def _detect_rRNA(data):
sample = dd.get_sample_name(data)
gtf_file = dd.get_gtf_file(data)
tidy_file = dd.get_sailfish_tidy(data)
rrna_features = gtf.get_rRNA(gtf_file)
transcripts = set([x[1] for x in rrna_features if x])
if not transcripts:
return {'rRNA': "NA", "rRNA_rate": "NA"}
count_table = pd.read_csv(tidy_file, sep="\t")
sample_table = count_table[count_table["sample"].isin([sample])]
rrna_exp = map(float, sample_table[sample_table["id"].isin(transcripts)]["numreads"])
total_exp = map(float, sample_table["numreads"])
rrna = sum(rrna_exp)
rrna_rate = float(rrna) / sum(total_exp)
return {'rRNA': str(rrna), 'rRNA_rate': str(rrna_rate)}
def _detect_rRNA(data):
sample = dd.get_sample_name(data)
gtf_file = dd.get_gtf_file(data)
tidy_file = dd.get_sailfish_tidy(data)
rrna_features = gtf.get_rRNA(gtf_file)
transcripts = set([x[1] for x in rrna_features if x])
if not transcripts:
return {'rRNA': "NA", "rRNA_rate": "NA"}
count_table = pd.read_csv(tidy_file, sep="\t")
sample_table = count_table[count_table["sample"].isin([sample])]
rrna_exp = map(
float, sample_table[sample_table["id"].isin(transcripts)]["numreads"])
total_exp = map(float, sample_table["numreads"])
rrna = sum(rrna_exp)
rrna_rate = float(rrna) / sum(total_exp)
return {'rRNA': str(rrna), 'rRNA_rate': str(rrna_rate)}
def _get_files_project(sample, upload_config):
"""Retrieve output files associated with an entire analysis project.
"""
out = [{"path": sample["provenance"]["programs"]}]
if os.path.exists(tz.get_in(["provenance", "data"], sample) or ""):
out.append({"path": sample["provenance"]["data"]})
for fname in ["bcbio-nextgen.log", "bcbio-nextgen-commands.log"]:
if os.path.exists(os.path.join(log.get_log_dir(sample["config"]), fname)):
out.append({"path": os.path.join(log.get_log_dir(sample["config"]), fname),
"type": "external_command_log",
"ext": ""})
if "summary" in sample and sample["summary"].get("project"):
out.append({"path": sample["summary"]["project"]})
mixup_check = tz.get_in(["summary", "mixup_check"], sample)
if mixup_check:
out.append({"path": sample["summary"]["mixup_check"],
"type": "directory", "ext": "mixup_check"})
report = os.path.join(dd.get_work_dir(sample), "report")
if utils.file_exists(report):
out.append({"path": report,
"type": "directory", "ext": "report"})
multiqc = tz.get_in(["summary", "multiqc"], sample)
if multiqc:
out.extend(_flatten_file_with_secondary(multiqc, "multiqc"))
if sample.get("seqcluster", None):
out.append({"path": sample["seqcluster"],
"type": "directory", "ext": "seqcluster"})
if sample.get("report", None):
out.append({"path": os.path.dirname(sample["report"]),
"type": "directory", "ext": "seqclusterViz"})
for x in sample.get("variants", []):
if "pop_db" in x:
out.append({"path": x["pop_db"],
"type": "sqlite",
"variantcaller": x["variantcaller"]})
for x in sample.get("variants", []):
if "population" in x:
pop_db = tz.get_in(["population", "db"], x)
if pop_db:
out.append({"path": pop_db,
"type": "sqlite",
"variantcaller": x["variantcaller"]})
out.extend(_get_variant_file(x, ("population", "vcf")))
for x in sample.get("variants", []):
if x.get("validate") and x["validate"].get("grading_summary"):
out.append({"path": x["validate"]["grading_summary"]})
break
if "coverage" in sample:
cov_db = tz.get_in(["coverage", "summary"], sample)
if cov_db:
out.append({"path": cov_db, "type": "sqlite", "ext": "coverage"})
all_coverage = tz.get_in(["coverage", "all"], sample)
if all_coverage:
out.append({"path": all_coverage, "type": "bed", "ext": "coverage"})
if dd.get_mirna_counts(sample):
out.append({"path": dd.get_mirna_counts(sample)})
if dd.get_isomir_counts(sample):
out.append({"path": dd.get_isomir_counts(sample)})
if dd.get_novel_mirna_counts(sample):
out.append({"path": dd.get_novel_mirna_counts(sample)})
if dd.get_novel_isomir_counts(sample):
out.append({"path": dd.get_novel_isomir_counts(sample)})
if dd.get_combined_counts(sample):
out.append({"path": dd.get_combined_counts(sample)})
if dd.get_annotated_combined_counts(sample):
out.append({"path": dd.get_annotated_combined_counts(sample)})
if dd.get_combined_fpkm(sample):
out.append({"path": dd.get_combined_fpkm(sample)})
if dd.get_combined_fpkm_isoform(sample):
out.append({"path": dd.get_combined_fpkm_isoform(sample)})
if dd.get_transcript_assembler(sample):
out.append({"path": dd.get_merged_gtf(sample)})
if dd.get_dexseq_counts(sample):
out.append({"path": dd.get_dexseq_counts(sample)})
if dd.get_express_counts(sample):
out.append({"path": dd.get_express_counts(sample)})
if dd.get_express_fpkm(sample):
out.append({"path": dd.get_express_fpkm(sample)})
if dd.get_express_tpm(sample):
out.append({"path": dd.get_express_tpm(sample)})
if dd.get_isoform_to_gene(sample):
out.append({"path": dd.get_isoform_to_gene(sample)})
if dd.get_square_vcf(sample):
out.append({"path": dd.get_square_vcf(sample)})
if dd.get_sailfish_tidy(sample):
out.append({"path": dd.get_sailfish_tidy(sample)})
if dd.get_sailfish_transcript_tpm(sample):
out.append({"path": dd.get_sailfish_transcript_tpm(sample)})
if dd.get_sailfish_gene_tpm(sample):
out.append({"path": dd.get_sailfish_gene_tpm(sample)})
if dd.get_tx2gene(sample):
out.append({"path": dd.get_tx2gene(sample)})
return _add_meta(out, config=upload_config)
def _get_files_project(sample, upload_config):
"""Retrieve output files associated with an entire analysis project.
