#!/usr/bin/python import os import sys import stat import massspec_toolbox_config as conf (db_name, filename_fasta) = conf.get_dbinfo() current_dirname = os.getcwd() tandem_bin = conf.get_TPP_path('tandem.exe') tandem2xml_bin = conf.get_TPP_path('Tandem2XML') filename_fasta_pro = filename_fasta+'.pro' filename_param_abs = '/home/taejoon/massspec-toolbox/config/tandem-isb_input_native.xml' def tandem_taxonomy_xml(dbname=None, fasta_pro=None): xml_list = [] xml_list.append('<?xml version="1.0"?>') xml_list.append(' <bioml label="x! taxon-to-file matching list">') xml_list.append(' <taxon label="%s">'%(dbname)) xml_list.append(' <file format="peptide" URL="%s" />'%(fasta_pro)) xml_list.append(' </taxon>') xml_list.append('</bioml>') return '\n'.join(xml_list) def tandem_config_xml(param=None, mzxml=None, output=None, log='', seq='', taxonomy=None, dbname=None): xml_list = [] xml_list.append('<?xml version="1.0" encoding="UTF-8"?>\n<bioml>') xml_list.append('<note type="input" label="list path, default parameters">%s</note>'%param) xml_list.append('<note type="input" label="spectrum, path">%s</note>'%mzxml)
#!/usr/bin/python import os import sys import massspec_toolbox_config as conf (db_name, filename_fasta) = conf.get_dbinfo() sys.stderr.write("Use %s as DB file\n" % filename_fasta) for filename_pepxml in os.listdir('sequest.pepxml/'): if (not filename_pepxml.endswith('.pepxml')): continue filename_pepxml = os.path.join('sequest.pepxml', filename_pepxml) filename_pepxml_tmp = filename_pepxml + '.tmp' f_tmp = open(filename_pepxml_tmp, 'w') f_pepxml = open(filename_pepxml, 'r') for line in f_pepxml: line = line.strip() if (line.startswith('<search_database local_path="')): f_tmp.write('<search_database local_path="%s" type="AA"/>\n' % filename_fasta) elif (line.startswith( '<parameter name="list path, sequence source #1" value"')): f_tmp.write( '<parameter name="list path, sequence source #1" value="%s"/>\n' % filename_fasta) elif (line.startswith('<parameter name="first_database_name" value"')): f_tmp.write( '<parameter name="first_database_name" value="%s"/>\n' % filename_fasta) else: f_tmp.write('%s\n' % line)