comparison gops_complement.py @ 3:e0a23ab32d7f draft

planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/complement commit a1517c9d22029095120643bbe2c8fa53754dd2b7

2:2221cf5f59aa

    -1, --cols1=N,N,N,N: Columns for chrom, start, end, strand in file
    -l, --lengths=N: Filename of .len file for species (chromosome lengths)
    -a, --all: Complement all chromosomes (Genome-wide complement)
"""

import sys, traceback, fileinput
from warnings import warn
from bx.intervals import *
from bx.intervals.io import *
from bx.intervals.operations.complement import complement
from bx.intervals.operations.subtract import subtract
from bx.cookbook import doc_optparse
from galaxy.tools.util.galaxyops import *

assert sys.version_info[:2] >= ( 2, 4 )

def main():
    allchroms = False
    upstream_pad = 0
    downstream_pad = 0

    options, args = doc_optparse.parse( __doc__ )
    try:
        chr_col_1, start_col_1, end_col_1, strand_col_1 = parse_cols_arg( options.cols1 )
        lengths = options.lengths
        if options.all: allchroms = True
        in_fname, out_fname = args
    except:
        doc_optparse.exception()

    g1 = NiceReaderWrapper( fileinput.FileInput( in_fname ),

    lens = dict()
    chroms = list()
    # dbfile is used to determine the length of each chromosome.  The lengths
    # are added to the lens dict and passed copmlement operation code in bx.
    dbfile = fileinput.FileInput( lengths )
    
    if dbfile:
        if not allchroms:
            try:
                for line in dbfile:
                    fields = line.split("\t")

        elif allchroms:
            try:
                for line in dbfile:
                    fields = line.split("\t")
                    end = int(fields[1])
                    chroms.append("\t".join([fields[0],"0",str(end)]))
            except:
                pass

    # Safety...if the dbfile didn't exist and we're on allchroms, then
    # default to generic complement

3:e0a23ab32d7f

    -1, --cols1=N,N,N,N: Columns for chrom, start, end, strand in file
    -l, --lengths=N: Filename of .len file for species (chromosome lengths)
    -a, --all: Complement all chromosomes (Genome-wide complement)
"""

import sys
import fileinput
from bx.intervals.io import GenomicInterval, GenomicIntervalReader, NiceReaderWrapper
from bx.intervals.operations.complement import complement
from bx.intervals.operations.subtract import subtract
from bx.cookbook import doc_optparse
from bx.tabular.io import ParseError
from galaxy.tools.util.galaxyops import fail, parse_cols_arg, skipped

assert sys.version_info[:2] >= ( 2, 4 )


def main():
    allchroms = False

    options, args = doc_optparse.parse( __doc__ )
    try:
        chr_col_1, start_col_1, end_col_1, strand_col_1 = parse_cols_arg( options.cols1 )
        lengths = options.lengths
        if options.all:
            allchroms = True
        in_fname, out_fname = args
    except:
        doc_optparse.exception()

    g1 = NiceReaderWrapper( fileinput.FileInput( in_fname ),

    lens = dict()
    chroms = list()
    # dbfile is used to determine the length of each chromosome.  The lengths
    # are added to the lens dict and passed copmlement operation code in bx.
    dbfile = fileinput.FileInput( lengths )

    if dbfile:
        if not allchroms:
            try:
                for line in dbfile:
                    fields = line.split("\t")

        elif allchroms:
            try:
                for line in dbfile:
                    fields = line.split("\t")
                    end = int(fields[1])
                    chroms.append("\t".join([fields[0], "0", str(end)]))
            except:
                pass

    # Safety...if the dbfile didn't exist and we're on allchroms, then
    # default to generic complement