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Thomas Weber
Mosaicatcher Update
Commits
8a1ad842
Commit
8a1ad842
authored
4 years ago
by
Maryam Ghareghani
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adjusted the syntax of agg function to the latest version of pandas
parent
d03faa65
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utils/call-complex-regions.py
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utils/call-complex-regions.py
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utils/call-complex-regions.py
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8a1ad842
...
...
@@ -38,7 +38,7 @@ def main():
calls
=
pd
.
read_csv
(
args
.
callset
,
sep
=
'
\t
'
)
# Identify "complex" intervals
segments
=
calls
.
groupby
(
by
=
[
'
chrom
'
,
'
start
'
,
'
end
'
]).
sv_call_name
.
agg
(
{
'
is_complex
'
:
partial
(
is_complex
,
ignore_haplotypes
=
args
.
ignore_haplotypes
,
min_cell_count
=
args
.
min_cell_count
)
}
).
reset_index
().
sort_values
([
'
chrom
'
,
'
start
'
,
'
end
'
])
segments
=
calls
.
groupby
(
by
=
[
'
chrom
'
,
'
start
'
,
'
end
'
]).
sv_call_name
.
agg
(
is_complex
=
partial
(
is_complex
,
ignore_haplotypes
=
args
.
ignore_haplotypes
,
min_cell_count
=
args
.
min_cell_count
)).
reset_index
().
sort_values
([
'
chrom
'
,
'
start
'
,
'
end
'
])
# merge complex segments if closer than args.merge_distance
...
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