| Previous changeset 2:702970e4a134 (2016-03-09) Next changeset 4:4822a36300fd (2017-01-13) |
|
Commit message:
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/extract_genomic_dna commit bd4fbe120288bf8452e479cbd82aa1bbf5c4bd31 |
|
modified:
extract_genomic_dna.py extract_genomic_dna_utils.py tool_data_table_conf.xml.sample |
|
added:
extract_genomic_dna_utils.pyc |
| b |
| 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: |
| b |
| 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 |
| b |
| @@ -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)) |
| b |
| diff -r 702970e4a134 -r b71579ad576c extract_genomic_dna_utils.pyc |
| b |
| Binary file extract_genomic_dna_utils.pyc has changed |
| b |
| 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 |
| b |
| @@ -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> |