# HG changeset patch
# User iuc
# Date 1482166657 18000
# Node ID b71579ad576c5bb4ef023aa222dd845d9f5b1d52
# Parent  702970e4a134ad829d57f90e5d8a67ddc4b5b7f4
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/extract_genomic_dna commit bd4fbe120288bf8452e479cbd82aa1bbf5c4bd31

diff -r 702970e4a134 -r b71579ad576c extract_genomic_dna.py
--- a/extract_genomic_dna.py	Wed Mar 09 05:07:21 2016 -0500
+++ b/extract_genomic_dna.py	Mon Dec 19 11:57:37 2016 -0500
@@ -2,11 +2,11 @@
 import argparse
 import os
 
-import extract_genomic_dna_utils as egdu
 import bx.seq.nib
 import bx.seq.twobit
-from bx.intervals.io import Header, Comment
+from bx.intervals.io import Comment, Header
 
+import extract_genomic_dna_utils as egdu
 
 parser = argparse.ArgumentParser()
 parser.add_argument('--input_format', dest='input_format', help="Input dataset format")
@@ -110,7 +110,7 @@
             nibs[chrom] = nib = bx.seq.nib.NibFile(open("%s/%s.nib" % (seq_path, chrom)))
         try:
             sequence = nib.get(start, end - start)
-        except Exception, e:
+        except Exception as e:
             warning = "Unable to fetch the sequence from '%d' to '%d' for build '%s'. " % (start, end - start, args.genome)
             warnings.append(warning)
             if not invalid_lines:
diff -r 702970e4a134 -r b71579ad576c extract_genomic_dna_utils.py
--- a/extract_genomic_dna_utils.py	Wed Mar 09 05:07:21 2016 -0500
+++ b/extract_genomic_dna_utils.py	Mon Dec 19 11:57:37 2016 -0500
@@ -4,7 +4,7 @@
 import sys
 import tempfile
 
-from bx.intervals.io import Comment, Header, GenomicInterval
+from bx.intervals.io import Comment, GenomicInterval, Header
 from bx.intervals.io import GenomicIntervalReader, NiceReaderWrapper, ParseError
 
 # Default chrom, start, end, strand cols for a bed file
@@ -288,7 +288,7 @@
             os.remove(tmp_name)
             stop_err(stderr)
         return seq_path
-    except Exception, e:
+    except Exception as e:
         stop_err('Error running faToTwoBit. ' + str(e))
 
 
diff -r 702970e4a134 -r b71579ad576c extract_genomic_dna_utils.pyc
Binary file extract_genomic_dna_utils.pyc has changed
diff -r 702970e4a134 -r b71579ad576c tool_data_table_conf.xml.sample
--- a/tool_data_table_conf.xml.sample	Wed Mar 09 05:07:21 2016 -0500
+++ b/tool_data_table_conf.xml.sample	Mon Dec 19 11:57:37 2016 -0500
@@ -1,5 +1,5 @@
 <tables>
-    <table name="twobit" comment_char="#">
+    <table name="twobit" comment_char="#" allow_duplicate_entries="False">
         <columns>dbkey, value</columns>
         <file path="tool-data/twobit.loc" />
     </table>