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biopet.biopet
Commits
a9beb867
Commit
a9beb867
authored
Jun 27, 2015
by
bow
Browse files
Add missing stats display in Gentrap report
parent
d6acc80f
Changes
2
Hide whitespace changes
Inline
Side-by-side
public/gentrap/src/main/resources/nl/lumc/sasc/biopet/pipelines/gentrap/scripts/pdf_report.py
View file @
a9beb867
...
...
@@ -418,6 +418,8 @@ 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
(
"CollectAlignmentSummaryMetrics"
,
{})
for
k
,
v
in
self
.
aln_metrics
.
items
():
self
.
aln_metrics
[
k
]
=
{
a
.
lower
():
b
for
a
,
b
in
v
.
items
()}
# insert size metrics files
self
.
inserts_metrics_files
=
\
summary
.
get
(
"bammetrics"
,
{}).
get
(
"files"
,
{}).
get
(
"multi_metrics"
,
{})
...
...
@@ -428,25 +430,26 @@ class GentrapLib(object):
if
"metrics"
in
_rmetrics
:
_rmetrics
=
_rmetrics
[
"metrics"
]
if
_rmetrics
:
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
))
_rmetrics
=
{
k
.
lower
():
v
for
k
,
v
in
_rmetrics
.
items
()
}
self
.
rna_metrics
=
_rmetrics
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
))
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
,
"
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
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
(
...
...
@@ -463,9 +466,11 @@ class GentrapSample(object):
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
(
"CollectAlignmentSummaryMetrics"
,
{})
for
k
,
v
in
self
.
aln_metrics
.
items
():
self
.
aln_metrics
[
k
]
=
{
a
.
lower
():
b
for
a
,
b
in
v
.
items
()}
# insert size metrics files
self
.
inserts_metrics_files
=
\
summary
.
get
(
"bammetrics"
,
{}).
get
(
"files"
,
{}).
get
(
"
CollectInsertSizeMetrics"
,
{}).
get
(
"
metrics"
,
{})
summary
.
get
(
"bammetrics"
,
{}).
get
(
"files"
,
{}).
get
(
"
multi_
metrics"
,
{})
# rna metrics files and stats
self
.
rna_metrics_files
=
summary
.
get
(
"bammetrics"
,
{}).
get
(
"files"
,
{}).
get
(
"rna"
,
{})
_rmetrics
=
summary
.
get
(
"bammetrics"
,
{}).
get
(
"stats"
,
{}).
get
(
"rna"
,
{})
...
...
@@ -473,25 +478,26 @@ class GentrapSample(object):
if
"metrics"
in
_rmetrics
:
_rmetrics
=
_rmetrics
[
"metrics"
]
if
_rmetrics
:
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
))
_rmetrics
=
{
k
.
lower
():
v
for
k
,
v
in
_rmetrics
.
items
()
}
self
.
rna_metrics
=
_rmetrics
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
))
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
,
"
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
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
=
\
...
...
public/gentrap/src/main/resources/nl/lumc/sasc/biopet/pipelines/gentrap/templates/pdf/sample_mapping.tex
View file @
a9beb867
...
...
@@ -47,11 +47,11 @@
% inferred insert size distribution
\subsubsection
{
Insert size distribution
}
\IfFileExists
{
((( sample.inserts
_
metrics
_
files.
output
_
histogram.path )))
}
\IfFileExists
{
((( sample.inserts
_
metrics
_
files.
insert
_
size
_
histogram.path )))
}
{
\begin{figure}
[h!]
\centering
\includegraphics
[width=0.7\textwidth]
{
((( sample.inserts
_
metrics
_
files.
output
_
histogram.path )))
}
\includegraphics
[width=0.7\textwidth]
{
((( sample.inserts
_
metrics
_
files.
insert
_
size
_
histogram.path )))
}
\caption
{
Distribution of insert size length of paired-end reads mapped to opposite strands.
}
\end{figure}
}
...
...
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