hotfix for antismash

EBI-Metagenomics · Jul 16, 2020 · 1e8e721 · 1e8e721
1 parent f4c671c
commit 1e8e721
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Showing 2 changed files with 10 additions and 9 deletions.
diff --git a/.../Assembly/antismash/chunking_antismash_with_conditionals/antismash/run_antismash_short.sh b/.../Assembly/antismash/chunking_antismash_with_conditionals/antismash/run_antismash_short.sh
@@ -9,4 +9,4 @@ done
 
 echo "run antismash"
 source ${CONDA_ENV} antismash && \
-antismash --smcogs --asf --disable-svg --knownclusterblast --outputfolder ${OUTFOLDER} ${INPUT}  # --subclusterblast -v
+antismash --genefinding prodigal-m --smcogs --asf --disable-svg --knownclusterblast --outputfolder ${OUTFOLDER} ${INPUT}  # --subclusterblast -v
diff --git a/...smash_with_conditionals/post-processing/fix_geneclusters_js/change_geneclusters_ctg_js.py b/...smash_with_conditionals/post-processing/fix_geneclusters_js/change_geneclusters_ctg_js.py
@@ -24,15 +24,16 @@
             for cluster in data:
                 for locus in data[cluster]['orfs']:
                     old_locus_tag = locus['locus_tag']
-                    number = old_locus_tag.split('_')[0].split('ctg')[1]
-                    postfix = old_locus_tag.split('_')[1]
+                    if len(old_locus_tag.split('_')[0].split('ctg')) > 1:
+                        number = old_locus_tag.split('_')[0].split('ctg')[1]
+                        postfix = old_locus_tag.split('_')[1]
 
-                    limit = min(NAME_LIMIT - 1 - len(number), len(accession) - 1)
-                    name = accession[0:limit]
+                        limit = min(NAME_LIMIT - 1 - len(number), len(accession) - 1)
+                        name = accession[0:limit]
 
-                    new_locus_tag = name + '-' + number + '_' + postfix
-                    locus['locus_tag'] = new_locus_tag
-                    description = locus['description']
-                    locus['description'] = description.replace(old_locus_tag, new_locus_tag)
+                        new_locus_tag = name + '-' + number + '_' + postfix
+                        locus['locus_tag'] = new_locus_tag
+                        description = locus['description']
+                        locus['description'] = description.replace(old_locus_tag, new_locus_tag)
             json.dump(data, out_json)