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Paul Igor Costea
metaSNV
Commits
6fb74df4
Commit
6fb74df4
authored
May 12, 2017
by
Paul Igor Costea
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parent
a0a9c160
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metaSNV_post.py
metaSNV_post.py
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metaSNV_post.py
View file @
6fb74df4
...
...
@@ -43,7 +43,7 @@ def get_arguments():
# OPTIONAL arguments:
parser
.
add_argument
(
'-b'
,
metavar
=
'FLOAT'
,
type
=
float
,
default
=
40.0
)
parser
.
add_argument
(
'-b'
,
metavar
=
'FLOAT'
,
type
=
float
,
default
=
40.0
,
help
=
"Coverage breadth: minimal horizontal genome coverage percentage per sample per species"
)
parser
.
add_argument
(
'-d'
,
metavar
=
'FLOAT'
,
type
=
float
,
default
=
5.0
,
help
=
"Coverage depth: minimal average vertical genome coverage per sample per species"
)
...
...
@@ -85,8 +85,8 @@ def debugging(taxids_of_interest, header_cov):
def
file_check
():
''' Check if required files exist (True / False)'''
args
.
projdir
=
args
.
projdir
.
rstrip
(
'/'
)
args
.
coverage_file
=
args
.
projdir
+
'/'
+
args
.
projdir
+
'.all_cov.tab'
args
.
percentage_file
=
args
.
projdir
+
'/'
+
args
.
projdir
+
'.all_perc.tab'
args
.
coverage_file
=
args
.
projdir
+
'/'
+
args
.
projdir
.
split
(
'/'
)[
-
1
]
+
'.all_cov.tab'
args
.
percentage_file
=
args
.
projdir
+
'/'
+
args
.
projdir
.
spit
(
'/'
)[
-
1
]
+
'.all_perc.tab'
args
.
all_samples
=
args
.
projdir
+
'/'
+
'all_samples'
print
(
"Checking for necessary input files..."
)
...
...
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