Merge remote-tracking branch 'origin/hotfix'

Author: susannasiebert

docs/conf.py

@@ -69,7 +69,7 @@
 # The short X.Y version.
 version = '1.5'
 # The full version, including alpha/beta/rc tags.
-release = '1.5.1'
+release = '1.5.2'
 
 # The language for content autogenerated by Sphinx. Refer to documentation
 # for a list of supported languages.

docs/index.rst

@@ -52,12 +52,9 @@ New in release |release|
 
 This is a hotfix release. It fixes the following issues:
 
-- There was a syntax error in
-  ``tools/pvacseq/generate_condensed_ranked_report.py`` that would result in
-  an error when running the ``pvacseq generate-condensed-ranked-report``
-  commands.
-- We were previously not correctly catching cases where the intermediate fasta for
-  making binding prediction was empty. This would result in errors downstream.
+- AGFusion exon files may be comma-delimited. Previously, the file parser
+  assumed the files were tab-delimited. This release now allows AGFusion
+  inputs that are comma- or tab-delimited.
 
 New in version |version|
 ------------------------

docs/releases/1_5.rst

@@ -76,3 +76,24 @@ This version adds the following features:
   where the cache file contains conflicting data compared to the actual
   process outputs which results in errors. Clearing the cache using the ``pvacapi clear_cache``
   function can be used in that situation to resolve these errors.
+
+1.5.1
+-----
+
+This is a hotfix release. It fixes the following issues:
+
+- There was a syntax error in
+  ``tools/pvacseq/generate_condensed_ranked_report.py`` that would result in
+  an error when running the ``pvacseq generate-condensed-ranked-report``
+  commands.
+- We were previously not correctly catching cases where the intermediate fasta for
+  making binding prediction was empty. This would result in errors downstream.
+
+1.5.2
+-----
+
+This is a hotfix release. It fixes the following issues:
+
+- AGFusion exon files may be comma-delimited. Previously, the file parser
+  assumed the files were tab-delimited. This release now allows AGFusion
+  inputs that are comma- or tab-delimited.

lib/input_file_converter.py

@@ -469,7 +469,7 @@ def parse_integrate_neo_file(self):
 
     def determine_fusion_sequence(self, full_sequence, variant_type):
         if '*' not in full_sequence:
-            sys.exit("Fusion position marker '*' not found in fusion sequence. Please rerun AGfusion using the `--middlestar` option.")
+            sys.exit("Fusion position marker '*' not found in fusion sequence. Please rerun AGFusion using the `--middlestar` option.")
         else:
             fusion_position = full_sequence.find('*')
             sequence = full_sequence.replace('*', '')
@@ -479,7 +479,9 @@ def parse_exon_file(self, input_file):
         exon_file = input_file.replace('_protein.fa', '.exons.txt')
         five_prime_positions, three_prime_positions = [], []
         with open(exon_file, 'r') as fh:
-            reader = csv.DictReader(fh, delimiter='\t')
+            dialect = csv.Sniffer().sniff(fh.read())
+            fh.seek(0)
+            reader = csv.DictReader(fh, delimiter=dialect.delimiter)
             for record in reader:
                 exon_start = int(record['exon_start'])
                 exon_end = int(record['exon_end'])

setup.py

@@ -61,7 +61,7 @@
 
 setup(
     name="pvactools",
-    version="1.5.1",
+    version="1.5.2",
     packages=[
         "tools",
         "tools.pvacbind",

tests/test_data/input_file_converter/agfusion/WHSC1L1-38347497_ESRP1-94705925/WHSC1L1-ESRP1.exons.txt

@@ -1,4 +1,4 @@
-5'_gene	3'_gene	5'_transcript	3'_transcript	exon_gene_source	exon_number	exon_chr	exon_start	exon_end
-WHSC1L1	ESRP1	ENST00000317025	ENST00000433389	'5 gene	1	8	38381799	38382272
-WHSC1L1	ESRP1	ENST00000317025	ENST00000433389	'5 gene	2	8	38347497	38348215
-WHSC1L1	ESRP1	ENST00000317025	ENST00000433389	'3 gene	16	8	94705925	94707423
+5'_gene,3'_gene,5'_transcript,3'_transcript,exon_gene_source,exon_number,exon_chr,exon_start,exon_end
+WHSC1L1,ESRP1,ENST00000317025,ENST00000433389,'5 gene,1,8,38381799,38382272
+WHSC1L1,ESRP1,ENST00000317025,ENST00000433389,'5 gene,2,8,38347497,38348215
+WHSC1L1,ESRP1,ENST00000317025,ENST00000433389,'3 gene,16,8,94705925,94707423