Metaquast: fixed bug with references with same names

ablab · Mar 17, 2017 · e64e7ed · e64e7ed
1 parent d28c640
commit e64e7ed
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Showing 2 changed files with 4 additions and 6 deletions.
diff --git a/quast_libs/metautils.py b/quast_libs/metautils.py
@@ -154,15 +154,13 @@ def _proceed_seq(seq_name, seq, ref_name, ref_fasta_ext, total_references, ref_f
     for ref_fname in ref_fnames:
         ref_name, ref_fasta_ext = qutils.splitext_for_fasta_file(ref_fname)
         ref_names.append(ref_name)
-    dupl_ref_names = [ref_name for ref_name in ref_names if ref_names.count(ref_name) > 1]
 
     excluded_ref_fpaths = []
-    for ref_fpath in ref_fpaths:
+    ref_names = qutils.process_labels(ref_fpaths)
+    for ref_fpath, ref_name in zip(ref_fpaths, ref_names):
         total_references = 0
         ref_fname = os.path.basename(ref_fpath)
-        ref_name, ref_fasta_ext = qutils.splitext_for_fasta_file(ref_fname)
-        if ref_name in dupl_ref_names:
-            ref_name = qutils.get_label_from_par_dir_and_fname(ref_fpath)
+        _, ref_fasta_ext = qutils.splitext_for_fasta_file(ref_fname)
 
         chromosomes_by_refs[ref_name] = []
         used_seq_names = defaultdict(int)

diff --git a/quast_libs/qutils.py b/quast_libs/qutils.py
@@ -439,7 +439,7 @@ def get_labels_from_par_dirs(contigs_fpaths):
     return labels
 
 
-def process_labels(contigs_fpaths, labels, all_labels_from_dirs):
+def process_labels(contigs_fpaths, labels=None, all_labels_from_dirs=False):
     # 1. labels if the provided by -l options
     if labels:
         # process duplicates, empties