From ee04ad64defaf04bec690beb6dcab9bdd9c637b2 Mon Sep 17 00:00:00 2001
From: Jakob Nybo Nissen <jakobnybonissen@gmail.com>
Date: Tue, 12 Sep 2023 16:15:56 +0200
Subject: [PATCH] Fix bugs in scripts

---
 src/cmd_benchmark.py                   | 58 --------------------------
 workflow_avamb/src/write_abundances.py |  6 ++-
 2 files changed, 5 insertions(+), 59 deletions(-)
 delete mode 100644 src/cmd_benchmark.py

diff --git a/src/cmd_benchmark.py b/src/cmd_benchmark.py
deleted file mode 100644
index daa81add..00000000
--- a/src/cmd_benchmark.py
+++ /dev/null
@@ -1,58 +0,0 @@
-#!/usr/bin/python
-import sys
-import argparse
-import vamb
-import os
-
-parser = argparse.ArgumentParser(
-    description="""Command-line benchmark utility.""",
-    formatter_class=argparse.RawDescriptionHelpFormatter,
-    add_help=False,
-)
-
-parser.add_argument("clusterspath", help="Path to clusters.tsv")
-parser.add_argument("refpath", help="Path to reference file")
-parser.add_argument("--tax", dest="taxpath", help="Path to taxonomic maps")
-parser.add_argument(
-    "-m",
-    dest="min_bin_size",
-    metavar="",
-    type=int,
-    default=200000,
-    help="Minimum size of bins [200000]",
-)
-parser.add_argument("-s", dest="separator", help="Binsplit separator", default=None)
-parser.add_argument("--disjoint", action="store_true", help="Enforce disjoint clusters")
-
-if len(sys.argv) == 1:
-    parser.print_help()
-    sys.exit()
-
-args = parser.parse_args()
-
-# Check that files exist
-for path in args.clusterspath, args.refpath, args.taxpath:
-    if path is not None and not os.path.isfile(path):
-        raise FileNotFoundError(path)
-
-with open(args.clusterspath) as file:
-    clusters = vamb.vambtools.read_clusters(file)
-
-with open(args.refpath) as file:
-    reference = vamb.benchmark.Reference.from_file(file)
-
-if args.taxpath is not None:
-    with open(args.taxpath) as file:
-        reference.load_tax_file(file)
-
-binning = vamb.benchmark.Binning(
-    clusters,
-    reference,
-    minsize=args.min_bin_size,
-    disjoint=args.disjoint,
-    binsplit_separator=args.separator,
-)
-
-for rank in range(len(binning.counters)):
-    binning.print_matrix(rank)
-    print("")
diff --git a/workflow_avamb/src/write_abundances.py b/workflow_avamb/src/write_abundances.py
index 58493765..5ab33606 100644
--- a/workflow_avamb/src/write_abundances.py
+++ b/workflow_avamb/src/write_abundances.py
@@ -13,7 +13,11 @@ def write_abundances(
     mask = loadnpz["mask"]
     refhash = refhash.reshape(1)[0]
     (abundance, _) = vamb.parsebam.Abundance.run_pycoverm(
-        paths=[bampath], minid=min_identity, target_refhash=refhash, mask=mask
+        paths=[bampath],
+        minid=min_identity,
+        target_refhash=refhash,
+        target_identifiers=None,
+        mask=mask,
     )
     vamb.vambtools.write_npz(outfile, abundance.ravel())