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 056a0ea7f07cffb999a7a89aecb4e97ef4b49c94..5206e98cf6ceb6896e1d2668f30b34e02b812036 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
@@ -419,6 +419,31 @@ 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("alignment_metrics", {})
+ # insert size metrics files
+ self.inserts_metrics_files = summary.get("bammetrics", {}).get("files", {}).get("insert_size_metrics", {})
+ # rna metrics files and stats
+ _rmetrics = summary.get("gentrap", {}).get("stats", {}).get("rna_metrics", {})
+ if _rmetrics:
+ self.rna_metrics_files = summary.get("gentrap", {}).get("files", {}).get("rna_metrics", {})
+ 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))
+ # 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))
+ 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,
+ })
+ 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(
@@ -436,6 +461,30 @@ class GentrapSample(object):
self.libs = \
{l: GentrapLib(self.run, self, l, summary["libraries"][l]) \
for l in self.lib_names}
+ # rna metrics files and stats
+ _rmetrics = summary.get("gentrap", {}).get("stats", {}).get("rna_metrics", {})
+ if _rmetrics:
+ self.rna_metrics_files = summary.get("gentrap", {}).get("files", {}).get("rna_metrics", {})
+ 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))
+ # 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))
+ 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,
+ })
+ 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}(\"{1}\")".format(self.__class__.__name__, self.name)
diff --git a/public/gentrap/src/main/resources/nl/lumc/sasc/biopet/pipelines/gentrap/templates/pdf/lib_mapping.tex b/public/gentrap/src/main/resources/nl/lumc/sasc/biopet/pipelines/gentrap/templates/pdf/lib_mapping.tex
index 8026fed7bd9dc08bcccecbe44a87ec2c0b50cb5b..0d862bc9b649157cef7fe5640fbc1948681968fe 100644
--- a/public/gentrap/src/main/resources/nl/lumc/sasc/biopet/pipelines/gentrap/templates/pdf/lib_mapping.tex
+++ b/public/gentrap/src/main/resources/nl/lumc/sasc/biopet/pipelines/gentrap/templates/pdf/lib_mapping.tex
@@ -1,18 +1,15 @@
\subsection{Mapping}
-\label{sec:map}
+\label{sec:map-((( lib.sample.name )))-((( lib.name )))}
\subsubsection{Mapping statistics}
-Table~\ref{tab:bamstat-((( lib.sample.name )))-((( lib.name ))))} shows the overview statistics of the
-generated alignment file.
-
\indent
% number + percentage of reads mapped to genome
% number + percentage of properly paired reads
\begin{center}
\captionof{table}{Mapping Overview}
- \label{tab:bamstat-((( lib.sample.name )))-((( lib.name ))))}
+ \label{tab:bamstat-((( lib.sample.name )))-((( lib.name )))}
\setlength{\tabcolsep}{11pt}
((* if lib.is_paired_end *))
\begin{tabular}{ l r r r }
@@ -46,34 +43,19 @@ generated alignment file.
\end{tabular}
\end{center}
-((=
-%((* if run.is_paired_end *))
-%% inferred insert size distribution
-%\subsection{Insert size distribution}
-%
-%This section contains a quick overview of the insert size distribution
-%of the mapped reads.
-%
-%\indent
-%
-%There are three possible types of inserts the graph may denote:
-%\begin{description}
-% \item[\textit{inward}] \hfill \\
-% Each read pair maps to opposite strands and point towards each other.
-% \item[\textit{outward}] \hfill \\
-% Each read pair maps to opposite strands and point away from each other.
-% \item[\textit{same directions}] \hfill \\
-% Both read pair map to the same strand.
-%\end{description}
-%
-%\IfFileExists{((( vars['OUT_DIR'] )))/((( vars['SAMPLE'] ))).insertsizes.png}
-%{
-% \begin{figure}[h!]
-% \centering
-% \includegraphics[width=0.7\textwidth]{((( vars['OUT_DIR'] )))/((( vars['SAMPLE'] ))).insertsizes.png}
-% \caption{Distribution of insert size length of paired-end reads mapped to opposite strands.}
-% \end{figure}
-%}
+((* if lib.is_paired_end *))
+% inferred insert size distribution
+\subsubsection{Insert size distribution}
+
+\IfFileExists{((( lib.inserts_metrics_files.output_histogram.path )))}
+{
+ \begin{figure}[h!]
