changeset 1:da1ac511a473 draft

planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/metagene_annotator commit 4765a3ed5db56cfc7e743148ab9d1ea190c2486f-dirty

--- a/convert_mga.py	Fri Mar 16 12:13:43 2018 -0400
+++ b/convert_mga.py	Mon Mar 19 20:47:09 2018 -0400
@@ -7,11 +7,12 @@
 import re
 import sys
 
+
 def __main__():
     parser = argparse.ArgumentParser(
         description='Convert mga output to bed and tsv')
     parser.add_argument(
-        'input_mga', 
+        'input_mga',
         help="mga output to convert,  '-' for stdin")
     parser.add_argument(
         '-t', '--tsv', default=None,
@@ -29,9 +30,9 @@
     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', 
+            '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']))
 
     seq_count = 0
@@ -42,14 +43,16 @@
         # self: -
         if line.startswith('# gc'):
             try:
-                m = re.match('# gc = (-?[0-9]*[.]?[0-9]+), rbs = (-?[0-9]*[.]?[0-9]+)',line.strip())
-                seq_gc,seq_rbs = m.groups()
+                m = re.match('# gc = (-?[0-9]*[.]?[0-9]+)',
+                             'rbs = (-?[0-9]*[.]?[0-9]+)',
+                             line.strip())
+                seq_gc, seq_rbs = m.groups()
             except:
                 seq_gc = seq_rbs = ''
         elif line.startswith('# self:'):
-            seq_type = re.sub('# self:','',line.rstrip())
+            seq_type = re.sub('# self:', '', line.rstrip())
         elif line.startswith('# '):
-            seq_name = re.sub('# (\S+).*$','\\1',line.rstrip())
+            seq_name = re.sub('# (\S+).*$', '\\1', line.rstrip())
             seq_count += 1
         else:
             fields = line.split('\t')
@@ -65,25 +68,24 @@
                         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))
+                    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)
-
-        
+              % (seq_count, gene_count), file=sys.stdout)
 
 
 if __name__ == "__main__":

--- a/metagene_annotator.xml	Fri Mar 16 12:13:43 2018 -0400
+++ b/metagene_annotator.xml	Mon Mar 19 20:47:09 2018 -0400
@@ -2,6 +2,7 @@
     <description>gene-finding program for prokaryote and phage</description>
     <requirements>
         <requirement type="package">metagene_annotator</requirement>
+        <requirement type="package">python</requirement>
     </requirements>
     <command detect_errors="exit_code"><![CDATA[
         mga $input $multiple_species > mga_output