Merge pull request #88 from rrwick/main

Fix two bugs: macOS MMseqs2 version and integer contig names
gbouras13 · Nov 22, 2024 · af14bac · af14bac
2 parents f5def91 + c516810
commit af14bac
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Showing 4 changed files with 30 additions and 12 deletions.
diff --git a/src/dnaapler/utils/all.py b/src/dnaapler/utils/all.py
@@ -62,7 +62,11 @@ def all_process_MMseqs2_output_and_reorient(
     # read in the dataframe from MMseqs2
     try:
         MMseqs2_df = pd.read_csv(
-            MMseqs2_file, delimiter="\t", index_col=False, names=col_list
+            MMseqs2_file,
+            delimiter="\t",
+            index_col=False,
+            names=col_list,
+            dtype={"qseqid": "object"},
         )
 
     except Exception:

diff --git a/src/dnaapler/utils/bulk.py b/src/dnaapler/utils/bulk.py
@@ -153,7 +153,11 @@ def bulk_process_MMseqs2_output_and_reorient(
     # read in the dataframe from MMseqs2
     try:
         MMseqs2_df = pd.read_csv(
-            MMseqs2_file, delimiter="\t", index_col=False, names=col_list
+            MMseqs2_file,
+            delimiter="\t",
+            index_col=False,
+            names=col_list,
+            dtype={"qseqid": "object"},
         )
 
     except Exception:

diff --git a/src/dnaapler/utils/processing.py b/src/dnaapler/utils/processing.py
@@ -50,7 +50,11 @@ def process_MMseqs2_output_and_reorient(
     # read in the dataframe from MMseqs2
     try:
         MMseqs2_df = pd.read_csv(
-            MMseqs2_file, delimiter="\t", index_col=False, names=col_list
+            MMseqs2_file,
+            delimiter="\t",
+            index_col=False,
+            names=col_list,
+            dtype={"qseqid": "object"},
         )
     except Exception:
         logger.error("There was an issue with parsing the MMseqs2 output file.")

diff --git a/src/dnaapler/utils/util.py b/src/dnaapler/utils/util.py
@@ -129,17 +129,23 @@ def check_mmseqs2_version():
         else:
             raise ValueError("MMseqs2 version not found")
 
-        mmseqs_major_version = int(mmseqs_version.split(".")[0])
-        mmseqs_minor_version = mmseqs_version.split(".")[1]
+        # The pre-built binary on GitHub reports its version using the commit hash instead of
+        # a version number.
+        if mmseqs_version.startswith("45111b6"):
+            logger.info(f"MMseqs2 version found is {mmseqs_version}")
 
-        logger.info(
-            f"MMseqs2 version found is v{mmseqs_major_version}.{mmseqs_minor_version}"
-        )
+        else:
+            mmseqs_major_version = int(mmseqs_version.split(".")[0])
+            mmseqs_minor_version = mmseqs_version.split(".")[1]
+
+            logger.info(
+                f"MMseqs2 version found is v{mmseqs_major_version}.{mmseqs_minor_version}"
+            )
 
-        if mmseqs_major_version != 13:
-            logger.error("MMseqs2 is the wrong version. Please install v13.45111")
-        if mmseqs_minor_version != "45111":
-            logger.error("MMseqs2 is the wrong version. Please install v13.45111")
+            if mmseqs_major_version != 13:
+                logger.error("MMseqs2 is the wrong version. Please install v13.45111")
+            if mmseqs_minor_version != "45111":
+                logger.error("MMseqs2 is the wrong version. Please install v13.45111")
 
         logger.info("MMseqs2 version is ok.")