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changeset 3:78afc81ab244 draft default tip

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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/pi_db_tools commit decb06dc90d7069d317968b979f649a04720b264
author galaxyp
date Thu, 14 Sep 2017 11:55:02 -0400
parents 77ddaee887a8
children
files __pycache__/peptide_pi_annotator.cpython-36.pyc delta_pi_calc.xml peptide_pi_annotator.py pi_dbspec_align.xml test-data/peptable.txt test-data/peptable_deltapi.txt test-data/peptable_missed_ox.txt
diffstat 7 files changed, 28 insertions(+), 13 deletions(-) [+]
line wrap: on
line diff
Binary file __pycache__/peptide_pi_annotator.cpython-36.pyc has changed
--- a/delta_pi_calc.xml	Fri Sep 01 03:14:54 2017 -0400
+++ b/delta_pi_calc.xml	Thu Sep 14 11:55:02 2017 -0400
@@ -1,4 +1,4 @@
-<tool id="calc_delta_pi" name="Add delta pI" version="1.2">
+<tool id="calc_delta_pi" name="Add delta pI" version="1.3">
     <description>to peptide table</description>
     <requirements>
         <requirement type="package" version="3.6">python</requirement>
--- a/peptide_pi_annotator.py	Fri Sep 01 03:14:54 2017 -0400
+++ b/peptide_pi_annotator.py	Thu Sep 14 11:55:02 2017 -0400
@@ -43,10 +43,10 @@
             fp.write('\n')
 
 
-def get_first_matching_pattern(patterns, string):
-    for pattern in patterns:
+def get_strip(strips, string):
+    for pattern in strips.keys():
         if re.search(pattern, string):
-            return pattern
+            return strips[pattern]
     return False
 
 
@@ -71,11 +71,6 @@
         yield header + ['Experimental pI', 'Predicted pI', 'Delta pI']
         for line in fp:
             line = line.strip('\n').split('\t')
-            strip = strips[get_first_matching_pattern(strips.keys(),
-                                                      line[stripcol])]
-            exp_pi = (strip['fr_width'] * int(line[frac_col]) +
-                      strip['intercept'])
-
             sequence = line[seqcol]
             for weight in ignoremods:
                 if weight == '*':
@@ -90,12 +85,26 @@
                 not_predicted_count += 1
                 pred_pi, delta_pi = 'NA', 'NA'
             else:
-                delta_pi = exp_pi - pred_pi
                 predicted_count += 1
+            strip = get_strip(strips, line[stripcol])
+            if not strip:
+                exp_pi, delta_pi = 'NA', 'NA'
+            else:
+                try:
+                    exp_pi = (strip['fr_width'] * int(line[frac_col]) +
+                              strip['intercept'])
+                except ValueError:
+                    print('Cannot detect fraction for PSM {}'.format(sequence))
+                    exp_pi, delta_pi = 'NA', 'NA'
+                else:
+                    if pred_pi != 'NA':
+                        delta_pi = exp_pi - pred_pi
+                    else:
+                        delta_pi = 'NA'
             yield line + [exp_pi, pred_pi, delta_pi]
     print('Number of peptides without pI prediction: {}\n'
-          'Number of peptides with predicion: {}\n'.format(not_predicted_count,
-                                                           predicted_count))
+          'Number of peptides predicted: {}\n'.format(not_predicted_count,
+                                                      predicted_count))
 
 
 def parse_commandline():
--- a/pi_dbspec_align.xml	Fri Sep 01 03:14:54 2017 -0400
+++ b/pi_dbspec_align.xml	Thu Sep 14 11:55:02 2017 -0400
@@ -2,7 +2,7 @@
     <description>to resemble spectra fraction scheme</description>
     <requirements>
         <requirement type="package" version="3.6">python</requirement>
-	<requirement type="package" version="1.62">biopython</requirement>
+	<requirement type="package" version="1.70">biopython</requirement>
     </requirements>
     <command detect_errors="exit_code">
 	    <![CDATA[
--- a/test-data/peptable.txt	Fri Sep 01 03:14:54 2017 -0400
+++ b/test-data/peptable.txt	Thu Sep 14 11:55:02 2017 -0400
@@ -3,3 +3,5 @@
 FLWLKIIVYIM+15.994915IILSFLCNCLLLCVDFLK	strip1_fr50	0.3	50
 IIVYIMIILSFLCNCLLLCVDFLK	strip2_fr50	0	50
 IIVYIMIILSFLCNCLLLCVDFLKISFEVNTNPISCGFLSFT	strip2_fr43	0.01	43
+TSESLIPKSLNL	cannotfind_strip	0.1	NA
+TSESLIPKSLNL	strip1_nofr_fr20	0.1	NA
--- a/test-data/peptable_deltapi.txt	Fri Sep 01 03:14:54 2017 -0400
+++ b/test-data/peptable_deltapi.txt	Thu Sep 14 11:55:02 2017 -0400
@@ -3,3 +3,5 @@
 FLWLKIIVYIM+15.994915IILSFLCNCLLLCVDFLK	strip1_fr50	0.3	50	8.860000000000001	7.6171	1.2429000000000014
 IIVYIMIILSFLCNCLLLCVDFLK	strip2_fr50	0	50	8.11	5.99038	2.1196199999999994
 IIVYIMIILSFLCNCLLLCVDFLKISFEVNTNPISCGFLSFT	strip2_fr43	0.01	43	7.83	4.55361	3.27639
+TSESLIPKSLNL	cannotfind_strip	0.1	NA	NA	6.13955	NA
+TSESLIPKSLNL	strip1_nofr_fr20	0.1	NA	NA	6.13955	NA
--- a/test-data/peptable_missed_ox.txt	Fri Sep 01 03:14:54 2017 -0400
+++ b/test-data/peptable_missed_ox.txt	Thu Sep 14 11:55:02 2017 -0400
@@ -3,3 +3,5 @@
 FLWLKIIVYIM+15.994915IILSFLCNCLLLCVDFLK	strip1_fr50	0.3	50	8.860000000000001	NA	NA
 IIVYIMIILSFLCNCLLLCVDFLK	strip2_fr50	0	50	8.11	5.99038	2.1196199999999994
 IIVYIMIILSFLCNCLLLCVDFLKISFEVNTNPISCGFLSFT	strip2_fr43	0.01	43	7.83	4.55361	3.27639
+TSESLIPKSLNL	cannotfind_strip	0.1	NA	NA	6.13955	NA
+TSESLIPKSLNL	strip1_nofr_fr20	0.1	NA	NA	6.13955	NA