abutils - npm Package Compare versions

Comparing version 0.5.2 to 0.5.3

abutils.egg-info/PKG-INFO

 Metadata-Version: 2.4
 Name: abutils
-Version: 0.5.2
+Version: 0.5.3
 Summary: Utilities for analysis of adaptive immune receptor repertoire (AIRR) data
@@ -5,0 +5,0 @@ Home-page: https://github.com/briney/abutils

abutils/tools/cluster.py

@@ -217,4 +217,4 @@ #!/usr/bin/env python
             for name, cdata in clusts.items():
-                seqs = cdata["seqs"]
-                centroid = cdata["centroid"]
+                seqs = cdata.get("seqs", [])
+                centroid = cdata.get("centroid", None)
                 clusters.append(Cluster(name, seqs, centroid=centroid))
@@ -250,2 +250,3 @@ return clusters
     as_dict: bool = False,
+    quiet: bool = False,
     debug: bool = False,
@@ -361,2 +362,5 @@ ) -> Union[dict, Clusters]:
 
+    quiet : bool, default=False
+        If ``True``, suppresses all output from the clustering algorithm.
+
     debug : bool, default=False
@@ -414,2 +418,3 @@ If ``True``, prints MAFFT's standard output and standard error.
             as_dict=True,
+            quiet=quiet,
             debug=debug,
@@ -425,2 +430,3 @@ )
             as_dict=True,
+            quiet=quiet,
             debug=debug,
@@ -438,2 +444,3 @@ )
             as_dict=True,
+            quiet=quiet,
             debug=debug,
@@ -465,2 +472,3 @@ )
     as_dict: bool = False,
+    quiet: bool = False,
     debug: bool = False,
@@ -516,2 +524,5 @@ ) -> Union[dict, Clusters]:
 
+    quiet : bool, default=False
+        If ``True``, suppresses all output from the clustering algorithm.
+
     debug : bool, default=False
@@ -558,6 +569,7 @@ If ``True``, prints standard output and standard error from ``vsearch``.
     if os.stat(uc_file).st_size == 0:
-        err = f"WARNING: the VSEARCH output file ({uc_file}) is empty. "
-        err += "Please verify that the input data is valid."
-        print(err)
-        return None
+        if not quiet:
+            err = f"WARNING: the VSEARCH output file ({uc_file}) is empty. "
+            err += "Please verify that the input data is valid."
+            print(err)
+        return {}
     if as_dict:
@@ -581,2 +593,3 @@ cluster_info = {}
             os.remove(uc_file)
+            os.remove(centroid_file)
         return cluster_info
@@ -599,2 +612,3 @@ else:
     as_dict: bool = False,
+    quiet: bool = False,
     debug: bool = False,
@@ -676,2 +690,5 @@ ):
 
+    quiet : bool, default=False
+        If ``True``, suppresses all output from the clustering algorithm.
+
     debug : bool, default=False
@@ -758,2 +775,4 @@ If ``True``, prints standard output and standard error from ``mmseqs``.
             os.remove(tsv_file)
+            os.remove(db_file)
+            os.remove(clu_file)
         return cluster_info
@@ -771,2 +790,3 @@ else:
     as_dict: bool = False,
+    quiet: bool = False,
     debug: bool = False,
@@ -812,2 +832,5 @@ ):
 
+    quiet : bool, default=False
+        If ``True``, suppresses all output from the clustering algorithm.
+
     debug : bool, default=False
@@ -855,6 +878,7 @@ If ``True``, prints standard output and standard error from ``mmseqs``.
     if os.stat(clusters_file).st_size == 0:
-        err = f"WARNING: the CD-HIT output file ({clusters_file}) is empty. "
-        err += "Please verify that the input data is valid."
-        print(err)
-        return None
+        if not quiet:
+            err = f"WARNING: the CD-HIT output file ({clusters_file}) is empty. "
+            err += "Please verify that the input data is valid."
+            print(err)
+        return {}
     # parse CD-HIT output
@@ -861,0 +885,0 @@ if as_dict:

abutils/version.py

@@ -6,2 +6,2 @@ # Store the version here so:
 
-__version__ = "0.5.2"
+__version__ = "0.5.3"

PKG-INFO

 Metadata-Version: 2.4
 Name: abutils
-Version: 0.5.2
+Version: 0.5.3
 Summary: Utilities for analysis of adaptive immune receptor repertoire (AIRR) data
@@ -5,0 +5,0 @@ Home-page: https://github.com/briney/abutils

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Total package byte prevSize

228936454

0

Lines of code

28753

0.07%