comparison extract_genomic_dna_utils.py @ 2:702970e4a134 draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/extract_genomic_dna commit 9192c1e90e2fd5017e6044884bcc6f2e80ba8b31

1:9af3f57e50b9

        return seq_path
    except Exception, e:
        stop_err('Error running faToTwoBit. ' + str(e))


def get_lines(feature):
    # Get feature's line(s).
    if isinstance(feature, GFFFeature):
        return feature.lines()
    else:

2:702970e4a134

        return seq_path
    except Exception, e:
        stop_err('Error running faToTwoBit. ' + str(e))


def get_bedtools_getfasta_default_header(chrom, start, end, strand, includes_strand_col):
    """
    Return a fasta header that is the default produced by the bedtools
    getfasta tool, assuming "force strandedness".  This will produce a
    header with this format: <chrom>:<start>-<end>(strand).  If the input
    data includes a strand column and the strand is '+' or '-', then use it.
    If the input data includes a strand column and the value of strand is
    anything but '+' or '-', set strand to '.' in the header.  If the input
    data does not include a strand column, set strand to '.' in the header.
    """
    if includes_strand_col and strand in ['+', '-']:
        strand_val = strand
    else:
        strand_val = '.'
    return '%s:%s-%s(%s)' % (chrom, start, end, strand_val)


def get_fasta_header_delimiter(delimiter):
    # Return a specified fasta header delimiter.
    if delimiter == 'underscore':
        return '_'
    if delimiter == 'semicolon':
        return ';'
    if delimiter == 'comma':
        return ','
    if delimiter == 'tilde':
        return '~'
    if delimiter == 'vertical_bar':
        return '|'
    # Set the default to underscore.
    return '_'


def get_lines(feature):
    # Get feature's line(s).
    if isinstance(feature, GFFFeature):
        return feature.lines()
    else: