.read_conf( os.path.join(CWD,'mstb.conf') ) if( len(conf) == 0 ): sys.exit(1) helper.check_conf_term(conf,'DB_NAME') helper.check_conf_file(conf,'PATH_OMSSACL') path_dir = os.path.join(CWD,dirname) if( not os.access(path_dir,os.R_OK) ): sys.stderr.write("Create %s.\n"%(path_dir)) os.mkdir(path_dir) if( not os.path.isdir(path_dir) ): sys.stderr.write('\n%s is not a directory.\n'%path_dir) sys.stderr.write('Rename it and make %s directory.\n\n'%path_dir) sys.exit(1) filename_cmd_tmpl = os.path.join(MSTB_HOME,'tmpl','omssa.cmd') f_cmd_tmpl = open(filename_cmd_tmpl,'r') cmd_tmpl = ''.join( f_cmd_tmpl.readlines() ) f_cmd_tmpl.close()
import sys import stat import mstb_helper as helper usage_mesg = 'Usage: prepare-inspect.py' dirname = 'inspect' MSTB_HOME = helper.get_mstb_home() CWD = helper.get_cwd() conf = helper.read_conf( os.path.join(CWD, 'mstb.conf') ) if( len(conf) == 0 ): sys.exit(1) helper.check_conf_file(conf,'DB_TRIE') helper.check_conf_file(conf,'PATH_INSPECT') helper.check_conf_file(conf,'DIR_INSPECT') path_dir = os.path.join(CWD,dirname) if( not os.access(path_dir,os.R_OK) ): sys.stderr.write('Create %s.\n'%(path_dir)) os.mkdir(path_dir) if( not os.path.isdir(path_dir) ): sys.stderr.write('\n%s is not a directory.\n'%path_dir) sys.stderr.write('Rename it and make %s directory.\n\n'%path_dir) sys.exit(1) filename_cmd_tmpl = os.path.join(MSTB_HOME,'tmpl','inspect.cmd') f_cmd_tmpl = open(filename_cmd_tmpl,'r')
#!/usr/bin/env python import os import sys import stat import mstb_helper as helper usage_mesg = 'Usage: prepare-mzxml_gz2mgf.py' MSTB_HOME = helper.get_mstb_home() CWD = helper.get_cwd() conf = helper.read_conf( os.path.join(CWD,'mstb.conf') ) if( len(conf) == 0 ): sys.exit(1) helper.check_conf_file(conf,'PATH_MSCONVERT') filename_sh = os.path.join(CWD,'scripts','run-mzxml_gz2mgf.sh') f_sh = open(filename_sh,'w') f_sh.write('#!/bin/bash\n') for basename_mzxml in helper.get_mzxml_list(): filename_base = basename_mzxml.replace('.mzXML.gz','') filename_mzxml = os.path.join(CWD,'mzXML',basename_mzxml) f_sh.write('%s %s -z -o mgf\n'%(conf['PATH_MSCONVERT'],filename_mzxml)) f_sh.close() os.chmod(filename_sh,stat.S_IRWXU) sys.stderr.write('\nmzXML.gz-to-mgf is ready. Run %s.\n\n'%(filename_sh))
import mstb_helper as helper usage_mesg = 'Usage: prepare-tandemK.py' dirname = 'tandemK' filename_taxon_xml = 'tandem-taxonomy.xml' MSTB_HOME = helper.get_mstb_home() CWD = helper.get_cwd() conf = helper.read_conf( os.path.join(CWD,'mstb.conf') ) if( len(conf) == 0 ): sys.exit(1) helper.check_conf_term(conf,'DB_NAME') helper.check_conf_file(conf,'DB_FASTAPRO') helper.check_conf_file(conf,'PATH_TANDEMK_EXE') helper.check_conf_file(conf,'PATH_TANDEM2XML') helper.check_conf_file(conf,'PATH_TANDEMK_DEFAULT_PARAM') path_dir = os.path.join(CWD,dirname) if( not os.access(path_dir,os.R_OK) ): sys.stderr.write("Create %s.\n"%(path_dir)) os.mkdir(path_dir) if( not os.path.isdir(path_dir) ): sys.stderr.write('\n%s is not a directory.\n'%path_dir) sys.stderr.write('Rename it and make %s directory.\n\n'%path_dir) sys.exit(1) filename_taxon_tmpl = os.path.join(MSTB_HOME,'tmpl',filename_taxon_xml)
import sys import stat import mstb_helper as helper usage_mesg = 'Usage: prepare-MSGFDB.py' dirname = 'MSGFDB' MSTB_HOME = helper.get_mstb_home() CWD = helper.get_cwd() conf = helper.read_conf( os.path.join(CWD,'mstb.conf') ) if( len(conf) == 0 ): sys.exit(1) helper.check_conf_file(conf,'DB_FASTA') helper.check_conf_file(conf,'PATH_MSGFDB_JAR') path_dir = os.path.join(CWD,dirname) if( not os.access(path_dir,os.R_OK) ): sys.stderr.write("Create %s.\n"%(path_dir)) os.mkdir(path_dir) if( not os.path.isdir(path_dir) ): sys.stderr.write('\n%s is not a directory.\n'%path_dir) sys.stderr.write('Rename it and make %s directory.\n\n'%path_dir) sys.exit(1) filename_cmd_tmpl = os.path.join(MSTB_HOME,'tmpl','MSGFDB.cmd') f_cmd_tmpl = open(filename_cmd_tmpl,'r') cmd_tmpl = ''.join( f_cmd_tmpl.readlines() )
import sys import stat import mstb_helper as helper usage_mesg = 'Usage: prepare-sequest-TPP.py' dirname = 'sequest' MSTB_HOME = helper.get_mstb_home() CWD = helper.get_cwd() conf = helper.read_conf( os.path.join(CWD,'mstb.conf') ) if( len(conf) == 0 ): sys.exit(1) helper.check_conf_file(conf,'PATH_XINTERACT') helper.check_conf_term(conf,'DB_DECOY_PREFIX') sample_list = dict() for basename_pepxml in os.listdir(dirname): if( not basename_pepxml.endswith('.pepxml') ): continue sample_name = '_'.join( basename_pepxml.split('_')[1:3]) if( not sample_list.has_key(sample_name) ): sample_list[sample_name] = [] sample_list[sample_name].append( os.path.join(CWD,dirname,basename_pepxml) ) filename_sh = os.path.join(CWD,'scripts','run-sequest-TPP.sh') f_sh = open(filename_sh,'w') f_sh.write('#!/bin/bash\n')