diff gff_to_prot.py @ 0:99810cf51f2e draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transit/ commit 73c6b2baf9dda26c6809a4f36582f7cbdb161ea1

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/gff_to_prot.py	Mon Apr 22 14:42:21 2019 -0400
@@ -0,0 +1,65 @@
+#!/usr/bin/env python
+import csv
+import os
+import sys
+
+
+def get_description(line, parent):
+    cols = line.split('\t')
+    labels = {}
+    for pair in cols[8].split(";"):
+        k, v = pair.split('=')
+        labels[k] = v
+
+    if (cols[2]) == "CDS" and labels["Parent"] == parent:
+        return labels.get("Note", '-')
+    return '-'
+
+
+def convert_to_prot_table(fname, output_name):
+    gff_file = open(fname)
+    output_file = open(output_name, 'w')
+    writer = csv.writer(output_file, delimiter='\t')
+    lines = gff_file.readlines()
+    gff_file.close()
+    for i, line in enumerate(lines):
+        line = line.strip()
+        if line.startswith('#'):
+            continue
+        cols = line.split('\t')
+        if (len(cols) < 9):
+            print("Ignoring invalid row with entries: {0}".format(cols))
+        elif (cols[2]) == "region":
+            continue
+        elif (cols[2]) == "CDS":
+            continue
+        elif (cols[2]) == "gene":
+            start = int(cols[3])
+            end = int(cols[4])
+            strand = cols[6].strip()
+            labels = {}
+            diff = int(abs(end - start) / 3)  # What is this called?
+            for pair in cols[8].split(";"):
+                k, v = pair.split('=')
+                labels[k.strip()] = v.strip()
+
+            Rv = labels["locus_tag"].strip()  # error out if not found
+            gene = labels.get('Name', '')
+            desc = get_description(lines[i + 1], labels.get("ID", "")) if (i + 1) < len(lines) else '-'
+            vals = [desc, start, end, strand, diff, '-', '-', gene, Rv, '-']
+            writer.writerow(vals)
+    output_file.close()
+
+
+if __name__ == "__main__":
+    usage_string = "Usage: python gff-prot-converter.py <gff filename> <output filename>"
+
+    if len(sys.argv) < 3:
+        print(usage_string)
+        sys.exit(0)
+    file_name = sys.argv[1]
+    if not os.path.exists(file_name):
+        print("File not found. Exiting...")
+        print(usage_string)
+        sys.exit(0)
+    convert_to_prot_table(file_name, sys.argv[2])