comparison extract_genomic_dna_utils.py @ 7:3088e7e70888 draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/extract_genomic_dna commit 4a3c9f195ba5d899b1a1ce5e80281cdf230f456a

6:53db9cb721f1

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

        for interval in self.intervals:
            lines.append('\t'.join(interval.fields))
        return lines


class GFFReaderWrapper(NiceReaderWrapper):
    """
    Reader wrapper for GFF files which has two major functions:
    1. group entries for GFF file (via group column), GFF3 (via id attribute),
       or GTF (via gene_id/transcript id);
    2. convert coordinates from GFF format--starting and ending coordinates

        interval = GFFInterval(self, line.split("\t"), self.chrom_col, self.feature_col, self.start_col,
                               self.end_col, self.strand_col, self.score_col, self.default_strand,
                               fix_strand=self.fix_strand)
        return interval

    def next(self):
        """
        Returns next GFFFeature.
        """

        def handle_parse_error(parse_error):
            """
            Actions to take when ParseError found.
            """
            if self.outstream:
                if self.print_delegate and hasattr(self.print_delegate, "__call__"):

    if cols:
        # Handle case where no strand column included - in this case, cols
        # looks something like 1,2,3,
        if cols.endswith(','):
            cols += '0'
        col_list = map(lambda x: int(x) - 1, cols.split(","))
        return col_list
    else:
        return BED_DEFAULT_COLS

7:3088e7e70888

import sys
import tempfile

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

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

        for interval in self.intervals:
            lines.append('\t'.join(interval.fields))
        return lines


class GFFReaderWrapper(Iterator, NiceReaderWrapper):
    """
    Reader wrapper for GFF files which has two major functions:
    1. group entries for GFF file (via group column), GFF3 (via id attribute),
       or GTF (via gene_id/transcript id);
    2. convert coordinates from GFF format--starting and ending coordinates

        interval = GFFInterval(self, line.split("\t"), self.chrom_col, self.feature_col, self.start_col,
                               self.end_col, self.strand_col, self.score_col, self.default_strand,
                               fix_strand=self.fix_strand)
        return interval

    def __next__(self):
        """
        Returns next GFFFeature.
        """

        def handle_parse_error(e):
            """
            Actions to take when ParseError found.
            """
            if self.outstream:
                if self.print_delegate and hasattr(self.print_delegate, "__call__"):

    if cols:
        # Handle case where no strand column included - in this case, cols
        # looks something like 1,2,3,
        if cols.endswith(','):
            cols += '0'
        col_list = [int(x) - 1 for x in cols.split(",")]
        return col_list
    else:
        return BED_DEFAULT_COLS