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()