--- a/GCMS/combine_output.py	Fri Mar 20 17:11:04 2015 +0100
+++ b/GCMS/combine_output.py	Thu Mar 26 09:27:51 2015 +0100
@@ -5,7 +5,6 @@
 '''
 
 import csv
-import re
 import sys
 import math
 import pprint
@@ -81,13 +80,15 @@
     # The ID in the RankFilter output contains the following 5 fields:
     rf_id = rankfilter['ID'].split('-')
     try:
+        if 'Formula' not in rankfilter:
+            raise Exception("Error: old Rankfilter format detected (the selected Rankfilter data does not contain the column 'Formula'). Solution: rerun Rankfilter again.")
         hit = [rf_id[0], # Centrotype
                rf_id[1], # cent.Factor
                rf_id[2], # scan nr
                rf_id[3], # R.T. (umin)
                rf_id[4], # nr. Peaks
+               rankfilter['R.T.'],
                # Appending other fields
-               rankfilter['R.T.'],
                rankfilter['Name'],
                rankfilter['Formula'],
                rankfilter['Library'].strip(),

--- a/GCMS/combine_output.xml	Fri Mar 20 17:11:04 2015 +0100
+++ b/GCMS/combine_output.xml	Thu Mar 26 09:27:51 2015 +0100
@@ -15,13 +15,13 @@
     <data format="tabular" label="${tool.name} (Multi) on ${on_string}" name="out_multi" />
   </outputs>
   <help>
-Performs a combination of output files from the 'RankFilter' and 'Lookup RI for CAS' tools into two tab-separated files.
+Performs a combination of given 'RankFilter' and 'Lookup RI for CAS' files into two tab-separated files.
 
-Merges data from both input dictionaries based on the Centrotype field.
+This combination is a merge of the given files based on the Centrotype field.
 In the 'RIQC-RankFilter output' the centrotype is found in the 'ID' field (first part before the "-"). In the 'RIQC-Lookup RI for CAS output'
 the centrotype is found in the 'Centrotype' field. 
 
-The files produced are contain either all hits for a compound on a single line (Single) or on separate lines 
+The files produced contain either all hits for a compound on a single line (Single) or on separate lines 
 (Multi). 
 
