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Amandine PERRIN
panacota
Commits
23333d25
Commit
23333d25
authored
5 years ago
by
Amandine PERRIN
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Write absolute path for annotate_path in LSTINFO file
parent
874291a0
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PanACoTA/utils.py
+1
-4
1 addition, 4 deletions
PanACoTA/utils.py
with
1 addition
and
4 deletions
PanACoTA/utils.py
+
1
−
4
View file @
23333d25
...
@@ -484,16 +484,13 @@ def write_lstinfo(list_file, genomes, outdir):
...
@@ -484,16 +484,13 @@ def write_lstinfo(list_file, genomes, outdir):
"""
"""
_
,
name_lst
=
os
.
path
.
split
(
list_file
)
_
,
name_lst
=
os
.
path
.
split
(
list_file
)
outlst
=
os
.
path
.
join
(
outdir
,
"
LSTINFO-
"
+
"
.
"
.
join
(
name_lst
.
split
(
"
.
"
)[:
-
1
])
+
"
.lst
"
)
outlst
=
os
.
path
.
join
(
outdir
,
"
LSTINFO-
"
+
"
.
"
.
join
(
name_lst
.
split
(
"
.
"
)[:
-
1
])
+
"
.lst
"
)
with
open
(
outlst
,
"
w
"
)
as
outf
:
with
open
(
outlst
,
"
w
"
)
as
outf
:
outf
.
write
(
"
\t
"
.
join
([
"
gembase_name
"
,
"
orig_name
"
,
"
to_annotate
"
,
"
gsize
"
,
outf
.
write
(
"
\t
"
.
join
([
"
gembase_name
"
,
"
orig_name
"
,
"
to_annotate
"
,
"
gsize
"
,
"
nb_conts
"
,
"
L90
"
])
+
"
\n
"
)
"
nb_conts
"
,
"
L90
"
])
+
"
\n
"
)
for
genome
,
values
in
sorted
(
genomes
.
items
(),
key
=
sort_genomes_byname_l90_nbcont
):
for
genome
,
values
in
sorted
(
genomes
.
items
(),
key
=
sort_genomes_byname_l90_nbcont
):
gembase
,
_
,
to_annote
,
gsize
,
nbcont
,
l90
=
[
str
(
x
)
for
x
in
values
]
gembase
,
_
,
to_annote
,
gsize
,
nbcont
,
l90
=
[
str
(
x
)
for
x
in
values
]
to_annote_file
=
os
.
path
.
basename
(
to_annote
)
outf
.
write
(
"
\t
"
.
join
([
gembase
,
genome
,
to_annote
,
gsize
,
nbcont
,
l90
])
+
"
\n
"
)
outf
.
write
(
"
\t
"
.
join
([
gembase
,
genome
,
to_annote_file
,
gsize
,
nbcont
,
l90
])
+
"
\n
"
)
def
sort_genomes_by_name
(
x
):
def
sort_genomes_by_name
(
x
):
"""
"""
...
...
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