"""
out = [{"path": sample["provenance"]["programs"]}]
if os.path.exists(tz.get_in(["provenance", "data"], sample) or ""):
out.append({"path": sample["provenance"]["data"]})
for fname in ["bcbio-nextgen.log", "bcbio-nextgen-commands.log"]:
if os.path.exists(os.path.join(log.get_log_dir(sample["config"]), fname)):
out.append({"path": os.path.join(log.get_log_dir(sample["config"]), fname),
"type": "external_command_log",
"ext": ""})
if "summary" in sample and sample["summary"].get("project"):
out.append({"path": sample["summary"]["project"]})
mixup_check = tz.get_in(["summary", "mixup_check"], sample)
if mixup_check:
out.append({"path": sample["summary"]["mixup_check"],
"type": "directory", "ext": "mixup_check"})
report = os.path.join(dd.get_work_dir(sample), "report")
if utils.file_exists(report):
out.append({"path": report,
"type": "directory", "ext": "report"})
multiqc = tz.get_in(["summary", "multiqc"], sample)
if multiqc:
out.extend(_flatten_file_with_secondary(multiqc, "multiqc"))
if sample.get("seqcluster", {}):
out.append({"path": sample["seqcluster"].get("out_dir"),
"type": "directory", "ext": "seqcluster"})
if sample.get("report", None):
out.append({"path": os.path.dirname(sample["report"]),
"type": "directory", "ext": "seqclusterViz"})
for x in sample.get("variants", []):
if "pop_db" in x:
out.append({"path": x["pop_db"],
"type": "sqlite",
"variantcaller": x["variantcaller"]})
for x in sample.get("variants", []):
if "population" in x:
pop_db = tz.get_in(["population", "db"], x)
if pop_db:
out.append({"path": pop_db,
"type": "sqlite",
"variantcaller": x["variantcaller"]})
suffix = "-annotated-decomposed" if tz.get_in(("population", "decomposed"), x) else "-annotated"
out.extend([_add_batch(x, sample)
for x in _get_variant_file(x, ("population", "vcf"), suffix=suffix)])
for x in sample.get("variants", []):
if x.get("validate") and x["validate"].get("grading_summary"):
out.append({"path": x["validate"]["grading_summary"]})
break
if "coverage" in sample:
cov_db = tz.get_in(["coverage", "summary"], sample)
if cov_db:
out.append({"path": cov_db, "type": "sqlite", "ext": "coverage"})
all_coverage = tz.get_in(["coverage", "all"], sample)
if all_coverage:
out.append({"path": all_coverage, "type": "bed", "ext": "coverage"})
if dd.get_mirna_counts(sample):
out.append({"path": dd.get_mirna_counts(sample)})
if dd.get_isomir_counts(sample):
out.append({"path": dd.get_isomir_counts(sample)})
if dd.get_novel_mirna_counts(sample):
out.append({"path": dd.get_novel_mirna_counts(sample)})
if dd.get_novel_isomir_counts(sample):
out.append({"path": dd.get_novel_isomir_counts(sample)})
if dd.get_combined_counts(sample):
count_file = dd.get_combined_counts(sample)
if sample["analysis"].lower() == "scrna-seq":
out.append({"path": count_file,
"type": "mtx"})
out.append({"path": count_file + ".rownames",
"type": "rownames"})
out.append({"path": count_file + ".colnames",
"type": "colnames"})
else:
out.append({"path": dd.get_combined_counts(sample)})
if dd.get_annotated_combined_counts(sample):
out.append({"path": dd.get_annotated_combined_counts(sample)})
if dd.get_combined_fpkm(sample):
out.append({"path": dd.get_combined_fpkm(sample)})
if dd.get_combined_fpkm_isoform(sample):
out.append({"path": dd.get_combined_fpkm_isoform(sample)})
if dd.get_transcript_assembler(sample):
out.append({"path": dd.get_merged_gtf(sample)})
if dd.get_dexseq_counts(sample):
out.append({"path": dd.get_dexseq_counts(sample)})
if dd.get_express_counts(sample):
out.append({"path": dd.get_express_counts(sample)})
if dd.get_express_fpkm(sample):
out.append({"path": dd.get_express_fpkm(sample)})
if dd.get_express_tpm(sample):
out.append({"path": dd.get_express_tpm(sample)})
if dd.get_isoform_to_gene(sample):
out.append({"path": dd.get_isoform_to_gene(sample)})
if dd.get_square_vcf(sample):
out.append({"path": dd.get_square_vcf(sample)})
if dd.get_sailfish_tidy(sample):
out.append({"path": dd.get_sailfish_tidy(sample)})
if dd.get_sailfish_transcript_tpm(sample):
out.append({"path": dd.get_sailfish_transcript_tpm(sample)})
if dd.get_sailfish_gene_tpm(sample):
out.append({"path": dd.get_sailfish_gene_tpm(sample)})
if dd.get_tx2gene(sample):
out.append({"path": dd.get_tx2gene(sample)})
if dd.get_spikein_counts(sample):
out.append({"path": dd.get_spikein_counts(sample)})
return _add_meta(out, config=upload_config)
def _get_files_project(sample, upload_config):
"""Retrieve output files associated with an entire analysis project.
