def generate_transcript_counts(data):
"""Generate counts per transcript and per exon from an alignment"""
data["count_file"] = featureCounts.count(data)
if dd.get_transcriptome_align(data):
# to create a disambiguated transcriptome file realign with bowtie2
if dd.get_disambiguate(data):
logger.info("Aligning to the transcriptome with bowtie2 using the "
"disambiguated reads.")
bam_path = data["work_bam"]
fastq_paths = alignprep._bgzip_from_bam(
bam_path,
data["dirs"],
data,
is_retry=False,
output_infix='-transcriptome')
if len(fastq_paths) == 2:
file1, file2 = fastq_paths
else:
file1, file2 = fastq_paths[0], None
ref_file = dd.get_ref_file(data)
data = bowtie2.align_transcriptome(file1, file2, ref_file, data)
else:
file1, file2 = dd.get_input_sequence_files(data)
if not dd.get_transcriptome_bam(data):
ref_file = dd.get_ref_file(data)
logger.info(
"Transcriptome alignment was flagged to run, but the "
"transcriptome BAM file was not found. Aligning to the "
"transcriptome with bowtie2.")
data = bowtie2.align_transcriptome(file1, file2, ref_file, data)
data = spikein.counts_spikein(data)
return [[data]]
def generate_transcript_counts(data):
"""Generate counts per transcript and per exon from an alignment"""
data["count_file"] = featureCounts.count(data)
if dd.get_fusion_mode(data, False):
oncofuse_file = oncofuse.run(data)
if oncofuse_file:
data = dd.set_oncofuse_file(data, oncofuse_file)
if dd.get_transcriptome_align(data):
# to create a disambiguated transcriptome file realign with bowtie2
if dd.get_disambiguate(data):
logger.info("Aligning to the transcriptome with bowtie2 using the "
"disambiguated reads.")
bam_path = data["work_bam"]
fastq_paths = alignprep._bgzip_from_bam(bam_path, data["dirs"], data["config"], is_retry=False, output_infix='-transcriptome')
if len(fastq_paths) == 2:
file1, file2 = fastq_paths
else:
file1, file2 = fastq_paths[0], None
ref_file = dd.get_ref_file(data)
data = bowtie2.align_transcriptome(file1, file2, ref_file, data)
else:
file1, file2 = dd.get_input_sequence_files(data)
if not dd.get_transcriptome_bam(data):
ref_file = dd.get_ref_file(data)
logger.info("Transcriptome alignment was flagged to run, but the "
"transcriptome BAM file was not found. Aligning to the "
"transcriptome with bowtie2.")
data = bowtie2.align_transcriptome(file1, file2, ref_file, data)
return [[data]]
def generate_transcript_counts(data):
"""Generate counts per transcript and per exon from an alignment"""
data["count_file"] = featureCounts.count(data)
if dd.get_fusion_mode(data, False):
oncofuse_file = oncofuse.run(data)
if oncofuse_file:
data = dd.set_oncofuse_file(data, oncofuse_file)
if dd.get_transcriptome_align(data) and not dd.get_transcriptome_bam(data):
file1, file2 = None, None
if dd.get_disambiguate(data):
bam_path = data["work_bam"]
fastq_paths = alignprep._bgzip_from_bam(
bam_path,
data["dirs"],
data["config"],
is_retry=False,
output_infix='-transcriptome')
if len(fastq_paths) == 2:
file1, file2 = fastq_paths
else:
file1, file2 = fastq_paths[0], None
else:
file1, file2 = dd.get_input_sequence_files(data)
ref_file = dd.get_ref_file(data)
logger.info("Transcriptome alignment was flagged to run, but the "
"transcriptome BAM file was not found. Aligning to the "
"transcriptome with bowtie2.")
data = bowtie2.align_transcriptome(file1, file2, ref_file, data)
return [[data]]
def generate_transcript_counts(data):
"""Generate counts per transcript and per exon from an alignment"""
data["count_file"] = featureCounts.count(data)
if dd.get_fusion_mode(data, False):
oncofuse_file = oncofuse.run(data)
if oncofuse_file:
data = dd.set_oncofuse_file(data, oncofuse_file)
# if RSEM set to run, but the aligner didn't create the transcriptome BAM
# file, make one with bwa
if dd.get_rsem(data) and not dd.get_transcriptome_bam(data):
file1, file2 = dd.get_input_sequence_files(data)
ref_file = dd.get_ref_file(data)
logger.info("RSEM was flagged to run, but the transcriptome BAM file "
"was not found. Aligning to the transcriptome with bowtie2.")
data = bowtie2.align_transcriptome(file1, file2, ref_file, data)
return [[data]]
def generate_transcript_counts(data):
"""Generate counts per transcript and per exon from an alignment"""
data["count_file"] = featureCounts.count(data)
if dd.get_fusion_mode(data, False):
oncofuse_file = oncofuse.run(data)
if oncofuse_file:
data = dd.set_oncofuse_file(data, oncofuse_file)
# if RSEM set to run, but the aligner didn't create the transcriptome BAM
# file, make one with bwa
if dd.get_rsem(data) and not dd.get_transcriptome_bam(data):
file1, file2 = dd.get_input_sequence_files(data)
ref_file = dd.get_ref_file(data)
logger.info(
"RSEM was flagged to run, but the transcriptome BAM file "
"was not found. Aligning to the transcriptome with bowtie2.")
data = bowtie2.align_transcriptome(file1, file2, ref_file, data)
return [[data]]
def generate_transcript_counts(data):
"""Generate counts per transcript and per exon from an alignment"""
data["count_file"] = featureCounts.count(data)
if dd.get_fusion_mode(data, False):
oncofuse_file = oncofuse.run(data)
if oncofuse_file:
data = dd.set_oncofuse_file(data, oncofuse_file)
# if RSEM set to run, but the aligner didn't create the transcriptome BAM
# file, make one with bwa
if dd.get_disambiguate(data):
logger.info("RSEM is not supported yet for disambiguation protocols. "
"See https://github.com/chapmanb/bcbio-nextgen/issues/859")
return [[data]]
if dd.get_rsem(data) and not dd.get_transcriptome_bam(data):
file1, file2 = dd.get_input_sequence_files(data)
ref_file = dd.get_ref_file(data)
logger.info("RSEM was flagged to run, but the transcriptome BAM file "
"was not found. Aligning to the transcriptome with bowtie2.")
data = bowtie2.align_transcriptome(file1, file2, ref_file, data)
return [[data]]
