diff merge_cut_up_clustering.py @ 0:b9d37d30731e draft

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/concoct commit 40a09cbfd6052f7b0295946621db1bdf58228b09"

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/merge_cut_up_clustering.py	Sun Mar 13 08:43:39 2022 +0000
@@ -0,0 +1,56 @@
+#!/usr/bin/env python
+
+import argparse
+import re
+import sys
+from collections import Counter
+from collections import defaultdict
+
+
+CONTIG_PART_EXPR = re.compile(r'(.*)\.concoct_part_([0-9]*)')
+
+
+def original_contig_name_special(contig_id):
+    try:
+        original_id, part_index = CONTIG_PART_EXPR.match(contig_id).group(1, 2)
+        return original_id, part_index
+    except AttributeError:
+        # No matches for concoct_part regex.
+        return contig_id, 0
+
+
+parser = argparse.ArgumentParser()
+parser.add_argument("--input", action="store", dest="input", help="Tabular file with cut up clusters")
+parser.add_argument("--output", action="store", dest="output", help="Output file with merged clusters")
+
+args = parser.parse_args()
+
+# Get cut up clusters
+all_seqs = {}
+all_originals = defaultdict(dict)
+with open(args.input, 'r') as ifh:
+    for i, line in enumerate(ifh):
+        if i == 0:
+            if 'contig_id' not in line:
+                sys.stderr.write("ERROR nvalid clustering file, 'contig_id' is not found in the header.")
+                sys.exit(-1)
+            # Skip header.
+            continue
+        line = line.rstrip('\r\n')
+        contig_id, cluster_id = line.split('\t')
+        original_contig_name, part_id = original_contig_name_special(contig_id)
+        all_originals[original_contig_name][part_id] = cluster_id
+
+# Merge cut up clusters.
+with open(args.output, 'w') as ofh:
+    ofh.write("contig_id\tcluster_id\n")
+    for original_contig_id, part_ids_d in all_originals.items():
+        if len(part_ids_d) > 1:
+            c = Counter(part_ids_d.values())
+            cluster_id = c.most_common(1)[0][0]
+            c_string = [(a, b) for a, b in c.items()]
+            # Here if len(c.values()) > 1,
+            # then no cluster for contig.
+        else:
+            cluster_id = list(part_ids_d.values())[0]
+        ofh.write(f"{original_contig_id}\t{cluster_id}\n")