#!/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)