Handling and error msg for using gzipped fasta file and hmmsearch

gamcil · May 4, 2022 · 4c63fa5 · 4c63fa5
1 parent 1c16caa
commit 4c63fa5
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Showing 2 changed files with 8 additions and 2 deletions.
diff --git a/cblaster/helpers.py b/cblaster/helpers.py
@@ -18,7 +18,10 @@
 
 
 def find_sqlite_db(path):
-    sqlite_db = Path(path).with_suffix(".sqlite3")
+    sqlite_db = Path(path)
+    if sqlite_db.suffix == ".gz":
+        sqlite_db = sqlite_db.with_suffix("")
+    sqlite_db = sqlite_db.with_suffix(".sqlite3")
     if not sqlite_db.exists():
         LOG.error("Could not find matching SQlite3 database, exiting")
         raise SystemExit

diff --git a/cblaster/hmm_search.py b/cblaster/hmm_search.py
@@ -158,7 +158,10 @@ def run_hmmsearch(fasta, query):
             check=True,
         )
     except subprocess.CalledProcessError:
-        LOG.exception("hmmsearch failed!")
+        add_msg=""
+        if fasta.endswith("gz"):
+            add_msg = " Try running:  \n  gunzip {0} \nand then resubmit your cblaster command command, specifying:\n  -db {1}.\n\n".format(fasta, fasta.replace(".gz",""))
+        LOG.exception("hmmsearch failed!"+add_msg)
     return output