Python convert_to_kallisto示例

示例#1

文件： kallisto.py 项目： skanwal/bcbio-nextgen

def kallisto_singlecell(fq1, kallisto_dir, gtf_file, fasta_file, data):
    samplename = dd.get_sample_name(data)
    quant_dir = os.path.join(kallisto_dir, "quant")
    safe_makedir(kallisto_dir)
    num_cores = dd.get_num_cores(data)
    strandedness = dd.get_strandedness(data).lower()
    kallisto = config_utils.get_program("kallisto", dd.get_config(data))
    # unsure how to estimate from single end data, so go with a reasonable default
    frag_length = 250
    batch_file = umi.convert_to_kallisto(data)
    index = kallisto_index(gtf_file, fasta_file, data, kallisto_dir)
    cmd = ("{kallisto} pseudo --umi "
           "-t {num_cores} -o {tx_out_dir} -b {batch_file} -i {index}")
    with chdir(os.path.dirname(batch_file)):
        with file_transaction(data, quant_dir) as tx_out_dir:
            message = ("Quantifying transcripts with Kallisto.")
            do.run(cmd.format(**locals()), message, None)
    kallisto_table(kallisto_dir, index)
    return quant_dir

示例#2

文件： kallisto.py 项目： biocyberman/bcbio-nextgen

def kallisto_singlecell(fq1, kallisto_dir, gtf_file, fasta_file, data):
    samplename = dd.get_sample_name(data)
    quant_dir = os.path.join(kallisto_dir, "quant")
    safe_makedir(kallisto_dir)
    num_cores = dd.get_num_cores(data)
    strandedness = dd.get_strandedness(data).lower()
    kallisto = config_utils.get_program("kallisto", dd.get_config(data))
    # unsure how to estimate from single end data, so go with a reasonable default
    frag_length = 250
    batch_file = umi.convert_to_kallisto(data)
    index = kallisto_index(gtf_file, fasta_file, data, kallisto_dir)
    cmd = ("{kallisto} pseudo --umi "
           "-t {num_cores} -o {tx_out_dir} -b {batch_file} -i {index}")
    with chdir(os.path.dirname(batch_file)):
        with file_transaction(data, quant_dir) as tx_out_dir:
            message = ("Quantifying transcripts with Kallisto.")
            do.run(cmd.format(**locals()), message, None)
    kallisto_table(kallisto_dir, index)
    return quant_dir