#!/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 stat import massspec_toolbox_config as conf path_xinteract = conf.get_TPP_path('xinteract') path_prot_prophet = conf.get_TPP_path('ProteinProphet') path_APEX_parser = conf.get_TPP2APEX_parser() TPP_cutoff = 0.05 filename_script = 'run-inspect.xinteract-combined.sh'; f_script = open(filename_script,'w') f_script.write('#!/bin/bash\n') f_script.write('SAMPLE_NAME="tmp"\n') for filename_pepxml in os.listdir('inspect'): filename_pepxml = filename_pepxml.strip() if( not filename_pepxml.endswith('.inspect.pepxml') ): continue filename_base = filename_pepxml.replace('.pepxml','') filename_pepxml = os.path.join('inspect',filename_pepxml) f_script.write('cp %s %s\n'%(filename_pepxml,'tmp/')) filename_base = os.path.join('inspect.xinteract','$SAMPLE_NAME') filename_xinteract = filename_base+'.xinteract.xml' filename_prot = filename_base+'.xinteract.prot.xml' filename_summary = filename_base+'.xinteract.summary'
#!/usr/bin/python import os import sys import stat import massspec_toolbox_config as conf path_xinteract = conf.get_TPP_path('xinteract') path_prot_prophet = conf.get_TPP_path('ProteinProphet') path_APEX_parser = conf.get_TPP2APEX_parser() TPP_cutoff = 0.05 filename_script = 'run-inspect.xinteract-combined.sh' f_script = open(filename_script, 'w') f_script.write('#!/bin/bash\n') f_script.write('SAMPLE_NAME="tmp"\n') for filename_pepxml in os.listdir('inspect'): filename_pepxml = filename_pepxml.strip() if (not filename_pepxml.endswith('.inspect.pepxml')): continue filename_base = filename_pepxml.replace('.pepxml', '') filename_pepxml = os.path.join('inspect', filename_pepxml) f_script.write('cp %s %s\n' % (filename_pepxml, 'tmp/')) filename_base = os.path.join('inspect.xinteract', '$SAMPLE_NAME') filename_xinteract = filename_base + '.xinteract.xml' filename_prot = filename_base + '.xinteract.prot.xml' filename_summary = filename_base + '.xinteract.summary'
#!/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_kscore.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,
#!/usr/bin/python import os import sys import stat import massspec_toolbox_config as conf path_xinteract = conf.get_TPP_path('xinteract') path_APEX_parser = conf.get_TPP2APEX_parser() TPP_cutoff = 0.05 filename_script = 'run-sequest.xinteract.sh' f_script = open(filename_script, 'w') f_script.write('#!/bin/bash\n') for filename_pepxml in os.listdir('sequest.pepxml'): filename_pepxml = filename_pepxml.strip() if (not filename_pepxml.endswith('.sequest.pepxml')): continue filename_base = filename_pepxml.replace('.pepxml', '') filename_pepxml = os.path.join('sequest.pepxml', filename_pepxml) filename_base = os.path.join('sequest.xinteract', filename_base) filename_xinteract = filename_base + '.xinteract.xml' filename_prot = filename_base + '.xinteract.prot.xml' filename_summary = filename_base + '.xinteract.summary' f_script.write("%s -N%s -dxf_ -Op %s\n" % (path_xinteract, filename_xinteract, filename_pepxml)) f_script.write( "%s %s %.2f %s\n" % (path_APEX_parser, filename_prot, TPP_cutoff, filename_summary)) f_script.close() os.chmod(filename_script, stat.S_IRWXU)
#!/usr/bin/python import os import sys import stat import massspec_toolbox_config as conf path_xinteract = conf.get_TPP_path('xinteract') path_APEX_parser = conf.get_TPP2APEX_parser() TPP_cutoff = 0.05 filename_script = 'run-sequest.xinteract.sh'; f_script = open(filename_script,'w') f_script.write('#!/bin/bash\n') for filename_pepxml in os.listdir('sequest.pepxml'): filename_pepxml = filename_pepxml.strip() if( not filename_pepxml.endswith('.sequest.pepxml') ): continue filename_base = filename_pepxml.replace('.pepxml','') filename_pepxml = os.path.join('sequest.pepxml',filename_pepxml) filename_base = os.path.join('sequest.xinteract',filename_base) filename_xinteract = filename_base+'.xinteract.xml' filename_prot = filename_base+'.xinteract.prot.xml' filename_summary = filename_base+'.xinteract.summary' f_script.write("%s -N%s -dxf_ -Op %s\n"%(path_xinteract,filename_xinteract,filename_pepxml)) f_script.write("%s %s %.2f %s\n"%(path_APEX_parser,filename_prot,TPP_cutoff,filename_summary)) f_script.close() os.chmod(filename_script,stat.S_IRWXU)