diff convert_mga.py @ 0:b04960a7abf5 draft

planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/metagene_annotator commit 6d8b6e0fa2f1b47b337dbf21f5bc320586ccbd4c

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/convert_mga.py	Wed Mar 21 17:15:25 2018 -0400
@@ -0,0 +1,91 @@
+#!/usr/bin/env python
+
+from __future__ import print_function
+
+import argparse
+import math
+import re
+import sys
+
+
+def __main__():
+    parser = argparse.ArgumentParser(
+        description='Convert mga output to bed and tsv')
+    parser.add_argument(
+        'input_mga',
+        help="mga output to convert,  '-' for stdin")
+    parser.add_argument(
+        '-t', '--tsv', default=None,
+        help='Path to output mga.tsv')
+    parser.add_argument(
+        '-b', '--bed', default=None,
+        help='Path to output mga.bed')
+    parser.add_argument('-v', '--verbose', action='store_true', help='Verbose')
+    args = parser.parse_args()
+
+    input_rdr = open(args.input_mga, 'r')\
+        if args.input_mga != '-' else sys.stdin
+
+    bed_wtr = open(args.bed, 'w') if args.bed is not None else None
+    tsv_wtr = open(args.tsv, 'w') if args.bed is not None else None
+    if tsv_wtr:
+        tsv_wtr.write('#%s\n' % '\t'.join([
+            'seq_id', 'seq_model', 'seq_gc', 'seq_rbs',
+            'gene ID', 'start pos', 'end pos', 'strand', 'frame',
+            'complete/partial', 'gene score', 'used model',
+            'rbs start', 'rbs end', 'rbs score']))
+
+    gc_rbs_pat = '# gc = (-?[0-9]*[.]?[0-9]+), rbs = (-?[0-9]*[.]?[0-9]+)' 
+    seq_count = 0
+    gene_count = 0
+    for i, line in enumerate(input_rdr):
+        # 1317/1
+        # gc = 0.272955, rbs = -1
+        # self: -
+        if line.startswith('# gc'):
+            try:
+                m = re.match(gc_rbs_pat, line.strip())
+                seq_gc, seq_rbs = m.groups()
+            except:
+                seq_gc = seq_rbs = ''
+        elif line.startswith('# self:'):
+            seq_type = re.sub('# self:', '', line.rstrip())
+        elif line.startswith('# '):
+            seq_name = re.sub('# (\S+).*$', '\\1', line.rstrip())
+            seq_count += 1
+        else:
+            fields = line.split('\t')
+            if len(fields) == 11:
+                gene_count += 1
+                start = int(fields[1]) - 1
+                end = int(fields[2])
+                if tsv_wtr:
+                    tsv_wtr.write('%s\t%s\t%s\t%s\t%s' % (
+                        seq_name,
+                        seq_type,
+                        seq_gc,
+                        seq_rbs,
+                        line))
+                if bed_wtr:
+                    bed_wtr.write(
+                        '%s\t%d\t%d\t%s\t%s\t%s\t%d\t%d\t%s\t%s\t%s\t%s\n' % (
+                            seq_name,
+                            start,
+                            end,
+                            '%s:%s' % (seq_name, fields[0]),
+                            int(math.ceil(float(fields[6]))),
+                            fields[3],
+                            start,
+                            end,
+                            0,
+                            1,
+                            abs(end - start),
+                            0))
+
+    if args.verbose:
+        print("sequences: %d\tgenes: %d"
+              % (seq_count, gene_count), file=sys.stdout)
+
+
+if __name__ == "__main__":
+    __main__()