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 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)
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 [
@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():