"""
out = [{"path": sample["provenance"]["programs"]}]
for fname in ["bcbio-nextgen.log", "bcbio-nextgen-commands.log"]:
if os.path.exists(os.path.join(log.get_log_dir(sample["config"]), fname)):
out.append({"path": os.path.join(log.get_log_dir(sample["config"]), fname),
"type": "external_command_log",
"ext": ""})
if "summary" in sample and sample["summary"].get("project"):
out.append({"path": sample["summary"]["project"]})
mixup_check = tz.get_in(["summary", "mixup_check"], sample)
if mixup_check:
out.append({"path": sample["summary"]["mixup_check"],
"type": "directory", "ext": "mixup_check"})
report = os.path.join(dd.get_work_dir(sample), "report")
if utils.file_exists(report):
out.append({"path": report,
"type": "directory", "ext": "report"})
if sample.get("seqcluster", None):
out.append({"path": sample["seqcluster"],
"type": "directory", "ext": "seqcluster"})
for x in sample.get("variants", []):
if "pop_db" in x:
out.append({"path": x["pop_db"],
"type": "sqlite",
"variantcaller": x["variantcaller"]})
for x in sample.get("variants", []):
if "population" in x:
pop_db = tz.get_in(["population", "db"], x)
if pop_db:
out.append({"path": pop_db,
"type": "sqlite",
"variantcaller": x["variantcaller"]})
out.extend(_get_variant_file(x, ("population", "vcf")))
for x in sample.get("variants", []):
if x.get("validate") and x["validate"].get("grading_summary"):
out.append({"path": x["validate"]["grading_summary"]})
break
if "coverage" in sample:
cov_db = tz.get_in(["coverage", "summary"], sample)
if cov_db:
out.append({"path": cov_db, "type": "sqlite", "ext": "coverage"})
all_coverage = tz.get_in(["coverage", "all"], sample)
if all_coverage:
out.append({"path": all_coverage, "type": "bed", "ext": "coverage"})
if dd.get_mirna_counts(sample):
out.append({"path": dd.get_mirna_counts(sample)})
if dd.get_isomir_counts(sample):
out.append({"path": dd.get_isomir_counts(sample)})
if dd.get_combined_counts(sample):
out.append({"path": dd.get_combined_counts(sample)})
if dd.get_annotated_combined_counts(sample):
out.append({"path": dd.get_annotated_combined_counts(sample)})
if dd.get_combined_fpkm(sample):
out.append({"path": dd.get_combined_fpkm(sample)})
if dd.get_combined_fpkm_isoform(sample):
out.append({"path": dd.get_combined_fpkm_isoform(sample)})
if dd.get_assembled_gtf(sample):
out.append({"path": dd.get_assembled_gtf(sample)})
if dd.get_dexseq_counts(sample):
out.append({"path": dd.get_dexseq_counts(sample)})
if dd.get_express_counts(sample):
out.append({"path": dd.get_express_counts(sample)})
if dd.get_express_fpkm(sample):
out.append({"path": dd.get_express_fpkm(sample)})
if dd.get_express_tpm(sample):
out.append({"path": dd.get_express_tpm(sample)})
if dd.get_isoform_to_gene(sample):
out.append({"path": dd.get_isoform_to_gene(sample)})
if dd.get_square_vcf(sample):
out.append({"path": dd.get_square_vcf(sample)})
if dd.get_sailfish_tidy(sample):
out.append({"path": dd.get_sailfish_tidy(sample)})
if dd.get_sailfish_transcript_tpm(sample):
out.append({"path": dd.get_sailfish_transcript_tpm(sample)})
if dd.get_sailfish_gene_tpm(sample):
out.append({"path": dd.get_sailfish_gene_tpm(sample)})
return _add_meta(out, config=upload_config)