@files([Paths.nr_refseq_list] +
[Paths.genomespace_refseq_counts(sample)
for sample in Paths.ALL_SAMPLES],
Paths.genomespace_all_expressed_transcripts)
@follows(quantitate_refseq_in_gspace)
def make_list_of_expressed_transcripts(inputfiles, outputfile):
inputlist = ' '.join(inputfiles)
runproc("""
$ENV MINDEPTH=$GSPACE_STATS_MINIMUM_RAW_READS \
$REFSEQCNT_PICK_EXPRESSED $inputlist > $outputfile""", outputfile)
@files([Paths.nr_refseq_db, Paths.genomespace_all_expressed_transcripts,
Paths.genome_fasta,
Paths.genomespace_read_database(Options.SNPREF_SAMPLE)],
[Paths.reftranscriptome_sequences, Paths.reftranscriptome_cds_anno])
@follows(make_list_of_expressed_transcripts)
def generate_SNPfixed_transcriptome(inputfiles, outputfiles):
nrdb, expressed, genomeseq, gspace = inputfiles
outseq, outanno = outputfiles
runproc("""
$GENFASTA_MUTATED_TRANSCRIPTOME $nrdb $expressed $genomeseq $gspace \
$outseq $outanno""", outputfiles)
runproc("$SAMTOOLS faidx $outseq", outputfiles)
runproc("$FASIZE -detailed $outseq > $outseq.size", outputfiles)
@files(Paths.reftranscriptome_sequences, Paths.reftranscriptome_gmap_index)
@follows(generate_SNPfixed_transcriptome)
