Python get_kallisto_fusions Examples

Example #1

File: pizzly.py Project: biocyberman/bcbio-nextgen

def run_pizzly(data):
    work_dir = dd.get_work_dir(data)
    pizzlydir = os.path.join(work_dir, "pizzly")
    samplename = dd.get_sample_name(data)
    gtf = dd.get_gtf_file(data)
    if dd.get_transcriptome_fasta(data):
        gtf_fa = dd.get_transcriptome_fasta(data)
    else:
        gtf_fa = sailfish.create_combined_fasta(data)
    fraglength = get_fragment_length(data)
    cachefile = os.path.join(pizzlydir, "pizzly.cache")
    fusions = kallisto.get_kallisto_fusions(data)
    pizzlypath = config_utils.get_program("pizzly", dd.get_config(data))
    outdir = pizzly(pizzlypath, gtf, gtf_fa, fraglength, cachefile, pizzlydir,
                    fusions, samplename, data)
    return outdir

Example #2

def run_pizzly(data):
    work_dir = dd.get_work_dir(data)
    pizzlydir = os.path.join(work_dir, "pizzly")
    samplename = dd.get_sample_name(data)
    gtf = dd.get_gtf_file(data)
    if dd.get_transcriptome_fasta(data):
        gtf_fa = dd.get_transcriptome_fasta(data)
    else:
        gtf_fa = sailfish.create_combined_fasta(data)
    fraglength = get_fragment_length(data)
    cachefile = os.path.join(pizzlydir, "pizzly.cache")
    fusions = kallisto.get_kallisto_fusions(data)
    pizzlypath = config_utils.get_program("pizzly", dd.get_config(data))
    outdir = pizzly(pizzlypath, gtf, gtf_fa, fraglength, cachefile, pizzlydir,
                    fusions, samplename, data)
    return outdir

Example #3

File: pizzly.py Project: chapmanb/bcbio-nextgen

def run_pizzly(data):
    samplename = dd.get_sample_name(data)
    work_dir = dd.get_work_dir(data)
    pizzlydir = os.path.join(work_dir, "pizzly")
    gtf = dd.get_transcriptome_gtf(data)
    if not gtf:
        gtf = dd.get_gtf_file(data)
    if dd.get_transcriptome_fasta(data):
        gtf_fa = dd.get_transcriptome_fasta(data)
    else:
        gtf_fa = sailfish.create_combined_fasta(data)
    stripped_fa = os.path.splitext(os.path.basename(gtf_fa))[0] + "-noversions.fa"
    stripped_fa = os.path.join(pizzlydir, stripped_fa)
    gtf_fa = fasta.strip_transcript_versions(gtf_fa, stripped_fa)
    fraglength = get_fragment_length(data)
    cachefile = os.path.join(pizzlydir, "pizzly.cache")
    fusions = kallisto.get_kallisto_fusions(data)
    pizzlypath = config_utils.get_program("pizzly", dd.get_config(data))
    outdir = pizzly(pizzlypath, gtf, gtf_fa, fraglength, cachefile, pizzlydir,
                    fusions, samplename, data)
    return outdir

Example #4

File: pizzly.py Project: limbus-medtec/bcbio-nextgen-1

def run_pizzly(data):
    samplename = dd.get_sample_name(data)
    work_dir = dd.get_work_dir(data)
    pizzlydir = os.path.join(work_dir, "pizzly")
    gtf = dd.get_transcriptome_gtf(data)
    if not gtf:
        gtf = dd.get_gtf_file(data)
    if dd.get_transcriptome_fasta(data):
        gtf_fa = dd.get_transcriptome_fasta(data)
    else:
        gtf_fa = sailfish.create_combined_fasta(data)
    stripped_fa = os.path.splitext(
        os.path.basename(gtf_fa))[0] + "-noversions.fa"
    stripped_fa = os.path.join(pizzlydir, stripped_fa)
    gtf_fa = fasta.strip_transcript_versions(gtf_fa, stripped_fa)
    fraglength = get_fragment_length(data)
    cachefile = os.path.join(pizzlydir, "pizzly.cache")
    fusions = kallisto.get_kallisto_fusions(data)
    pizzlypath = config_utils.get_program("pizzly", dd.get_config(data))
    outdir = pizzly(pizzlypath, gtf, gtf_fa, fraglength, cachefile, pizzlydir,
                    fusions, samplename, data)
    return outdir