diff GCMS/combine_output.py @ 14:346ff9ad8c7a

fix for rankfilter, removed pfd read functional
author linda.bakker@wur.nl <linda.bakker@wur.nl>
date Fri, 20 Mar 2015 17:10:04 +0100
parents 4393f982d18f
children fe4682eb938c
line wrap: on
line diff
--- a/GCMS/combine_output.py	Thu Mar 19 15:04:56 2015 +0100
+++ b/GCMS/combine_output.py	Fri Mar 20 17:10:04 2015 +0100
@@ -81,7 +81,6 @@
     # The ID in the RankFilter output contains the following 5 fields:
     rf_id = rankfilter['ID'].split('-')
     try:
-        name, formula = _remove_formula(rankfilter['Name'])
         hit = [rf_id[0], # Centrotype
                rf_id[1], # cent.Factor
                rf_id[2], # scan nr
@@ -89,8 +88,8 @@
                rf_id[4], # nr. Peaks
                # Appending other fields
                rankfilter['R.T.'],
-               name,
-               caslookup['FORMULA'] if not formula else formula,
+               rankfilter['Name'],
+               rankfilter['Formula'],
                rankfilter['Library'].strip(),
                rankfilter['CAS'].strip(),
                rankfilter['Forward'],
@@ -120,18 +119,7 @@
     return hit
 
 
-def _remove_formula(name):
-    '''
-    The RankFilter Name field often contains the Formula as well, this function removes it from the Name
-    @param name: complete name of the compound from the RankFilter output
-    '''
-    name = name.split()
-    poss_formula = name[-1]
-    match = re.match("^(([A-Z][a-z]{0,2})(\d*))+$", poss_formula)
-    if match:
-        return ' '.join(name[:-1]), poss_formula
-    else:
-        return ' '.join(name), False
+
 
 
 def _get_default_caslookup():