fix #317 translation error with int contig id (also unicycler input)

gbouras13 · Jan 9, 2024 · 73703a5 · 73703a5
1 parent fa39696
commit 73703a5
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Showing 2 changed files with 5 additions and 5 deletions.
diff --git a/bin/post_processing.py b/bin/post_processing.py
@@ -1227,7 +1227,7 @@ def create_tbl(
                         + "\t"
                         + "locus_tag"
                         + "\t"
-                        + row["locus_tag"]
+                        + str(row["locus_tag"])
                         + "\n"
                     )
                     f.write(
@@ -1243,7 +1243,7 @@ def create_tbl(
                         + "\n"
                     )
                 if self.trna_empty == False:
-                    subset_trna_df = trna_df[trna_df["contig"] == contig]
+                    subset_trna_df = trna_df[str(trna_df["contig"]) == contig]
                     for index, row in subset_trna_df.iterrows():
                         start = str(row["start"])
                         stop = str(row["stop"])
@@ -1305,7 +1305,7 @@ def create_tbl(
                             + "\t"
                             + "locus_tag"
                             + "\t"
-                            + row["locus_tag"]
+                            + str(row["locus_tag"])
                             + "\n"
                         )
                         f.write(
@@ -1350,7 +1350,7 @@ def create_tbl(
                             + "\t"
                             + "locus_tag"
                             + "\t"
-                            + row["locus_tag"]
+                            + str(row["locus_tag"])
                             + "\n"
                         )
                         f.write(

diff --git a/bin/processes.py b/bin/processes.py
@@ -430,7 +430,7 @@ def tidy_prodigal_output(out_dir, gv_flag):
         prod_filt_df.loc[ixs, cols].reindex(columns=cols[::-1]).values
     )
     prod_filt_df["gene"] = (
-        prod_filt_df["contig"]
+        prod_filt_df["contig"].astype(str)
         + prod_filt_df.index.astype(str)
         + " "
         + prod_filt_df["start"].astype(str)