diff tbl2gff3.py @ 0:965674d88d34 draft

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tbl2gff3 commit 725ff8b6a4f01bf532052ce46400f529551a317d"

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tbl2gff3.py	Tue Jul 07 04:20:40 2020 -0400
@@ -0,0 +1,95 @@
+#!/usr/bin/env python
+import argparse
+import csv
+import sys
+
+from BCBio import GFF
+from Bio.Seq import Seq
+from Bio.SeqFeature import FeatureLocation, SeqFeature
+from Bio.SeqRecord import SeqRecord
+
+
+def c(row, v, default=None):
+    if v is None:
+        return default
+
+    try:
+        _ = int(v)
+        return row[int(v) - 1]
+    except ValueError:
+        return v
+
+
+def tbl2gff3(
+    table,
+    rid,
+    begin,
+    end,
+    source=None,
+    type=None,
+    score=None,
+    frame=None,
+    a=None,
+    strand_column=None,
+    strand_value=None,
+):
+
+    records = {}
+
+    for row in csv.reader(table, delimiter="\t"):
+        # print(', '.join(row))
+
+        # if we haven't seen this record before, populate it.
+        recid = c(row, rid)
+        if recid not in records:
+            records[recid] = SeqRecord(Seq("ACTG"), id=recid)
+
+        r = records[recid]
+        q = {}
+        if c(row, score) is not None:
+            q["score"] = float(c(row, score))
+
+        q["source"] = c(row, source, "tbl2gff3")
+
+        _str = None
+        if strand_column is not None:
+            _str = int(c(row, strand_column))
+        elif strand_value is not None:
+            _str = int(strand_value)
+
+        for x in a:
+            k, v = x.split(":", 1)
+            _v = c(row, v)
+            if k in q:
+                q[k].append(_v)
+            else:
+                q[k] = [_v]
+
+        f = SeqFeature(
+            FeatureLocation(int(c(row, begin)), int(c(row, end))),
+            type=c(row, type),
+            strand=_str,
+            qualifiers=q,
+        )
+        r.features.append(f)
+
+    return records
+
+
+if __name__ == "__main__":
+    parser = argparse.ArgumentParser(description="Convert tables to gff3", epilog="")
+    parser.add_argument("table", type=argparse.FileType("r"), help="Tabular Input")
+    parser.add_argument("rid", help="id column")
+    parser.add_argument("begin", help="begin column")
+    parser.add_argument("end", help="end column")
+    parser.add_argument("--type", help="feature type column")
+    parser.add_argument("--score", help="score column")
+    parser.add_argument("--source", help="source column")
+    parser.add_argument("--strand_column", help="strand column")
+    parser.add_argument("--strand_value", help="strand value")
+    # parser.add_argument('--frame', help='frame column')
+    parser.add_argument("-a", action="append", help="attribute column (-a k:v)")
+    args = parser.parse_args()
+
+    for rid, rec in tbl2gff3(**vars(args)).items():
+        GFF.write([rec], sys.stdout)