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Konstantin Volzhenin
SENSE-PPI
Commits
78f70acf
Commit
78f70acf
authored
Aug 08, 2023
by
Konstantin Volzhenin
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0.2.2 fixed tsv bug in predict
parent
4b1847e2
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3 changed files
with
13 additions
and
4 deletions
+13
-4
.gitignore
.gitignore
+2
-0
__init__.py
senseppi/__init__.py
+1
-1
predict.py
senseppi/commands/predict.py
+10
-3
No files found.
.gitignore
View file @
78f70acf
...
@@ -127,3 +127,5 @@ dmypy.json
...
@@ -127,3 +127,5 @@ dmypy.json
/esm2_embs_3B
/esm2_embs_3B
*.sh
*.sh
draft.py
draft.py
/data/string_species/mmseqs_dbs/
/data/human_virus/all_test_viruses.csv
senseppi/__init__.py
View file @
78f70acf
__version__
=
"0.2.
1
"
__version__
=
"0.2.
2
"
__author__
=
"Konstantin Volzhenin"
__author__
=
"Konstantin Volzhenin"
from
.
import
model
,
commands
,
esm2_model
,
dataset
,
utils
,
network_utils
from
.
import
model
,
commands
,
esm2_model
,
dataset
,
utils
,
network_utils
...
...
senseppi/commands/predict.py
View file @
78f70acf
...
@@ -99,13 +99,20 @@ def main(params):
...
@@ -99,13 +99,20 @@ def main(params):
logging
.
info
(
'Predicting...'
)
logging
.
info
(
'Predicting...'
)
preds
=
predict
(
params
)
preds
=
predict
(
params
)
data
=
pd
.
read_csv
(
params
.
pairs_file
,
delimiter
=
'
\t
'
,
names
=
[
"seq1"
,
"seq2"
])
data
=
pd
.
read_csv
(
params
.
pairs_file
,
delimiter
=
'
\t
'
)
#if 3 columns, then assign names ['seq1', 'seq2', 'label'] if 2 columns, then names ['seq1', 'seq2']
if
len
(
data
.
columns
)
==
3
:
data
.
columns
=
[
'seq1'
,
'seq2'
,
'label'
]
elif
len
(
data
.
columns
)
==
2
:
data
.
columns
=
[
'seq1'
,
'seq2'
]
else
:
raise
ValueError
(
'The pairs file must have 2 or 3 columns: seq1, seq2 and label(optional)'
)
data
[
'preds'
]
=
preds
data
[
'preds'
]
=
preds
data
.
to_csv
(
params
.
output
+
'.tsv'
,
sep
=
'
\t
'
,
index
=
False
,
header
=
Fals
e
)
data
.
to_csv
(
params
.
output
+
'.tsv'
,
sep
=
'
\t
'
,
index
=
False
,
header
=
Tru
e
)
data_positive
=
data
[
data
[
'preds'
]
>=
params
.
pred_threshold
]
data_positive
=
data
[
data
[
'preds'
]
>=
params
.
pred_threshold
]
data_positive
.
to_csv
(
params
.
output
+
'_positive_interactions.tsv'
,
sep
=
'
\t
'
,
index
=
False
,
header
=
Fals
e
)
data_positive
.
to_csv
(
params
.
output
+
'_positive_interactions.tsv'
,
sep
=
'
\t
'
,
index
=
False
,
header
=
Tru
e
)
if
__name__
==
'__main__'
:
if
__name__
==
'__main__'
:
...
...
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