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Paul Igor Costea
metaSNV
Commits
907adcf8
Commit
907adcf8
authored
Apr 27, 2017
by
Robin Erich Muench
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updated metaSNV.py
parent
a77a2318
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metaSNV.py
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metaSNV.py
View file @
907adcf8
...
...
@@ -95,10 +95,9 @@ def compute_summary(args):
'''This information is required by metaSNV_post.py'''
project_name
=
path
.
basename
(
args
.
project_dir
)
cov_dir
=
path
.
join
(
args
.
project_dir
,
'cov'
)
cov_files
=
glob
(
cov_dir
+
'/*.cov'
)
# project_name = path.basename(args.project_dir)
if
not
cov_files
:
if
not
args
.
print_commands
:
stderr
.
write
(
"Coverage files not found.
\n
"
)
...
...
@@ -139,8 +138,8 @@ def split_opt(args):
# usage createOptimumSplit.sh <all_cov.tab> <all_perc.tab> <geneDefinitions> <INT_NrSplits> <.outfile>
cmd
=
[
'python'
,
'{}/src/createOptimumSplit.py'
.
format
(
basedir
),
"{}/{}.all_cov.tab"
.
format
(
args
.
project_dir
,
args
.
project_
dir
),
"{}/{}.all_perc.tab"
.
format
(
args
.
project_dir
,
args
.
project_
dir
),
"{}/{}.all_cov.tab"
.
format
(
args
.
project_dir
,
project_
name
),
"{}/{}.all_perc.tab"
.
format
(
args
.
project_dir
,
project_
name
),
args
.
ctg_len
,
str
(
args
.
n_splits
),
path
.
join
(
args
.
project_dir
,
"bestsplits"
,
"best_split"
)]
...
...
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