Initial report

public/gentrap/src/main/resources/nl/lumc/sasc/biopet/pipelines/gentrap/scripts/pdf_report.py

@@ -30,6 +30,7 @@ from os import path
 
 from jinja2 import Environment, FileSystemLoader
 
+
 # set locale for digit grouping
 locale.setlocale(locale.LC_ALL, "")
 
@@ -68,11 +69,15 @@ class LongTable(object):
 
 
 # filter functions for the jinja environment
-def nice_int(num):
+def nice_int(num, default="None"):
+    if num is None:
+        return default
     return locale.format("%i", int(num), grouping=True)
 
 
-def nice_flt(num):
+def nice_flt(num, default="None"):
+    if num is None:
+        return default
     return locale.format("%.2f", float(num), grouping=True)
 
 
@@ -84,7 +89,7 @@ def natural_sort(inlist):
     return inlist
 
 
-def write_template(summary_file, template_file, logo_file):
+def write_template(run, template_file, logo_file):
 
     template_file = path.abspath(path.realpath(template_file))
     template_dir = path.dirname(template_file)
@@ -109,17 +114,74 @@ def write_template(summary_file, template_file, logo_file):
 
     # write tex template for pdflatex
     jinja_template = env.get_template(path.basename(template_file))
+    run.logo = logo_file
     render_vars = {
-        "gentrap": {
-            "version": "--testing--",
-            "logo": logo_file,
-        },
+        "run": run,
     }
     rendered = jinja_template.render(**render_vars)
 
     print(rendered, file=sys.stdout)
 
 
+class GentrapLib(object):
+
+    def __init__(self, run, sample, name, summary):
+        assert isinstance(run, GentrapRun)
+        assert isinstance(sample, GentrapSample)
+        self.run = run
+        self.sample = sample
+        self.name = name
+        self._raw = summary
+        self.flexiprep = summary.get("flexiprep", {})
+        self.clipping = not self.flexiprep["settings"]["skip_clip"]
+        self.trimming = not self.flexiprep["settings"]["skip_trim"]
+        self.is_paired_end = self.flexiprep["settings"]["paired"]
+
+    def __repr__(self):
+        return "{0}(sample=\"{1}\", lib=\"{2}\")".format(
+                self.__class__.__name__, self.sample.name, self.name)
+
+
+class GentrapSample(object):
+
+    def __init__(self, run, name, summary):
+        assert isinstance(run, GentrapRun)
+        self.run = run
+        self.name = name
+        self._raw = summary
+        self.lib_names = sorted(summary["libraries"].keys())
+        self.libs = \
+            {l: GentrapLib(self.run, self, l, summary["libraries"][l]) \
+                for l in self.lib_names}
+
+    def __repr__(self):
+        return "{0}(\"{1}\")".format(self.__class__.__name__, self.name)
+
+
+class GentrapRun(object):
+
+    def __init__(self, summary_file):
+
+        with open(summary_file, "r") as src:
+            summary = json.load(src)
+
+        self._raw = summary
+        self.summary_file = summary_file
+        self.sample_names = sorted(summary["samples"].keys())
+        self.samples = \
+            {s: GentrapSample(self, s, summary["samples"][s]) \
+                for s in self.sample_names}
+
+        self.files = summary["gentrap"]["files"]
+        self.executables = summary["gentrap"]["executables"]
+        self.settings = summary["gentrap"]["settings"]
+        self.version = self.settings["version"]
+
+    def __repr__(self):
+        return "{0}(\"{1}\")".format(self.__class__.__name__,
+                                        self.summary_file)
+
+
 if __name__ == "__main__":
 
     parser = argparse.ArgumentParser()
@@ -131,4 +193,5 @@ if __name__ == "__main__":
             help="Path to main logo file")
     args = parser.parse_args()
 