 .. class:: infomark

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/rankfilter_GCMS/pdfread.py	Thu Mar 26 09:27:51 2015 +0100
@@ -0,0 +1,203 @@
+"""
+Copyright (C) 2011 by Velitchka Mihaleva, Wageningen University 
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in
+all copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
+THE SOFTWARE.
+"""
+
+import sys
+import csv
+
+def getPDF(filename, print_progress):
+    '''
+    Parses NIST PDF file
+    @param filename: PDF file to parse
+    '''
+    NistInput = {}
+    NistInput_missed = {}
+    nist_input = open(filename, 'r').read()
+
+    hitid = []
+    rt = []
+    name = []
+    forward = []
+    cas = []
+    reverse = []
+    prob = []
+    lib_id = []
+    nist_id = []
+    missed_compounds = []
+    id_missed_compounds = []
+    formula = []
+
+    hit_list = nist_input.split('** Search Report Page 1 of 1 **')
+    hit_list.pop(0)
+    #number_hits = range(10)
+    line_id = 0
+    for line in hit_list:
+        line = line.strip().translate(None, '\r')
+        if line != '':
+            hits = line.replace('\n', ' ').replace('\x0c', '').replace('^L', '').split('Hit')  #solution? : if we wouldn't replace the \n by ' ' but by some special sign, then reading formula would be simpler! 
+                                                                                                #strange....code seems fine actually...debug! See test/data/download.pdf 
+                                                                                                # strange thing is that it looks like the new line does not end up in the text file, eventhough it looks like there is a new line in the pdf...perhaps a bug in the pdf2text command in linux?
+            spec_id = hits.pop(0).split(' ')[1]
+            j = 0
+            for hh in hits:
+                cell = hh.split(';')
+                if print_progress == True:
+                    print 'Processing line: ', line_id, ' with length: ', len(cell), ':\n\t', cell
+                line_id += 1
+                if len(cell) == 7:  # the compound has CAS number
+                    if len(cell[1].split(':')) == 2:
+                        forward.append((cell[1].split(':')[1]).strip())
+                        # indication that the name contains the ":". Should join the cells of name_tmp from 1 till end
+                        if len(cell[0].split(':')) > 2:
+                            name_tmp = ':'.join(cell[0].split(':')[1:])
+                        else:
+                            name_tmp = cell[0].split(':')[1]
+                            
+                        name.append(name_tmp.replace("  ", " ").strip())
+                        name_tmp = name_tmp.strip().split(' ')
+                        if name_tmp:
+                            # if the name ends with a word that starts with C, F or H, then assume this last word is a formula:
+                            if name_tmp[-1][0] == 'C' or name_tmp[-1][0] == 'F' or name_tmp[-1][0] == 'H':
+                                formule = (name_tmp[-1])
+                            else:
+                                formule = ('not_def')
+                        else:
+                            formule = ('not_def')
+                        formula.append(formule.replace("  ", " "))
+                        reverse.append((cell[2].split(':')[1]).strip())
+                        prob.append(cell[3].split(' ')[2].replace('%', ''))
+                        cas.append((cell[4].split(':')[1]).strip())
+                        lib_id.append((cell[5].split(':')[1]).strip())
+                        nist_id.append(cell[6].split(':')[1].replace('.', '').strip())
+                        j = j + 1
+                    else:
+                        missed_compounds.append(hh)
+                        id_missed_compounds.append(spec_id)
+
+                elif len(cell) == 6:  # the compound has no CAS number
+                    if len(cell[1].split(':')) == 2:
+
+                        forward.append((cell[1].split(':')[1]).strip())
+                        # indication that the name contains the ":". Should join the cells of name_tmp from 1 till end
+                        if len(cell[0].split(':')) > 2:
+                            name_tmp = ':'.join(cell[0].split(':')[1:])
+                        else:
+                            name_tmp = cell[0].split(':')[1]
+                        
+                        name.append(name_tmp.replace("  ", " ").strip())
+                        name_tmp = name_tmp.strip().split(' ')
+                        if name_tmp:
+                            # if the name ends with a word that starts with C, F or H, then assume this last word is a formula:
+                            if name_tmp[-1][0] == 'C' or name_tmp[-1][0] == 'F' or name_tmp[-1][0] == 'H':
+                                formule = (name_tmp[-1])
+                            else:
+                                formule = ('not_def')
+                        else:
+                            formule = ('not_def')
+                        formula.append(formule.replace("  ", " "))
+                        reverse.append((cell[2].split(':')[1]).strip())
+                        prob.append(cell[3].split(' ')[2].replace('%', ''))
+                        cas.append('undef')
+                        lib_id.append((cell[4].split(':')[1]).strip())
+                        nist_id.append(cell[5].split(':')[1].replace('.', '').strip())
+                        j = j + 1
+
+                    else:
+                        missed_compounds.append(hh)
+                        id_missed_compounds.append(spec_id)
+
+                else: # Missing columns, report and quit
+                    missed_compounds.append(hh)
+                    id_missed_compounds.append(spec_id)
+
+            for _ in range(j):
+                hitid.append(str(spec_id.replace("  ", " ")))
+                #NB: this is the RT as found in the "id" generated by e.g. msclust, so NOT the RT of the library hit:
+                rt.append(str(float(spec_id.split('-')[3]) / 1e+06))
+
+    NistInput['ID'] = hitid
+    NistInput['R.T.'] = rt
+    NistInput['Name'] = name
+    NistInput['CAS'] = cas
+    NistInput['Formula'] = formula
+    NistInput['Forward'] = forward
+    NistInput['Reverse'] = reverse
+    NistInput['Probability'] = prob
+    NistInput['Library'] = lib_id
+    NistInput['Library ID'] = nist_id
+    NistInput_missed['Missed Compounds'] = missed_compounds
+    NistInput_missed['ID missed Compounds'] = id_missed_compounds
+
+    return NistInput, NistInput_missed
+
+
+def convert_pdftotext2tabular(filename, output_file, error_file, print_progress):
+    '''
+    Converts NIST PDF file to tabular format
+    @param filename: PDF file to parse
+    @param output_file: output file for the hits
+    @param error_file: output file for failed hits
+    '''
+    [HitList, HitList_missed] = getPDF(filename, print_progress)
+    # save Hitlist as tab seperate file
+    Hitlist_as_text = "\t".join(HitList.keys()) + "\n"
+    Hitlist_array_of_array = ([HitList[row] for row in HitList.keys()])
+    Hitlist_as_text += str("\n".join(["\t".join(e) for e in zip(*Hitlist_array_of_array)]))
+    output_fh = open(output_file, 'wb')
+    output_fh.write(Hitlist_as_text)
+    output_fh.close()
+
+    out_missed_pdf = open(error_file, 'wb')
+    for x, y in zip(HitList_missed['Missed Compounds'], HitList_missed['ID missed Compounds']):
+        out_missed_pdf.write("Line with incorrect format or unexpected number of fields:\n")
+        out_missed_pdf.write('%s\n' % '\t'.join([y, x]))
+    out_missed_pdf.close()
+
+
+
+
+
+def read_tabular_old(filename):
+    '''
+    Function to read tabular format (created by convert_pdftotext2tabular)
+    and output a dict with header of columns as key and value is columns of tabular as list
+    @param filename: tabular file to read
+    '''
+    input_fh = None
+    try:
+        input_fh = open(filename, 'r')
+    except IOError, error:
+        raise error
+    colnames = input_fh.readline().strip().split('\t')
+    cells = []
+    for line in input_fh.readlines():
+        cells.append(line.strip().split('\t'))
+    #transform from row oriented structure to column oriented structure
+    cells = zip(*cells)
+    #store the list of list in form of final output
+    RankFilterGC_format = {}
+    for colnumber in range(len(colnames)):
+        RankFilterGC_format[colnames[colnumber]] = cells[colnumber]
+    return RankFilterGC_format
+
+
+if __name__ == '__main__':
+    convert_pdftotext2tabular(sys.argv[1], sys.argv[2], sys.argv[3], True)

--- a/rankfilter_GCMS/rankfilter.py	Fri Mar 20 17:11:04 2015 +0100
+++ b/rankfilter_GCMS/rankfilter.py	Thu Mar 26 09:27:51 2015 +0100
@@ -142,6 +142,8 @@
     # Convert 'Name' data to list in order to be indexed
     # library_data['Name']=list(library_data['Name'])
 
+    # tries to match on CAS first. If this is not possible (cas is 'undef' 
+    # or not found) then tries to match on name:
     for hit_cas, hit_name in zip(hit_list['CAS'], hit_list['Name']):
         index = 0
         if hit_cas != 'undef':