comparison extract_genomic_dna_utils.py @ 3:b71579ad576c draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/extract_genomic_dna commit bd4fbe120288bf8452e479cbd82aa1bbf5c4bd31

2:702970e4a134

import os
import subprocess
import sys
import tempfile

from bx.intervals.io import Comment, Header, GenomicInterval
from bx.intervals.io import GenomicIntervalReader, NiceReaderWrapper, ParseError

# Default chrom, start, end, strand cols for a bed file
BED_DEFAULT_COLS = 0, 1, 2, 5

                pass
            tmp_stderr.close()
            os.remove(tmp_name)
            stop_err(stderr)
        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):
    """

3:b71579ad576c

import os
import subprocess
import sys
import tempfile

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
BED_DEFAULT_COLS = 0, 1, 2, 5

                pass
            tmp_stderr.close()
            os.remove(tmp_name)
            stop_err(stderr)
        return seq_path
    except Exception as e:
        stop_err('Error running faToTwoBit. ' + str(e))


def get_bedtools_getfasta_default_header(chrom, start, end, strand, includes_strand_col):
    """