def runKallistoAddModels(infiles, outfiles): ''' Computes read counts across transcripts and genes based on a fastq file and an indexed transcriptome using Kallisto. Runs the kallisto "quant" function across transcripts with the specified options. Read counts across genes are counted as the total in all transcripts of that gene (based on the getTranscript2GeneMap table) ''' infiles, transcript2geneMap = infiles index, fastqfile = infiles transcript_outfile, gene_outfile = outfiles Quantifier = PipelineRnaseq.KallistoQuantifier( infile=fastqfile, transcript_outfile=transcript_outfile, gene_outfile=gene_outfile, annotations=index, job_threads=PARAMS["alignment_free_threads"], job_memory=PARAMS["kallisto_memory"], options=PARAMS["kallisto_options"], bootstrap=PARAMS["alignment_free_bootstrap"], fragment_length=PARAMS["kallisto_fragment_length"], fragment_sd=PARAMS["kallisto_fragment_sd"], transcript2geneMap=transcript2geneMap) Quantifier.run_all()
def runKallisto(infiles, outfiles): ''' Computes read counts across transcripts and genes based on a fastq file and an indexed transcriptome using Kallisto. Runs the kallisto "quant" function across transcripts with the specified options. Read counts across genes are counted as the total in all transcripts of that gene (based on the getTranscript2GeneMap table) Parameters ---------- infiles: list list with three components 0 - string - path to fastq file to quantify using Kallisto 1 - string - path to Kallisto index file 2 - string - path totable mapping transcripts to genes kallisto_threads: int :term: `PARAMS` the number of threads for Kallisto kallisto_memory: str :term: `PARAMS` the job memory for Kallisto kallisto_options: str :term: `PARAMS` string to append to the Kallisto quant command to provide specific options, see https://pachterlab.github.io/kallisto/manual kallisto_bootstrap: int :term: `PARAMS` number of bootstrap samples to run. Note, you need to bootstrap for differential expression with sleuth if there are no technical replicates. If you only need point estimates, set to 1. Note that bootstrap must be set to at least 1 kallisto_fragment_length: int :term: `PARAMS` Fragment length for Kallisto, required for single end reads only kallisto_fragment_sd: int :term: `PARAMS` Fragment length standard deviation for Kallisto, required for single end reads only. outfiles: list paths to output files for transcripts and genes ''' fastqfile, index, transcript2geneMap = infiles transcript_outfile, gene_outfile = outfiles Quantifier = PipelineRnaseq.KallistoQuantifier( infile=fastqfile, transcript_outfile=transcript_outfile, gene_outfile=gene_outfile, annotations=index, job_threads=PARAMS["alignment_free_threads"], job_memory=PARAMS["kallisto_memory"], options=PARAMS["kallisto_options"], bootstrap=PARAMS["alignment_free_bootstrap"], fragment_length=PARAMS["kallisto_fragment_length"], fragment_sd=PARAMS["kallisto_fragment_sd"], transcript2geneMap=transcript2geneMap) Quantifier.run_all()