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MICS_Biomathematics
bioinfo
VariantAnnotator
Commits
a08e9e4e
Commit
a08e9e4e
authored
Aug 28, 2020
by
Pradat Yoann
Browse files
minor fix remove redundant cols
parent
133cab8e
Changes
1
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Inline
Side-by-side
src/main.py
View file @
a08e9e4e
...
@@ -229,7 +229,7 @@ def run_annotator(vcf_folder: str, vcf_file: str, col_normal: str, col_tumor: st
...
@@ -229,7 +229,7 @@ def run_annotator(vcf_folder: str, vcf_file: str, col_normal: str, col_tumor: st
#### vcf2maf
#### vcf2maf
ddf_maf
[
"vcf2maf"
].
columns
=
[
"%s_VCF2MAF"
%
x
for
x
in
ddf_maf
[
"vcf2maf"
].
columns
]
ddf_maf
[
"vcf2maf"
].
columns
=
[
"%s_VCF2MAF"
%
x
for
x
in
ddf_maf
[
"vcf2maf"
].
columns
]
for
column
in
ddf_maf
[
"vcf2maf"
].
columns
:
for
column
in
ddf_maf
[
"vcf2maf"
].
columns
:
if
column
in
dt_identifiers
.
keys
():
if
column
in
dt_identifiers
.
keys
()
or
column
in
cols_manual
:
#### prioritize identifiers from input
#### prioritize identifiers from input
pass
pass
else
:
else
:
...
@@ -243,7 +243,7 @@ def run_annotator(vcf_folder: str, vcf_file: str, col_normal: str, col_tumor: st
...
@@ -243,7 +243,7 @@ def run_annotator(vcf_folder: str, vcf_file: str, col_normal: str, col_tumor: st
elif
vcf2maf_config
.
run
:
elif
vcf2maf_config
.
run
:
#### vcf2maf
#### vcf2maf
for
column
in
ddf_maf
[
"vcf2maf"
].
columns
:
for
column
in
ddf_maf
[
"vcf2maf"
].
columns
:
if
column
in
dt_identifiers
.
keys
():
if
column
in
dt_identifiers
.
keys
()
or
column
in
cols_manual
:
#### prioritize identifiers from input
#### prioritize identifiers from input
pass
pass
else
:
else
:
...
...
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