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Beatrice Tan
CNAprioritization
Commits
2d3389cc
Commit
2d3389cc
authored
Feb 02, 2018
by
Beatrice Tan
Browse files
Removed ensembl function.
parent
f7bc787b
Changes
2
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config.yaml
View file @
2d3389cc
#Directories to be specified
workdir
:
/home/bftan/CNA_results
#directory to write output
gisticdir
:
/home/bftan/Tools/GISTIC2
#directory to install GISTIC2
#
workdir: /home/bftan/CNA_results #directory to write output
#
gisticdir: /home/bftan/Tools/GISTIC2 #directory to install GISTIC2
#
workdir: /home/beatrice/CNA_analysis
#
gisticdir: /home/beatrice/CNA_analysis/run_gistic2
workdir
:
/home/beatrice/CNA_analysis
gisticdir
:
/home/beatrice/CNA_analysis/run_gistic2
#Input details to download from firehose
cancer_type
:
SKCM
...
...
scripts/ParseResults.py
View file @
2d3389cc
...
...
@@ -46,13 +46,30 @@ def parse_gistic_results(results_file, known_genes, census_genes):
start
,
end
=
bp
.
split
(
"-"
)
cnv_type
=
'amp'
if
stats
[
0
].
startswith
(
"Amplification"
)
else
'del'
qval
=
log10
(
float
(
stats
[
5
]))
*
-
1
#Convert q-value to log10(q-value)
list_genes
=
genes_locus
(
chrom
,
int
(
start
),
int
(
end
))
#list_genes = genes_locus(chrom, int(start), int(end))
result_dir
,
conf
=
results_file
.
split
(
"all_lesions"
)
gene_file
=
os
.
path
.
join
(
result_dir
,
cnv_type
+
"_genes"
+
conf
)
list_genes
=
gistic_genes
(
gene_file
,
CNV_id
)
known_overlap
=
set
(
list_genes
).
intersection
(
set
(
known_genes
))
census_overlap
=
set
(
list_genes
).
intersection
(
set
(
census_genes
))
cnv_data
=
[
chrom
,
start
,
end
,
cnv_type
,
qval
,
list
(
known_overlap
),
list
(
census_overlap
),
list_genes
]
regions
.
append
(
cnv_data
)
return
regions
def
gistic_genes
(
gene_file
,
CNV_id
):
"""Extract list of genes for a given recurrent CNV from GISTIC2 output."""
out_genes
=
[]
with
open
(
gene_file
,
'r'
)
as
genes
:
for
i
in
range
(
3
):
genes
.
readline
()
column_CNV
=
genes
.
readline
().
split
(
"
\t
"
).
index
(
CNV_id
)
for
line
in
genes
:
if
len
(
line
.
split
(
"
\t
"
))
>=
column_CNV
:
gene
=
line
.
split
(
"
\t
"
)[
column_CNV
]
if
gene
!=
''
:
out_genes
.
append
(
gene
)
return
out_genes
def
parse_rubic_results
(
results_gains
,
results_losses
,
known_genes
,
census_genes
):
"""Create a list of lists with the recurrent regions called by GISTIC2."""
regions
=
[]
...
...
@@ -63,21 +80,23 @@ def parse_rubic_results(results_gains, results_losses, known_genes, census_genes
chrom
,
start
,
end
,
qval_left
,
qval_right
,
genes
=
lesion
.
split
(
"
\t
"
)
CNV_id
=
"chr"
+
chrom
+
":"
+
start
+
"-"
+
end
cnv_type
=
'amp'
if
result_file
.
endswith
(
'gains.txt'
)
else
'del'
list_genes
=
genes_locus
(
chrom
,
int
(
start
),
int
(
end
))
#list_genes = genes_locus(chrom, int(start), int(end))
list_genes
=
genes
.
strip
().
split
(
","
)
print
(
list_genes
)
known_overlap
=
set
(
list_genes
).
intersection
(
set
(
known_genes
))
census_overlap
=
set
(
list_genes
).
intersection
(
set
(
census_genes
))
cnv_data
=
[
chrom
,
start
,
end
,
cnv_type
,
(
qval_left
,
qval_right
),
list
(
known_overlap
),
list
(
census_overlap
),
list_genes
]
regions
.
append
(
cnv_data
)
return
regions
def
genes_locus
(
chrom
,
start
,
end
):
"""Get list of gene IDs at certain location."""
IDs
=
[]
gene_info
=
ensembl
.
genes_at_locus
(
chrom
,
start
,
end
)
for
gene
in
gene_info
:
ID
=
gene
.
gene_id
IDs
.
append
(
ID
)
return
IDs
#
def genes_locus(chrom, start, end):
#
"""Get list of gene IDs at certain location."""
#
IDs = []
#
gene_info = ensembl.genes_at_locus(chrom, start, end)
#
for gene in gene_info:
#
ID = gene.gene_id
#
IDs.append(ID)
#
return IDs
def
gene_file_IDs
(
gene_file
,
top_nr
):
"""Parse a file with a list of genes (one gene per line or first column).
...
...
@@ -90,11 +109,12 @@ def gene_file_IDs(gene_file, top_nr):
continue
else
:
gene
=
line
.
split
(
"
\t
"
)[
0
]
try
:
gene_ID
=
ensembl
.
gene_ids_of_gene_name
(
gene
)
list_genes
=
list_genes
+
gene_ID
except
:
pass
list_genes
.
append
(
gene
)
#try:
# gene_ID = ensembl.gene_ids_of_gene_name(gene)
# list_genes = list_genes + gene_ID
#except:
# pass
if
top_nr
!=
np
.
inf
:
list_genes
=
list_genes
[
0
:
top_nr
]
return
list_genes
...
...
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