From a9beb86776bca66eedc95646ce957b638cefcd6e Mon Sep 17 00:00:00 2001
From: bow <bow@bow.web.id>
Date: Sat, 27 Jun 2015 17:32:11 +0200
Subject: [PATCH] Add missing stats display in Gentrap report
---
.../pipelines/gentrap/scripts/pdf_report.py | 72 ++++++++++---------
.../gentrap/templates/pdf/sample_mapping.tex | 4 +-
2 files changed, 41 insertions(+), 35 deletions(-)
diff --git a/public/gentrap/src/main/resources/nl/lumc/sasc/biopet/pipelines/gentrap/scripts/pdf_report.py b/public/gentrap/src/main/resources/nl/lumc/sasc/biopet/pipelines/gentrap/scripts/pdf_report.py
index e0931c4b3..b0c2b2e82 100755
--- a/public/gentrap/src/main/resources/nl/lumc/sasc/biopet/pipelines/gentrap/scripts/pdf_report.py
+++ b/public/gentrap/src/main/resources/nl/lumc/sasc/biopet/pipelines/gentrap/scripts/pdf_report.py
@@ -418,6 +418,8 @@ class GentrapLib(object):
self.fastqc_r2_qc = FastQC(self.fastqc_r2_qc_files["fastqc_data"]["path"])
# mapping metrics settings
self.aln_metrics = summary.get("bammetrics", {}).get("stats", {}).get("CollectAlignmentSummaryMetrics", {})
+ for k, v in self.aln_metrics.items():
+ self.aln_metrics[k] = {a.lower(): b for a, b in v.items()}
# insert size metrics files
self.inserts_metrics_files = \
summary.get("bammetrics", {}).get("files", {}).get("multi_metrics", {})
@@ -428,25 +430,26 @@ class GentrapLib(object):
if "metrics" in _rmetrics:
_rmetrics = _rmetrics["metrics"]
if _rmetrics:
- self.rna_metrics = {k: v for k, v in _rmetrics.items() }
- pf_bases = float(_rmetrics["PF_BASES"])
- exonic_bases = int(_rmetrics.get("CODING_BASES", 0)) + int(_rmetrics.get("UTR_BASES", 0))
+ _rmetrics = {k.lower(): v for k, v in _rmetrics.items() }
+ self.rna_metrics = _rmetrics
+ pf_bases = float(_rmetrics["pf_bases"])
+ exonic_bases = int(_rmetrics.get("coding_bases", 0)) + int(_rmetrics.get("utr_bases", 0))
# picard uses pct_ but it's actually ratio ~ we follow their convention
- pct_exonic_bases_all = exonic_bases / float(_rmetrics["PF_BASES"])
- pct_exonic_bases = exonic_bases / float(_rmetrics.get("PF_ALIGNED_BASES", 0))
+ pct_exonic_bases_all = exonic_bases / float(_rmetrics["pf_bases"])
+ pct_exonic_bases = exonic_bases / float(_rmetrics.get("pf_aligned_bases", 0))
self.rna_metrics.update({
- "EXONIC_BASES": exonic_bases,
- "PCT_EXONIC_BASES_ALL": pct_exonic_bases_all,
- "PCT_EXONIC_BASES": pct_exonic_bases,
- "PCT_ALIGNED_BASES": 1.0,
- "PCT_ALIGNED_BASES_ALL": float(_rmetrics.get("PF_ALIGNED_BASES", 0.0)) / pf_bases,
- "PCT_CODING_BASES_ALL": float(_rmetrics.get("CODING_BASES", 0.0)) / pf_bases,
- "PCT_UTR_BASES_ALL": float(_rmetrics.get("UTR_BASES", 0.0)) / pf_bases,
- "PCT_INTRONIC_BASES_ALL": float(_rmetrics.get("INTRONIC_BASES", 0.0)) / pf_bases,
- "PCT_INTERGENIC_BASES_ALL": float(_rmetrics.get("INTERGENIC_BASES", 0.0)) / pf_bases,
+ "exonic_bases": exonic_bases,
+ "pct_exonic_bases_all": pct_exonic_bases_all,
+ "pct_exonic_bases": pct_exonic_bases,
+ "pct_aligned_bases": 1.0,
+ "pct_aligned_bases_all": float(_rmetrics.get("pf_aligned_bases", 0.0)) / pf_bases,
+ "pct_coding_bases_all": float(_rmetrics.get("coding_bases", 0.0)) / pf_bases,
+ "pct_utr_bases_all": float(_rmetrics.get("utr_bases", 0.0)) / pf_bases,
+ "pct_intronic_bases_all": float(_rmetrics.get("intronic_bases", 0.0)) / pf_bases,
+ "pct_intergenic_bases_all": float(_rmetrics.get("intergenic_bases", 0.0)) / pf_bases,
})
- if _rmetrics.get("RIBOSOMAL_BASES", "") != "":
- self.rna_metrics["PCT_RIBOSOMAL_BASES_ALL"] = float(_rmetrics.get("PF_RIBOSOMAL_BASES", 0.0)) / pf_bases
+ if _rmetrics.get("ribosomal_bases", "") != "":
+ self.rna_metrics["pct_ribosomal_bases_all"] = float(_rmetrics.get("pf_ribosomal_bases", 0.0)) / pf_bases
def __repr__(self):
return "{0}(sample=\"{1}\", lib=\"{2}\")".format(
@@ -463,9 +466,11 @@ class GentrapSample(object):
self.is_paired_end = summary.get("gentrap", {}).get("stats", {}).get("pipeline", {})["all_paired"]
# mapping metrics settings
self.aln_metrics = summary.get("bammetrics", {}).get("stats", {}).get("CollectAlignmentSummaryMetrics", {})