+ \centering
+ \includegraphics[width=0.7\textwidth]{((( lib.inserts_metrics_files.output_histogram.path )))}
+ \caption{Distribution of insert size length of paired-end reads mapped to opposite strands.}
+ \end{figure}
+}
+((= TODO: strand-specific stats
%{
% \IfFileExists{((( vars['OUT_DIR'] )))/((( vars['SAMPLE'] ))).f.insertsizes.png}
% {
@@ -92,5 +74,42 @@ generated alignment file.
% \end{figure}
% }{}
%}
-%((* endif *))
=))
+((* endif *))
+
+((* if lib.sample.libs|length > 1 *))
+\subsubsection{RNA-specific metrics}
+
+\IfFileExists{((( lib.rna_metrics_files.output_chart.path )))}
+{
+ \begin{figure}[h!]
+ \centering
+ \includegraphics[width=0.7\textwidth]{((( lib.rna_metrics_files.output_chart.path )))}
+ \caption{Normalized coverage bias plot.}
+ \end{figure}
+}
+
+\begin{center}
+ \captionof{table}{Functional annotation metrics}
+ \label{tab:fannot-((( lib.sample.name )))-((( lib.name ))))}
+ \setlength{\tabcolsep}{11pt}
+ \begin{tabular}{ l r r r }
+ \hline
+ \multirow{2}{*}{Parameter} & \multicolumn{3}{c}{Value} \\
+ & Count & \% of all & \% of aligned \\
+ \hline \hline
+ Total bases & ((( lib.rna_metrics.pf_bases|nice_int ))) & 100\% & - \\
+ Aligned bases & ((( lib.rna_metrics.pf_aligned_bases|nice_int ))) & ((( lib.rna_metrics.pct_aligned_bases_all|float2nice_pct )))\% & ((( lib.rna_metrics.pct_aligned_bases|float2nice_pct )))\% \\
+ Exonic bases & ((( lib.rna_metrics.exonic_bases|nice_int ))) & ((( lib.rna_metrics.pct_exonic_bases_all|float2nice_pct )))\% & ((( lib.rna_metrics.pct_exonic_bases|float2nice_pct )))\% \\
+ \hspace*{4mm}Coding bases & ((( lib.rna_metrics.coding_bases|nice_int ))) & ((( lib.rna_metrics.pct_coding_bases_all|float2nice_pct )))\% & ((( lib.rna_metrics.pct_coding_bases|float2nice_pct )))\% \\
+ \hspace*{4mm}UTR bases & ((( lib.rna_metrics.utr_bases|nice_int ))) & ((( lib.rna_metrics.pct_utr_bases_all|float2nice_pct )))\% & ((( lib.rna_metrics.pct_utr_bases|float2nice_pct )))\% \\
+ Intronic bases & ((( lib.rna_metrics.intronic_bases|nice_int ))) & ((( lib.rna_metrics.pct_intronic_bases_all|float2nice_pct )))\% & ((( lib.rna_metrics.pct_intronic_bases|float2nice_pct )))\% \\
+ Intergenic bases & ((( lib.rna_metrics.intergenic_bases|nice_int ))) & ((( lib.rna_metrics.pct_intergenic_bases_all|float2nice_pct )))\% & ((( lib.rna_metrics.pct_intergenic_bases|float2nice_pct )))\% \\
+ ((* if lib.rna_metrics.ribosomal_bases != "" *))
+ Ribosomal bases & ((( lib.rna_metrics.ribosomal_bases|nice_int ))) & ((( lib.rna_metrics.pct_ribosomal_bases_all|float2nice_pct )))\% & ((( lib.rna_metrics.pct_ribosomal_bases|float2nice_pct )))\% \\
+ ((* endif *))
+ \hline
+ \end{tabular}
+\end{center}
+
+((* endif *))
diff --git a/public/gentrap/src/main/resources/nl/lumc/sasc/biopet/pipelines/gentrap/templates/pdf/sample.tex b/public/gentrap/src/main/resources/nl/lumc/sasc/biopet/pipelines/gentrap/templates/pdf/sample.tex
index 947049d2eea57196665a1f63212e7e121d47fd9c..39709550273ada4a8b0fd73d69b5e4982c883f57 100644
