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biopet.biopet
Commits
13647e73
Commit
13647e73
authored
Mar 13, 2015
by
bow
Browse files
Add missing CollectRnaSeqMetrics values
parent
40276768
Changes
3
Hide whitespace changes
Inline
Side-by-side
public/gentrap/src/main/resources/nl/lumc/sasc/biopet/pipelines/gentrap/scripts/pdf_report.py
View file @
13647e73
...
...
@@ -456,10 +456,6 @@ class GentrapSample(object):
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
}
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
(
"alignment_metrics"
,
{})
...
...
@@ -486,9 +482,16 @@ class GentrapSample(object):
"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
self
.
run
.
settings
[
"strand_protocol"
]
!=
"non_specific"
:
self
.
rna_metrics
.
update
({
})
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
=
\
{
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
)
...
...
@@ -503,19 +506,6 @@ class GentrapRun(object):
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
.
libs
=
[]
for
sample
in
self
.
samples
.
values
():
self
.
libs
.
extend
(
sample
.
libs
.
values
())
if
all
([
s
.
is_paired_end
for
s
in
self
.
samples
.
values
()]):
self
.
lib_type
=
"all paired end"
elif
all
([
not
s
.
is_paired_end
for
s
in
self
.
samples
.
values
()]):
self
.
lib_type
=
"all single end"
else
:
self
.
lib_type
=
"mixed (single end and paired end)"
self
.
files
=
summary
[
"gentrap"
].
get
(
"files"
,
{}).
get
(
"pipeline"
,
{})
self
.
settings
=
summary
[
"gentrap"
][
"settings"
]
...
...
@@ -550,6 +540,20 @@ class GentrapRun(object):
self
.
executables
[
"samtools"
]
=
self
.
all_executables
[
"samtoolsview"
]
self
.
executables
[
"samtools"
][
"desc"
]
=
"various post-alignment processing"
self
.
sample_names
=
sorted
(
summary
[
"samples"
].
keys
())
self
.
samples
=
\
{
s
:
GentrapSample
(
self
,
s
,
summary
[
"samples"
][
s
])
\
for
s
in
self
.
sample_names
}
self
.
libs
=
[]
for
sample
in
self
.
samples
.
values
():
self
.
libs
.
extend
(
sample
.
libs
.
values
())
if
all
([
s
.
is_paired_end
for
s
in
self
.
samples
.
values
()]):
self
.
lib_type
=
"all paired end"
elif
all
([
not
s
.
is_paired_end
for
s
in
self
.
samples
.
values
()]):
self
.
lib_type
=
"all single end"
else
:
self
.
lib_type
=
"mixed (single end and paired end)"
def
__repr__
(
self
):
return
"{0}(
\"
{1}
\"
)"
.
format
(
self
.
__class__
.
__name__
,
self
.
summary_file
)
...
...
public/gentrap/src/main/resources/nl/lumc/sasc/biopet/pipelines/gentrap/templates/pdf/lib_mapping.tex
View file @
13647e73
...
...
@@ -108,5 +108,14 @@
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
Median 5' bias
&
((( lib.rna
_
metrics.median
_
5prime
_
bias )))
&
-
&
-
\\
Median 3' bias
&
((( lib.rna
_
metrics.median
_
3prime
_
bias )))
&
-
&
-
\\
Median 5' to 3' bias
&
((( lib.rna
_
metrics.median
_
5prime
_
to
_
3prime
_
bias )))
&
-
&
-
\\
\hline
((* if lib.run.settings.strand
_
protocol != "non
_
specific" *))
Correct strand reads
&
((( lib.rna
_
metrics.correct
_
strand
_
reads|nice
_
int )))
&
-
&
-
\\
Incorrect strand reads
&
((( lib.rna
_
metrics.incorrect
_
strand
_
reads|nice
_
int )))
&
-
&
-
\\
((* endif *))
\hline
\end{tabular}
\end{center}
public/gentrap/src/main/resources/nl/lumc/sasc/biopet/pipelines/gentrap/templates/pdf/sample_mapping.tex
View file @
13647e73
...
...
@@ -109,5 +109,14 @@
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
Median 5' bias
&
((( sample.rna
_
metrics.median
_
5prime
_
bias )))
&
-
&
-
\\
Median 3' bias
&
((( sample.rna
_
metrics.median
_
3prime
_
bias )))
&
-
&
-
\\
Median 5' to 3' bias
&
((( sample.rna
_
metrics.median
_
5prime
_
to
_
3prime
_
bias )))
&
-
&
-
\\
\hline
((* if sample.run.settings.strand
_
protocol != "non
_
specific" *))
Correct strand reads
&
((( sample.rna
_
metrics.correct
_
strand
_
reads|nice
_
int )))
&
-
&
-
\\
Incorrect strand reads
&
((( sample.rna
_
metrics.incorrect
_
strand
_
reads|nice
_
int )))
&
-
&
-
\\
((* endif *))
\hline
\end{tabular}
\end{center}
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