+ for k, v in self.aln_metrics.items():
+ self.aln_metrics[k] = {a.lower(): b for a, b in v.items()}
# insert size metrics files
self.inserts_metrics_files = \
- summary.get("bammetrics", {}).get("files", {}).get("CollectInsertSizeMetrics", {}).get("metrics", {})
+ summary.get("bammetrics", {}).get("files", {}).get("multi_metrics", {})
# rna metrics files and stats
self.rna_metrics_files = summary.get("bammetrics", {}).get("files", {}).get("rna", {})
_rmetrics = summary.get("bammetrics", {}).get("stats", {}).get("rna", {})
@@ -473,25 +478,26 @@ class GentrapSample(object):
if "metrics" in _rmetrics:
_rmetrics = _rmetrics["metrics"]
if _rmetrics:
- self.rna_metrics = {k: v for k, v in _rmetrics.items() }
- pf_bases = float(_rmetrics["PF_BASES"])
- exonic_bases = int(_rmetrics.get("CODING_BASES", 0)) + int(_rmetrics.get("UTR_BASES", 0))
+ _rmetrics = {k.lower(): v for k, v in _rmetrics.items() }
+ self.rna_metrics = _rmetrics
+ pf_bases = float(_rmetrics["pf_bases"])
+ exonic_bases = int(_rmetrics.get("coding_bases", 0)) + int(_rmetrics.get("utr_bases", 0))
# picard uses pct_ but it's actually ratio ~ we follow their convention
- pct_exonic_bases_all = exonic_bases / float(_rmetrics["PF_BASES"])
- pct_exonic_bases = exonic_bases / float(_rmetrics.get("PF_ALIGNED_BASES", 0))
+ pct_exonic_bases_all = exonic_bases / float(_rmetrics["pf_bases"])
+ pct_exonic_bases = exonic_bases / float(_rmetrics.get("pf_aligned_bases", 0))
self.rna_metrics.update({
- "EXONIC_BASES": exonic_bases,
- "PCT_EXONIC_BASES_ALL": pct_exonic_bases_all,
- "PCT_EXONIC_BASES": pct_exonic_bases,
- "PCT_ALIGNED_BASES": 1.0,
- "PCT_ALIGNED_BASES_ALL": float(_rmetrics.get("PF_ALIGNED_BASES", 0.0)) / pf_bases,
- "PCT_CODING_BASES_ALL": float(_rmetrics.get("CODING_BASES", 0.0)) / pf_bases,
- "PCT_UTR_BASES_ALL": float(_rmetrics.get("UTR_BASES", 0.0)) / pf_bases,
- "PCT_INTRONIC_BASES_ALL": float(_rmetrics.get("INTRONIC_BASES", 0.0)) / pf_bases,
- "PCT_INTERGENIC_BASES_ALL": float(_rmetrics.get("INTERGENIC_BASES", 0.0)) / pf_bases,
+ "exonic_bases": exonic_bases,
+ "pct_exonic_bases_all": pct_exonic_bases_all,
+ "pct_exonic_bases": pct_exonic_bases,
+ "pct_aligned_bases": 1.0,
+ "pct_aligned_bases_all": float(_rmetrics.get("pf_aligned_bases", 0.0)) / pf_bases,
+ "pct_coding_bases_all": float(_rmetrics.get("coding_bases", 0.0)) / pf_bases,
+ "pct_utr_bases_all": float(_rmetrics.get("utr_bases", 0.0)) / pf_bases,
+ "pct_intronic_bases_all": float(_rmetrics.get("intronic_bases", 0.0)) / pf_bases,
+ "pct_intergenic_bases_all": float(_rmetrics.get("intergenic_bases", 0.0)) / pf_bases,
})
- if _rmetrics.get("RIBOSOMAL_BASES", "") != "":
- self.rna_metrics["PCT_RIBOSOMAL_BASES_ALL"] = float(_rmetrics.get("PF_RIBOSOMAL_BASES", 0.0)) / pf_bases
+ if _rmetrics.get("ribosomal_bases", "") != "":
+ self.rna_metrics["pct_ribosomal_bases_all"] = float(_rmetrics.get("pf_ribosomal_bases", 0.0)) / pf_bases
self.lib_names = sorted(summary["libraries"].keys())
self.libs = \
diff --git a/public/gentrap/src/main/resources/nl/lumc/sasc/biopet/pipelines/gentrap/templates/pdf/sample_mapping.tex b/public/gentrap/src/main/resources/nl/lumc/sasc/biopet/pipelines/gentrap/templates/pdf/sample_mapping.tex
index da99f47d2..4f4da850d 100644
--- a/public/gentrap/src/main/resources/nl/lumc/sasc/biopet/pipelines/gentrap/templates/pdf/sample_mapping.tex
+++ b/public/gentrap/src/main/resources/nl/lumc/sasc/biopet/pipelines/gentrap/templates/pdf/sample_mapping.tex
@@ -47,11 +47,11 @@
% inferred insert size distribution
\subsubsection{Insert size distribution}
-\IfFileExists{((( sample.inserts_metrics_files.output_histogram.path )))}
+\IfFileExists{((( sample.inserts_metrics_files.insert_size_histogram.path )))}
{
\begin{figure}[h!]
\centering
- \includegraphics[width=0.7\textwidth]{((( sample.inserts_metrics_files.output_histogram.path )))}
+ \includegraphics[width=0.7\textwidth]{((( sample.inserts_metrics_files.insert_size_histogram.path )))}
\caption{Distribution of insert size length of paired-end reads mapped to opposite strands.}
\end{figure}
}
--
GitLab