Skip to content
GitLab
Projects
Groups
Snippets
/
Help
Help
Support
Community forum
Keyboard shortcuts
?
Submit feedback
Contribute to GitLab
Sign in
Toggle navigation
Menu
Open sidebar
Mirrors
biopet.biopet
Commits
fb8373ab
Commit
fb8373ab
authored
Mar 06, 2015
by
bow
Browse files
Initial report
parent
66bf4e3f
Changes
6
Expand all
Hide whitespace changes
Inline
Side-by-side
public/gentrap/src/main/resources/nl/lumc/sasc/biopet/pipelines/gentrap/scripts/pdf_report.py
View file @
fb8373ab
...
...
@@ -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
0 → 100644
View file @
fb8373ab
\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/lib_seqeval.tex
0 → 100644
View file @
fb8373ab
This diff is collapsed.
Click to expand it.
public/gentrap/src/main/resources/nl/lumc/sasc/biopet/pipelines/gentrap/templates/pdf/main.tex
View file @
fb8373ab
...
...
@@ -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 Transcript
ome
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
0 → 100644
View file @
fb8373ab
\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
deleted
100644 → 0
View file @
66bf4e3f
FROM THE MODULE
Write
Preview
Supports
Markdown
0%
Try again
or
attach a new file
.
Cancel
You are about to add
0
people
to the discussion. Proceed with caution.
Finish editing this message first!
Cancel
Please
register
or
sign in
to comment