comparison gops_join.py @ 3:860e7e4899b1 draft

planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734

2:83c18f310619

    -1, --cols1=N,N,N,N: Columns for start, end, strand in first file
    -2, --cols2=N,N,N,N: Columns for start, end, strand in second file
    -m, --mincols=N: Require this much overlap (default 1bp)
    -f, --fill=N: none, right, left, both
"""
import sys, traceback, fileinput
from warnings import warn
from bx.intervals import *
from bx.intervals.io import *
from bx.intervals.operations.join import *
from bx.cookbook import doc_optparse
from galaxy.tools.util.galaxyops import *

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

def main():
    mincols = 1
    upstream_pad = 0
    downstream_pad = 0
    leftfill = False
    rightfill = 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 )
        chr_col_2, start_col_2, end_col_2, strand_col_2 = parse_cols_arg( options.cols2 )      
        if options.mincols: mincols = int( options.mincols )
        if options.fill:
            if options.fill == "both":
                rightfill = leftfill = True
            else:
                rightfill = options.fill == "right"

3:860e7e4899b1

    -1, --cols1=N,N,N,N: Columns for start, end, strand in first file
    -2, --cols2=N,N,N,N: Columns for start, end, strand in second file
    -m, --mincols=N: Require this much overlap (default 1bp)
    -f, --fill=N: none, right, left, both
"""
import fileinput
import sys
from bx.intervals.io import NiceReaderWrapper
from bx.intervals.operations.join import join
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():
    mincols = 1
    leftfill = False
    rightfill = 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 )
        chr_col_2, start_col_2, end_col_2, strand_col_2 = parse_cols_arg( options.cols2 )
        if options.mincols:
            mincols = int( options.mincols )
        if options.fill:
            if options.fill == "both":
                rightfill = leftfill = True
            else:
                rightfill = options.fill == "right"