Python get_bed_from_GeneMarkHMM Examples

Example #1

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

Example #2

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

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

Example #3

File: harvest_bacteria.py Project: kidaak/galaxy

def process_GeneMarkHMM( filename, org_num, refseq ):
    try:
        geneMarkHMM_bed = get_bed_from_GeneMarkHMM( filename, refseq )
    except Exception, e:
        print "Converting GeneMarkHMM to bed FAILED! For chrom:", refseq, "file:", filename, e
        geneMarkHMM_bed = []

Example #4

def process_GeneMarkHMM(filename, org_num, refseq):
    try:
        geneMarkHMM_bed = get_bed_from_GeneMarkHMM(filename, refseq)
    except Exception, e:
        print "Converting GeneMarkHMM to bed FAILED! For chrom:", refseq, "file:", filename, e
        geneMarkHMM_bed = []