MRG: enable loading lineages from annotated gather with match_name in…

…stead of name (#3078)

This PR enables loading from gather lineages files that contain
'match_name' instead of name. Rationale:
- we generally plan to replace 'name' with 'match_name' in gather output
(#1555)
- branchwater plugin's fastmultigather already uses 'match_name'

---------

Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>

src/sourmash/tax/tax_utils.py

@@ -1274,7 +1274,9 @@ def load(
                 elif "accession" in header:
                     identifier = "accession"
                     header = ["ident" if "accession" == x else x for x in header]
-                elif "name" in header and "lineage" in header:
+                elif "lineage" in header and any(
+                    ["name" in header, "match_name" in header]
+                ):
                     return cls.load_from_gather_with_lineages(
                         filename, force=force, lins=lins, ictv=ictv
                     )
@@ -1390,9 +1392,14 @@ def load_from_gather_with_lineages(
             if not header:
                 raise ValueError(f"cannot read taxonomy assignments from {filename}")
 
-            if "name" not in header or "lineage" not in header:
+            ident_col = None
+            if "name" in header:
+                ident_col = "name"
+            elif "match_name" in header:
+                ident_col = "match_name"
+            if "lineage" not in header or ident_col is None:
                 raise ValueError(
-                    "Expected headers 'name' and 'lineage' not found. Is this a with-lineages file?"
+                    "Expected headers 'name'/'match_name' and 'lineage' not found. Is this a with-lineages file?"
                 )
 
             ranks = None
@@ -1405,7 +1412,7 @@ def load_from_gather_with_lineages(
             for n, row in enumerate(r):
                 num_rows += 1
 
-                name = row["name"]
+                name = row[ident_col]
                 ident = get_ident(name)
 
                 if lins:

tests/test-data/tax/test1.gather.with-lineages.csv

@@ -0,0 +1,5 @@
+intersect_bp,f_orig_query,f_match,f_unique_to_query,f_unique_weighted,average_abund,median_abund,std_abund,name,filename,md5,f_match_orig,unique_intersect_bp,gather_result_rank,remaining_bp,query_name,query_md5,query_filename,query_bp,ksize,scaled,query_n_hashes,lineage
+442000,0.08815317112086159,0.08438335242458954,0.08815317112086159,0.05815279361459521,1.6153846153846154,1.0,1.1059438185997785,"GCF_001881345.1 Escherichia coli strain=SF-596, ASM188134v1",/group/ctbrowngrp/gtdb/databases/ctb/gtdb-rs202.genomic.k31.sbt.zip,683df1ec13872b4b98d59e98b355b52c,0.042779713511420826,442000,0,4572000,test1,md5,test1.sig,5014000,31,1000,2507,Bacteria;Pseudomonadota;Gammaproteobacteria;Enterobacterales;Enterobacteriaceae;Escherichia;Escherichia coli
+390000,0.07778220981252493,0.10416666666666667,0.07778220981252493,0.050496823586903404,1.5897435897435896,1.0,0.8804995294906566,"GCF_009494285.1 Prevotella copri strain=iAK1218, ASM949428v1",/group/ctbrowngrp/gtdb/databases/ctb/gtdb-rs202.genomic.k31.sbt.zip,1266c86141e3a5603da61f57dd863ed0,0.052236806857755155,390000,1,4182000,test1,md5,test1.sig,5014000,31,1000,2507,Bacteria;Bacteroidota;Bacteroidia;Bacteroidales;Prevotellaceae;Prevotella;Prevotella copri
+138000,0.027522935779816515,0.024722321748477247,0.027522935779816515,0.015637726014008795,1.391304347826087,1.0,0.5702120455914782,"GCF_013368705.1 Bacteroides vulgatus strain=B33, ASM1336870v1",/group/ctbrowngrp/gtdb/databases/ctb/gtdb-rs202.genomic.k31.sbt.zip,7d5f4ba1d01c8c3f7a520d19faded7cb,0.012648945921173235,138000,2,4044000,test1,md5,test1.sig,5014000,31,1000,2507,Bacteria;Bacteroidota;Bacteroidia;Bacteroidales;Bacteroidaceae;Phocaeicola;Phocaeicola vulgatus
+338000,0.06741124850418827,0.013789581205311542,0.010769844435580374,0.006515719172503665,1.4814814814814814,1.0,0.738886568268889,"GCF_003471795.1 Prevotella copri strain=AM16-54, ASM347179v1",/group/ctbrowngrp/gtdb/databases/ctb/gtdb-rs202.genomic.k31.sbt.zip,0ebd36ff45fc2810808789667f4aad84,0.04337782340862423,54000,3,3990000,test1,md5,test1.sig,5014000,31,1000,2507,Bacteria;Bacteroidota;Bacteroidia;Bacteroidales;Prevotellaceae;Prevotella;Prevotella copri

tests/test_tax_utils.py

@@ -1014,7 +1014,7 @@ def test_check_and_load_gather_lineage_csvs_bad_header(runtmp):
     with pytest.raises(ValueError) as exc:
         LineageDB.load_from_gather_with_lineages(g_res)
     assert (
-        "Expected headers 'name' and 'lineage' not found. Is this a with-lineages file?"
+        "Expected headers 'name'/'match_name' and 'lineage' not found. Is this a with-lineages file?"
         in str(exc.value)
     )
 
@@ -1038,6 +1038,29 @@ def test_check_and_load_gather_lineage_csvs_isdir(runtmp):
     assert "is a directory" in str(exc.value)
 
 
+def test_check_and_load_gather_lineage_csvs_name(runtmp):
+    # test loading a with-lineage file that has 'name', not 'match_name'
+    g_res = utils.get_test_data("tax/test1.gather.with-lineages.csv")
+
+    lins = LineageDB.load_from_gather_with_lineages(g_res)
+    assert len(lins) == 4
+
+
+def test_check_and_load_gather_lineage_csvs_match_name(runtmp):
+    # test loading a with-lineage file that has 'match_name' instead of 'name'
+    g_res = utils.get_test_data("tax/test1.gather.with-lineages.csv")
+    out_lins = runtmp.output("match-name.lineages.csv")
+    with open(g_res) as f_in:
+        first_line = f_in.readline().replace("name", "match_name")
+        with open(out_lins, "w") as f_out:
+            f_out.write(first_line)
+            for line in f_in:
+                f_out.write(line)
+
+    lins = LineageDB.load_from_gather_with_lineages(out_lins)
+    assert len(lins) == 4
+
+
 def test_check_and_load_gather_csvs_fail_on_missing(runtmp):
     g_csv = utils.get_test_data("tax/test1.gather.csv")
     # make gather results with taxonomy name not in tax_assign