--- a/public/gentrap/src/main/resources/nl/lumc/sasc/biopet/pipelines/gentrap/templates/pdf/sample.tex
+++ b/public/gentrap/src/main/resources/nl/lumc/sasc/biopet/pipelines/gentrap/templates/pdf/sample.tex
@@ -1,7 +1,7 @@
\part{Sample "((( sample.name )))" Results}
\label{sample:(((sample.name)))}
-Hello from module ((( sample ))) \\
+((* include "sample_mapping.tex" *))
((* for lib in sample.libs.values() *))
((* include "lib.tex" *))
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
new file mode 100644
index 0000000000000000000000000000000000000000..5e3ab9da745896723197f78ca8ba0d9d428f3667
--- /dev/null
+++ b/public/gentrap/src/main/resources/nl/lumc/sasc/biopet/pipelines/gentrap/templates/pdf/sample_mapping.tex
@@ -0,0 +1,41 @@
+\section{Mapping}
+\label{sec:map-((( sample.name )))}
+
+\subsection{Mapping statistics}
+
+\indent
+
+
+\subsection{RNA-specific metrics}
+
+\IfFileExists{((( sample.rna_metrics_files.output_chart.path )))}
+{
+ \begin{figure}[h!]
+ \centering
+ \includegraphics[width=0.7\textwidth]{((( sample.rna_metrics_files.output_chart.path )))}
+ \caption{Normalized coverage bias plot.}
+ \end{figure}
+}
+
+\begin{center}
+ \captionof{table}{Functional annotation metrics}
+ \label{tab:fannot-((( sample.name )))}
+ \setlength{\tabcolsep}{11pt}
+ \begin{tabular}{ l r r r }
+ \hline
+ \multirow{2}{*}{Parameter} & \multicolumn{3}{c}{Value} \\
+ & Count & \% of all & \% of aligned \\
+ \hline \hline
+ Total bases & ((( sample.rna_metrics.pf_bases|nice_int ))) & 100\% & - \\
+ Aligned bases & ((( sample.rna_metrics.pf_aligned_bases|nice_int ))) & ((( sample.rna_metrics.pct_aligned_bases_all|float2nice_pct )))\% & ((( sample.rna_metrics.pct_aligned_bases|float2nice_pct )))\% \\
+ Exonic bases & ((( sample.rna_metrics.exonic_bases|nice_int ))) & ((( sample.rna_metrics.pct_exonic_bases_all|float2nice_pct )))\% & ((( sample.rna_metrics.pct_exonic_bases|float2nice_pct )))\% \\
+ \hspace*{4mm}Coding bases & ((( sample.rna_metrics.coding_bases|nice_int ))) & ((( sample.rna_metrics.pct_coding_bases_all|float2nice_pct )))\% & ((( sample.rna_metrics.pct_coding_bases|float2nice_pct )))\% \\
+ \hspace*{4mm}UTR bases & ((( sample.rna_metrics.utr_bases|nice_int ))) & ((( sample.rna_metrics.pct_utr_bases_all|float2nice_pct )))\% & ((( sample.rna_metrics.pct_utr_bases|float2nice_pct )))\% \\
+ Intronic bases & ((( sample.rna_metrics.intronic_bases|nice_int ))) & ((( sample.rna_metrics.pct_intronic_bases_all|float2nice_pct )))\% & ((( sample.rna_metrics.pct_intronic_bases|float2nice_pct )))\% \\
+ Intergenic bases & ((( sample.rna_metrics.intergenic_bases|nice_int ))) & ((( sample.rna_metrics.pct_intergenic_bases_all|float2nice_pct )))\% & ((( sample.rna_metrics.pct_intergenic_bases|float2nice_pct )))\% \\
+ ((* if sample.rna_metrics.ribosomal_bases != "" *))
+ Ribosomal bases & ((( sample.rna_metrics.ribosomal_bases|nice_int ))) & ((( sample.rna_metrics.pct_ribosomal_bases_all|float2nice_pct )))\% & ((( sample.rna_metrics.pct_ribosomal_bases|float2nice_pct )))\% \\
+ ((* endif *))
+ \hline
+ \end{tabular}
+\end{center}