Ejemplos de Paths.cds_read_count_table en Python

Ejemplo n.º 1

Archivo: RPFStatistics.py Proyecto: hyeshik/nrclip

def summarize_rpf_counts(inputfiles, outputfile):
    filemapping = ' '.join('%s:%s' % (s, Paths.cds_read_count_table(s))
                           for s in Options.SHORTTAG_SAMPLES)
    pairs = ' '.join('%s:%s:%s' % (grpname, polya, rpf)
                     for grpname, (rpf, polya) in Options.RPF_PAIRS)

    runproc("""
        $SUMMARIZE_RPF_COUNTS "$filemapping" "$pairs" > $outputfile""",
        outputfile)

Ejemplo n.º 2

def summarize_rpf_counts(inputfiles, outputfile):
    filemapping = ' '.join('%s:%s' % (s, Paths.cds_read_count_table(s))
                           for s in Options.SHORTTAG_SAMPLES)
    pairs = ' '.join('%s:%s:%s' % (grpname, polya, rpf)
                     for grpname, (rpf, polya) in Options.RPF_PAIRS)

    runproc(
        """
        $SUMMARIZE_RPF_COUNTS "$filemapping" "$pairs" > $outputfile""",
        outputfile)

Ejemplo n.º 3

Archivo: RPFStatistics.py Proyecto: hyeshik/nrclip

from rnarry.nrclip.PipelineControl import *


@files(for_each([Paths.nr_refseq_db, Paths.tspace_read_database],
                Paths.cds_read_count_table,
                Options.SHORTTAG_SAMPLES))
@follows(DataPreparation.build_nonredundant_refseq_database)
@follows(TranscriptomeAnalysis.build_tspace_read_database)
def count_cds_reads(inputfiles, outputfile, sample):
    nr_refseq_db, tspace = inputfiles

    runproc("""
        $TSPACE_COUNT_CDS $nr_refseq_db $tspace > $outputfile""", outputfile)


@files([Paths.cds_read_count_table(s) for s in Options.SHORTTAG_SAMPLES],
       Paths.rpf_summarized_table)
@follows(count_cds_reads)
def summarize_rpf_counts(inputfiles, outputfile):
    filemapping = ' '.join('%s:%s' % (s, Paths.cds_read_count_table(s))
                           for s in Options.SHORTTAG_SAMPLES)
    pairs = ' '.join('%s:%s:%s' % (grpname, polya, rpf)
                     for grpname, (rpf, polya) in Options.RPF_PAIRS)

    runproc("""
        $SUMMARIZE_RPF_COUNTS "$filemapping" "$pairs" > $outputfile""",
        outputfile)


def tasks():
    return [

Ejemplo n.º 4

@files(
    for_each([Paths.nr_refseq_db, Paths.tspace_read_database],
             Paths.cds_read_count_table, Options.SHORTTAG_SAMPLES))
@follows(DataPreparation.build_nonredundant_refseq_database)
@follows(TranscriptomeAnalysis.build_tspace_read_database)
def count_cds_reads(inputfiles, outputfile, sample):
    nr_refseq_db, tspace = inputfiles

    runproc(
        """
        $TSPACE_COUNT_CDS $nr_refseq_db $tspace > $outputfile""", outputfile)


@files([Paths.cds_read_count_table(s) for s in Options.SHORTTAG_SAMPLES],
       Paths.rpf_summarized_table)
@follows(count_cds_reads)
def summarize_rpf_counts(inputfiles, outputfile):
    filemapping = ' '.join('%s:%s' % (s, Paths.cds_read_count_table(s))
                           for s in Options.SHORTTAG_SAMPLES)
    pairs = ' '.join('%s:%s:%s' % (grpname, polya, rpf)
                     for grpname, (rpf, polya) in Options.RPF_PAIRS)

    runproc(
        """
        $SUMMARIZE_RPF_COUNTS "$filemapping" "$pairs" > $outputfile""",
        outputfile)


def tasks():