# HG changeset patch
# User iuc
# Date 1508779578 14400
# Node ID 3088e7e70888d09b70cb23683dccb34b3fa2124c
# Parent 53db9cb721f18ccca982dc8b180413d39aee53cf
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/extract_genomic_dna commit 4a3c9f195ba5d899b1a1ce5e80281cdf230f456a
diff -r 53db9cb721f1 -r 3088e7e70888 extract_genomic_dna.py
--- a/extract_genomic_dna.py Mon Jul 03 07:19:41 2017 -0400
+++ b/extract_genomic_dna.py Mon Oct 23 13:26:18 2017 -0400
@@ -1,4 +1,6 @@
#!/usr/bin/env python
+from __future__ import print_function
+
import argparse
import os
@@ -81,7 +83,7 @@
start, end = egdu.convert_gff_coords_to_bed([start, end])
if includes_strand_col:
strand = fields[strand_col]
- except:
+ except Exception:
warning = "Invalid chrom, start or end column values. "
warnings.append(warning)
if not invalid_lines:
@@ -129,7 +131,7 @@
sequence += twobitfile[interval.chrom][interval.start:interval.end]
else:
sequence = twobitfile[chrom][start:end]
- except:
+ except Exception:
warning = "Unable to fetch the sequence from '%d' to '%d' for chrom '%s'. " % (start, end - start, chrom)
warnings.append(warning)
if not invalid_lines:
@@ -156,8 +158,6 @@
if includes_strand_col and strand == "-":
sequence = egdu.reverse_complement(sequence)
if args.output_format == "fasta":
- l = len(sequence)
- c = 0
if input_is_gff:
start, end = egdu.convert_bed_coords_to_gff([start, end])
if args.fasta_header_type == "bedtools_getfasta_default":
@@ -175,8 +175,10 @@
out.write(">%s %s\n" % (meta_data, name))
else:
out.write(">%s\n" % meta_data)
- while c < l:
- b = min(c + 50, l)
+ c = 0
+ sequence_length = len(sequence)
+ while c < sequence_length:
+ b = min(c + 50, sequence_length)
out.write("%s\n" % str(sequence[c:b]))
c = b
else:
@@ -209,10 +211,10 @@
if warnings:
warn_msg = "%d warnings, 1st is: " % len(warnings)
warn_msg += warnings[0]
- print warn_msg
+ print(warn_msg)
if skipped_lines:
# Error message includes up to the first 10 skipped lines.
- print 'Skipped %d invalid lines, 1st is #%d, "%s"' % (skipped_lines, first_invalid_line, '\n'.join(invalid_lines[:10]))
+ print('Skipped %d invalid lines, 1st is #%d, "%s"' % (skipped_lines, first_invalid_line, '\n'.join(invalid_lines[:10])))
if args.reference_genome_source == "history":
os.remove(seq_path)
diff -r 53db9cb721f1 -r 3088e7e70888 extract_genomic_dna.xml
--- a/extract_genomic_dna.xml Mon Jul 03 07:19:41 2017 -0400
+++ b/extract_genomic_dna.xml Mon Oct 23 13:26:18 2017 -0400
@@ -2,6 +2,7 @@
using coordinates from assembled/unassembled genomes
bx-python
+ six
ucsc-fatotwobit