-    write_template(args.summary_file, args.template_file, args.logo_file)
+    run = GentrapRun(args.summary_file)
+    write_template(run, args.template_file, args.logo_file)

public/gentrap/src/main/resources/nl/lumc/sasc/biopet/pipelines/gentrap/templates/pdf/lib.tex

+\section{Library "((( lib.name )))" Results}
+\label{lib:(((lib.name)))}
+
+((* include "lib_seqeval.tex" *))

public/gentrap/src/main/resources/nl/lumc/sasc/biopet/pipelines/gentrap/templates/pdf/main.tex

@@ -43,46 +43,57 @@
 
 \begin{document}
 \setlength{\parindent}{0in}
-\title{\Huge Gentrap: Generic Transcriptome Analysis Pipeline}
+%\title{\Huge Gentrap Run Report}
+\title{\resizebox{0.7\linewidth}{!}{\itshape Gentrap Run Report}}
 \author{LUMC Sequencing Analysis Support Core}
 \maketitle
 \begin{center}
-    {\LARGE Run Report v((( gentrap.version )))}
+    {\LARGE version ((( run.version )))}
 \end{center}
 \begin{figure}[h!]
     \centering
-    \includegraphics[width=0.8\textwidth]{((( gentrap.logo )))}
+    \includegraphics[width=0.8\textwidth]{((( run.logo )))}
 \end{figure}
 \thispagestyle{empty}
 \clearpage
 
+\addtocontents{toc}{\protect\hypertarget{toc}{}}
 \tableofcontents
 \clearpage
 
 
-\section{Introduction}
+\part{Overview}
 \label{sec:intro}
 
 This document outlines the results obtained from running Gentrap, a generic
 pipeline for transcriptome analysis.
 
+\clearpage
 
-% TODO: contents ~ preferrably in modules!
-((* include "test.tex" *))
-
+((* for sample in run.samples.values() *))
+((* include "sample.tex" *))
+\clearpage
+((* endfor *))
 
 
-\section{About Gentrap}
+\part{About Gentrap}
 \label{apx:about}
 
-The Generic Transcript Analysis Pipeline (Gentrap) aims to to be a
-generic pipeline for analyzing transcripts from RNA-seq experiments.
+The Generic Transcriptome Analysis Pipeline (Gentrap) is a
+generic pipeline for analyzing transcripts from RNA-seq experiments. \\
 
 Gentrap was developed by Wibowo Arindrarto (\href{mailto:w.arindrarto@lumc.nl}{w.arindrarto@lumc.nl})
 based on raw scripts written by Jeroen Laros
 (\href{mailto:j.f.j.laros@lumc.nl}{j.f.j.laros@lumc.nl}) and
 Peter-Bram 't Hoen
-(\href{mailto:p.a.c._t_hoen@lumc.nl}{p.a.c._t_hoen@lumc.nl}).
+(\href{mailto:p.a.c._t_hoen@lumc.nl}{p.a.c._t_hoen@lumc.nl}) as part of the
+\href{https://git.lumc/nl/biopet/biopet}{Biopet framework}. \\
+
+The Biopet framework is developed by the
+\href{http://sasc.lumc.nl}{Sequencing Analysis Support Core} of the
+\href{http://lumc.nl}{Leiden University Medical Center}, by extending the
+\href{http://http://gatkforums.broadinstitute.org/discussion/1306/overview-of-queue}{Queue framework}.
+Please see the respective web sites for licensing information.
 
 \indent
 

public/gentrap/src/main/resources/nl/lumc/sasc/biopet/pipelines/gentrap/templates/pdf/sample.tex

+\part{Sample "((( sample.name )))" Results}
+\label{sample:(((sample.name)))}
+
+Hello from module ((( sample ))) \\
+
+((* for lib in sample.libs.values() *))
+((* include "lib.tex" *))
+\clearpage
+((* endfor *))

public/gentrap/src/main/resources/nl/lumc/sasc/biopet/pipelines/gentrap/templates/pdf/test.tex

-FROM THE MODULE