Update to 2.1.4 with bugfix for --run_intronerate

mossmatters · Jun 5, 2023 · 643e963 · 643e963
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diff --git a/README.md b/README.md
@@ -1,6 +1,6 @@
 # HybPiper
 
-Current version: 2.1.3 (March 2022)
+Current version: 2.1.4 (June 2023)
 
 [![DOI](https://zenodo.org/badge/6513/mossmatters/HybPiper.svg)](https://zenodo.org/badge/latestdoi/6513/mossmatters/HybPiper)
 

diff --git a/change_log.md b/change_log.md
@@ -1,5 +1,10 @@
 # Changelog
 
+**2.1.4** *5th June, 2023*
+
+- Bugfix: fixed an issue when using `--run_intronerate` that could cause an error and result in no `*.FNA` sequence being produced for some genes.  
+
+
 **2.1.3** *23rd March, 2023*
 
 - Log platform and ulimit details for debugging purposes.

diff --git a/hybpiper/assemble.py b/hybpiper/assemble.py
@@ -1,7 +1,7 @@
 #!/usr/bin/env python
 
 """
-HybPiper Version 2.1.3 (March 2023)
+HybPiper Version 2.1.4 (June 2023)
 
 ########################################################################################################################
 ############################################## NOTES ON VERSION 2.1.3 ##################################################
@@ -1780,7 +1780,7 @@ def parse_arguments():
     group_1.add_argument('--version', '-v',
                          dest='version',
                          action='version',
-                         version='%(prog)s 2.1.3',
+                         version='%(prog)s 2.1.4',
                          help='Print the HybPiper version number.')
 
     # Add subparsers:

diff --git a/hybpiper/exonerate_hits.py b/hybpiper/exonerate_hits.py
@@ -438,10 +438,13 @@ def intronerate(exonerate_object,
         intron_sequences.append(intron_seqrecord)
 
     # Only write an "introns.fasta" file in certain cases:
-    if exonerate_object.stitched_contig_seqrecord.description == 'single_hit' and \
-            len(exonerate_object.hits_subsumed_hits_removed_overlaps_trimmed_dict['hit_inter_ranges']) == 0:
-        logger.debug(f'Sequence for gene {gene_name} is derived from a single Exonerate hit with no introns - '
-                     f'only a supercontig sequence will be recovered (i.e. no "introns.fasta" file) will be recovered')
+    if exonerate_object.stitched_contig_seqrecord.description == 'single_hit':
+        single_hit_dict_values = list(exonerate_object.hits_subsumed_hits_removed_overlaps_trimmed_dict.values())[0]
+        single_hit_inter_ranges = single_hit_dict_values['hit_inter_ranges']
+        if len(single_hit_inter_ranges) == 0:
+            logger.debug(f'Sequence for gene {gene_name} is derived from a single Exonerate hit with no introns - '
+                         f'only a supercontig sequence will be recovered (i.e. no "introns.fasta" file) will be '
+                         f'recovered')
     elif len(intron_sequences) == 0:  # e.g. When Exonerate splits the intronerate_supercontig target
         logger.debug(f'No introns for gene {gene_name}! This is likely caused by Exonerate splitting the '
                      f'"intronerate_supercontig" target in to multiple HSPs (i.e. it could not find an '

diff --git a/setup.py b/setup.py
@@ -8,7 +8,7 @@
 hybpiper_entry_points = {'console_scripts': ['hybpiper = hybpiper.assemble:main']}
 
 setuptools.setup(name='hybpiper',
-                 version='2.1.3',
+                 version='2.1.4',
                  packages=setuptools.find_packages(),
                  author='Chris Jackson, Matt Johnson',
                  author_email='chris.jackson@rbg.vic.gov.au',