Fix Issue#350 (#353)

* Fix pandas version * :up-arrow: Update pandas to 1.5 🎨 Chage line_terminator to lineterminator in `summary.py` * Fix biopython error * Update bioython version
KwanLab · Feb 20, 2024 · a4a7af7 · a4a7af7
1 parent acbf86d
commit a4a7af7
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Showing 4 changed files with 6 additions and 6 deletions.
diff --git a/autometa-env.yml b/autometa-env.yml
@@ -6,14 +6,14 @@ channels:
 dependencies:
   - attrs # test-data requirement
   - bedtools
-  - biopython
+  - biopython>=1.82
   - bowtie2
   - diamond>=2.0
   - gdown
   - hmmer
   - numba>=0.47
   - numpy>=1.13
-  - pandas>=1.1
+  - pandas>=1.5
   - parallel
   - pip
   - prodigal # NOTE: 2.5 and 2.6 output format is different for sequence headers

diff --git a/autometa/binning/summary.py b/autometa/binning/summary.py
@@ -256,7 +256,7 @@ def get_metabin_taxonomies(
     outcols = [cluster_col, "length", "taxid", *canonical_ranks]
     tmp_lines = (
         bin_df[outcols]
-        .to_csv(sep="\t", index=False, header=False, line_terminator="\n")
+        .to_csv(sep="\t", index=False, header=False, lineterminator="\n")
         .split("\n")
     )
     taxonomies = {}

diff --git a/autometa/common/metagenome.py b/autometa/common/metagenome.py
@@ -139,7 +139,7 @@ def length_weighted_gc(self) -> float:
         for seq in self.sequences:
             weight = len(seq) / self.size
             add_weight(weight)
-            gc_content = SeqUtils.GC(seq)
+            gc_content = SeqUtils.gc_fraction(seq) * 100
             add_gc_contents(gc_content)
         return np.average(a=gc_contents, weights=weights)
 
@@ -312,7 +312,7 @@ def gc_content(self) -> pd.DataFrame:
             [
                 {
                     "contig": record.id,
-                    "gc_content": SeqUtils.GC(record.seq),
+                    "gc_content": SeqUtils.gc_fraction(seq) * 100,
                     "length": len(record.seq),
                 }
                 for record in self.seqrecords

diff --git a/tests/unit_tests/test_metagenome.py b/tests/unit_tests/test_metagenome.py
@@ -69,7 +69,7 @@ def test_length_weighted_gc(metagenome):
     if metagenome.nseqs == 3:
         expected = 65.3167472932504
     elif metagenome.nseqs == 4:
-        expected = 63.195548489666145
+        expected = 63.19554848966614
     else:
         expected = None
     assert isinstance(metagenome.length_weighted_gc, float)