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medema-group
BiG-SCAPE
Commits
8551a978
Commit
8551a978
authored
May 22, 2020
by
Jorge Navarro Muñoz
Browse files
Merge branch 'patch-1' into 'master'
Accesion --> Accession in 4 places See merge request
!46
parents
de1405cd
6062a7bb
Changes
1
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Inline
Side-by-side
bigscape.py
View file @
8551a978
...
...
@@ -2882,7 +2882,7 @@ if __name__=="__main__":
print
(
" Writing the complete Annotations file for the complete set"
)
network_annotation_path
=
os
.
path
.
join
(
network_files_folder
,
"Network_Annotations_Full.tsv"
)
with
open
(
network_annotation_path
,
"w"
)
as
network_annotation_file
:
network_annotation_file
.
write
(
"BGC
\t
Accesion ID
\t
Description
\t
Product Prediction
\t
BiG-SCAPE class
\t
Organism
\t
Taxonomy
\n
"
)
network_annotation_file
.
write
(
"BGC
\t
Acces
s
ion ID
\t
Description
\t
Product Prediction
\t
BiG-SCAPE class
\t
Organism
\t
Taxonomy
\n
"
)
for
bgc
in
clusterNames
:
product
=
bgc_info
[
bgc
].
product
network_annotation_file
.
write
(
"
\t
"
.
join
([
bgc
,
bgc_info
[
bgc
].
accession_id
,
bgc_info
[
bgc
].
description
,
product
,
sort_bgc
(
product
),
bgc_info
[
bgc
].
organism
,
bgc_info
[
bgc
].
taxonomy
])
+
"
\n
"
)
...
...
@@ -2983,7 +2983,7 @@ if __name__=="__main__":
print
(
" Writing annotation file"
)
network_annotation_path
=
os
.
path
.
join
(
network_files_folder
,
"mix"
,
"Network_Annotations_mix_QueryBGC.tsv"
)
with
open
(
network_annotation_path
,
"w"
)
as
network_annotation_file
:
network_annotation_file
.
write
(
"BGC
\t
Accesion ID
\t
Description
\t
Product Prediction
\t
BiG-SCAPE class
\t
Organism
\t
Taxonomy
\n
"
)
network_annotation_file
.
write
(
"BGC
\t
Acces
s
ion ID
\t
Description
\t
Product Prediction
\t
BiG-SCAPE class
\t
Organism
\t
Taxonomy
\n
"
)
for
idx
in
mix_set
:
bgc
=
clusterNames
[
idx
]
product
=
bgc_info
[
bgc
].
product
...
...
@@ -3136,7 +3136,7 @@ if __name__=="__main__":
print
(
" Writing annotation files"
)
network_annotation_path
=
os
.
path
.
join
(
network_files_folder
,
bgc_class
,
"Network_Annotations_"
+
bgc_class
+
".tsv"
)
with
open
(
network_annotation_path
,
"w"
)
as
network_annotation_file
:
network_annotation_file
.
write
(
"BGC
\t
Accesion ID
\t
Description
\t
Product Prediction
\t
BiG-SCAPE class
\t
Organism
\t
Taxonomy
\n
"
)
network_annotation_file
.
write
(
"BGC
\t
Acces
s
ion ID
\t
Description
\t
Product Prediction
\t
BiG-SCAPE class
\t
Organism
\t
Taxonomy
\n
"
)
for
idx
in
BGC_classes
[
bgc_class
]:
bgc
=
clusterNames
[
idx
]
product
=
bgc_info
[
bgc
].
product
...
...
@@ -3201,7 +3201,7 @@ if __name__=="__main__":
print
(
" Writing annotation file (Query BGC)"
)
network_annotation_path
=
os
.
path
.
join
(
network_files_folder
,
bgc_class
,
"Network_Annotations_"
+
bgc_class
+
"_QueryBGC.tsv"
)
with
open
(
network_annotation_path
,
"w"
)
as
network_annotation_file
:
network_annotation_file
.
write
(
"BGC
\t
Accesion ID
\t
Description
\t
Product Prediction
\t
BiG-SCAPE class
\t
Organism
\t
Taxonomy
\n
"
)
network_annotation_file
.
write
(
"BGC
\t
Acces
s
ion ID
\t
Description
\t
Product Prediction
\t
BiG-SCAPE class
\t
Organism
\t
Taxonomy
\n
"
)
for
idx
in
BGC_classes
[
bgc_class
]:
bgc
=
clusterNames
[
idx
]
product
=
bgc_info
[
bgc
].
product
...
...
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