| Previous changeset 15:05ff1c55db84 (2015-03-20) Next changeset 18:cc2f31d1bac0 (2015-03-26) |
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Commit message:
small improvement |
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modified:
GCMS/combine_output.py GCMS/combine_output.xml rankfilter_GCMS/rankfilter.py |
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| diff -r 05ff1c55db84 -r fe4682eb938c GCMS/combine_output.py --- a/GCMS/combine_output.py Fri Mar 20 17:11:04 2015 +0100 +++ b/GCMS/combine_output.py Mon Mar 23 08:40:42 2015 +0100 |
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| @@ -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(), |
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| diff -r 05ff1c55db84 -r fe4682eb938c GCMS/combine_output.xml --- a/GCMS/combine_output.xml Fri Mar 20 17:11:04 2015 +0100 +++ b/GCMS/combine_output.xml Mon Mar 23 08:40:42 2015 +0100 |
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| @@ -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 |
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| diff -r 05ff1c55db84 -r fe4682eb938c rankfilter_GCMS/rankfilter.py --- a/rankfilter_GCMS/rankfilter.py Fri Mar 20 17:11:04 2015 +0100 +++ b/rankfilter_GCMS/rankfilter.py Mon Mar 23 08:40:42 2015 +0100 |
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| @@ -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': |