def runSalmonAddModels(infiles, outfiles):
'''
Computes read counts across transcripts and genes based on a fastq
file and an indexed transcriptome using Salmon.
Runs the salmon "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.SalmonQuantifier(
infile=fastqfile,
transcript_outfile=transcript_outfile,
gene_outfile=gene_outfile,
annotations=index,
job_threads=PARAMS["alignment_free_threads"],
job_memory=PARAMS["salmon_memory"],
options=PARAMS["salmon_options"],
bootstrap=PARAMS["alignment_free_bootstrap"],
libtype=PARAMS['salmon_libtype'],
kmer=PARAMS['alignment_free_kmer'],
transcript2geneMap=transcript2geneMap)
Quantifier.run_all()
def runSalmon(infiles, outfiles):
'''
Computes read counts across transcripts and genes based on a fastq
file and an indexed transcriptome using Salmon.
Runs the salmon "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 - list of strings - paths to fastq files to merge then quantify
across using sailfish
1 - string - path to sailfish index file
2 - string - path to table mapping transcripts to genes
salmon_threads: int
:term: `PARAMS` the number of threads for salmon
salmon_memory: str
:term: `PARAMS` the job memory for salmon
salmon_options: str
:term: `PARAMS` string to append to the salmon quant command to
provide specific
options, see http://sailfish.readthedocs.io/en/master/salmon.html
salmon_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.
salmon_libtype: str
:term: `PARAMS` salmon library type
as for sailfish - use
http://sailfish.readthedocs.io/en/master/library_type.html#fraglibtype
outfiles: list
paths to output files for transcripts and genes
'''
fastqfile, index, transcript2geneMap = infiles
transcript_outfile, gene_outfile = outfiles
Quantifier = PipelineRnaseq.SalmonQuantifier(
infile=fastqfile,
transcript_outfile=transcript_outfile,
gene_outfile=gene_outfile,
annotations=index,
job_threads=PARAMS["alignment_free_threads"],
job_memory=PARAMS["salmon_memory"],
options=PARAMS["salmon_options"],
bootstrap=PARAMS["alignment_free_bootstrap"],
libtype=PARAMS['salmon_libtype'],
kmer=PARAMS['alignment_free_kmer'],
transcript2geneMap=transcript2geneMap)
Quantifier.run_all()
