Python get_bed_from_GeneMark Examples

Example #1

def process_GeneMark( filename, org_num, refseq ):
    try:
        geneMark_bed = get_bed_from_GeneMark( filename, refseq )
    except Exception as e:
        print "Converting GeneMark to bed FAILED! For chrom:", refseq, "file:", filename, e
        geneMark_bed = []
    geneMark_bed_bed_file = open( os.path.join( os.path.split( filename )[0], "%s.GeneMark.bed" % refseq ), 'wb+' )
    geneMark_bed_bed_file.write( '\n'.join( geneMark_bed ) )
    geneMark_bed_bed_file.close()

Example #2

File: harvest_bacteria.py Project: AAFC-MBB/galaxy-1

def process_GeneMark( filename, org_num, refseq ):
    try:
        geneMark_bed = get_bed_from_GeneMark( filename, refseq )
    except Exception as e:
        print "Converting GeneMark to bed FAILED! For chrom:", refseq, "file:", filename, e
        geneMark_bed = []
    geneMark_bed_bed_file = open( os.path.join( os.path.split( filename )[0], "%s.GeneMark.bed" % refseq ), 'wb+' )
    geneMark_bed_bed_file.write( '\n'.join( geneMark_bed ) )
    geneMark_bed_bed_file.close()

Example #3

File: harvest_bacteria.py Project: kidaak/galaxy

def process_GeneMark( filename, org_num, refseq ):
    try:
        geneMark_bed = get_bed_from_GeneMark( filename, refseq )
    except Exception, e:
        print "Converting GeneMark to bed FAILED! For chrom:", refseq, "file:", filename, e
        geneMark_bed = []

Example #4

def process_GeneMark(filename, org_num, refseq):
    try:
        geneMark_bed = get_bed_from_GeneMark(filename, refseq)
    except Exception, e:
        print "Converting GeneMark to bed FAILED! For chrom:", refseq, "file:", filename, e
        geneMark_bed = []