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Commit 1de28c56 authored by bow's avatar bow
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Add library-level and sample-level RNA metrics to report

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public/gentrap/src/main/resources/nl/lumc/sasc/biopet/pipelines/gentrap/scripts/pdf_report.py
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View file @ 1de28c56
...@@ -419,6 +419,31 @@ class GentrapLib(object): ...@@ -419,6 +419,31 @@ class GentrapLib(object):
self.fastqc_r2_qc = FastQC(self.fastqc_r2_qc_files["fastqc_data"]["path"]) self.fastqc_r2_qc = FastQC(self.fastqc_r2_qc_files["fastqc_data"]["path"])
# mapping metrics settings # mapping metrics settings
self.aln_metrics = summary.get("bammetrics", {}).get("stats", {}).get("alignment_metrics", {}) 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): def __repr__(self):
return "{0}(sample=\"{1}\", lib=\"{2}\")".format( return "{0}(sample=\"{1}\", lib=\"{2}\")".format(
...@@ -436,6 +461,30 @@ class GentrapSample(object): ...@@ -436,6 +461,30 @@ class GentrapSample(object):
self.libs = \ self.libs = \
{l: GentrapLib(self.run, self, l, summary["libraries"][l]) \ {l: GentrapLib(self.run, self, l, summary["libraries"][l]) \
for l in self.lib_names} 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): def __repr__(self):
return "{0}(\"{1}\")".format(self.__class__.__name__, self.name) return "{0}(\"{1}\")".format(self.__class__.__name__, self.name)
......
public/gentrap/src/main/resources/nl/lumc/sasc/biopet/pipelines/gentrap/templates/pdf/lib_mapping.tex
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View file @ 1de28c56
\subsection{Mapping} \subsection{Mapping}
\label{sec:map} \label{sec:map-((( lib.sample.name )))-((( lib.name )))}
\subsubsection{Mapping statistics} \subsubsection{Mapping statistics}
Table~\ref{tab:bamstat-((( lib.sample.name )))-((( lib.name ))))} shows the overview statistics of the
generated alignment file.
\indent \indent
% number + percentage of reads mapped to genome % number + percentage of reads mapped to genome
% number + percentage of properly paired reads % number + percentage of properly paired reads
\begin{center} \begin{center}
\captionof{table}{Mapping Overview} \captionof{table}{Mapping Overview}
\label{tab:bamstat-((( lib.sample.name )))-((( lib.name ))))} \label{tab:bamstat-((( lib.sample.name )))-((( lib.name )))}
\setlength{\tabcolsep}{11pt} \setlength{\tabcolsep}{11pt}
((* if lib.is_paired_end *)) ((* if lib.is_paired_end *))
\begin{tabular}{ l r r r } \begin{tabular}{ l r r r }
...@@ -46,34 +43,19 @@ generated alignment file. ...@@ -46,34 +43,19 @@ generated alignment file.
\end{tabular} \end{tabular}
\end{center} \end{center}
((= ((* if lib.is_paired_end *))
%((* if run.is_paired_end *)) % inferred insert size distribution
%% inferred insert size distribution \subsubsection{Insert size distribution}
%\subsection{Insert size distribution}
% \IfFileExists{((( lib.inserts_metrics_files.output_histogram.path )))}
%This section contains a quick overview of the insert size distribution {
%of the mapped reads. \begin{figure}[h!]
% \centering
%\indent \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.}
%There are three possible types of inserts the graph may denote: \end{figure}
%\begin{description} }
% \item[\textit{inward}] \hfill \\ ((= TODO: strand-specific stats
% 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}
%}
%{ %{
% \IfFileExists{((( vars['OUT_DIR'] )))/((( vars['SAMPLE'] ))).f.insertsizes.png} % \IfFileExists{((( vars['OUT_DIR'] )))/((( vars['SAMPLE'] ))).f.insertsizes.png}
% { % {
...@@ -92,5 +74,42 @@ generated alignment file. ...@@ -92,5 +74,42 @@ generated alignment file.
% \end{figure} % \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 *))
public/gentrap/src/main/resources/nl/lumc/sasc/biopet/pipelines/gentrap/templates/pdf/sample.tex
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\part{Sample "((( sample.name )))" Results} \part{Sample "((( sample.name )))" Results}
\label{sample:(((sample.name)))} \label{sample:(((sample.name)))}
Hello from module ((( sample ))) \\ ((* include "sample_mapping.tex" *))
((* for lib in sample.libs.values() *)) ((* for lib in sample.libs.values() *))
((* include "lib.tex" *)) ((* include "lib.tex" *))
......
public/gentrap/src/main/resources/nl/lumc/sasc/biopet/pipelines/gentrap/templates/pdf/sample_mapping.tex 0 → 100644
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\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}
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