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Mustafa Tekpinar
PRESCOTT
Commits
2eef3ef9
Commit
2eef3ef9
authored
Jun 14, 2022
by
Mustafa Tekpinar
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alphabet selection was added as an input argument!
parent
49d39490
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3 changed files
with
14 additions
and
7 deletions
+14
-7
computePred.R
computePred.R
+3
-1
gemme.py
gemme.py
+8
-3
gemmeAnal.py
gemmeAnal.py
+3
-3
No files found.
computePred.R
View file @
2eef3ef9
...
@@ -23,6 +23,7 @@ aliFile = args[2]
...
@@ -23,6 +23,7 @@ aliFile = args[2]
simple
=
args
[
3
]
simple
=
args
[
3
]
fname
=
args
[
4
]
fname
=
args
[
4
]
normWeightMode
=
args
[
5
]
normWeightMode
=
args
[
5
]
selectedAlphabet
=
args
[
6
]
# read alignment and convert to matrix
# read alignment and convert to matrix
ali
=
as.matrix.alignment
(
read.alignment
(
aliFile
,
format
=
"fasta"
))
ali
=
as.matrix.alignment
(
read.alignment
(
aliFile
,
format
=
"fasta"
))
...
@@ -241,7 +242,8 @@ print(alpha)
...
@@ -241,7 +242,8 @@ print(alpha)
alphabet
=
"lz-bl.7"
#alphabet = "lz-bl.7"
alphabet
=
selectedAlphabet
if
(
simple
){
if
(
simple
){
normPredCombi
=
normalizePredWithNbSeqsPC
(
pred
,
trace
,
wt
,
alpha
,
nbSeqs
,
alphabet
)
normPredCombi
=
normalizePredWithNbSeqsPC
(
pred
,
trace
,
wt
,
alpha
,
nbSeqs
,
alphabet
)
rownames
(
normPredCombi
)
=
aa
rownames
(
normPredCombi
)
=
aa
...
...
gemme.py
View file @
2eef3ef9
...
@@ -363,6 +363,10 @@ def parse_command_line():
...
@@ -363,6 +363,10 @@ def parse_command_line():
help
=
"If a jet file is provided, it will skip JET2 calculation and use the precalculated JET2 data in that file. Default is None"
,
help
=
"If a jet file is provided, it will skip JET2 calculation and use the precalculated JET2 data in that file. Default is None"
,
required
=
False
,
default
=
None
)
required
=
False
,
default
=
None
)
retMet_args
.
add_argument
(
'--alphabet'
,
dest
=
'alphabet'
,
type
=
str
,
\
help
=
"Which alphabet to use. Default is lz-bl.7"
,
required
=
False
,
default
=
"lz-bl.7"
)
retMet_args
.
add_argument
(
'-p'
,
'--pdbfile'
,
dest
=
'pdbfile'
,
type
=
str
,
\
retMet_args
.
add_argument
(
'-p'
,
'--pdbfile'
,
dest
=
'pdbfile'
,
type
=
str
,
\
help
=
"If a pdb file is provided, it will skip fake pdb file production step and use that file. Default is None"
,
help
=
"If a pdb file is provided, it will skip fake pdb file production step and use that file. Default is None"
,
required
=
False
,
default
=
None
)
required
=
False
,
default
=
None
)
...
@@ -384,7 +388,7 @@ def parse_command_line():
...
@@ -384,7 +388,7 @@ def parse_command_line():
return
args
return
args
def
doit
(
inAli
,
mutFile
,
retMet
,
bFile
,
fFile
,
n
,
N
,
jetfile
,
pdbfile
,
normWeightMode
):
def
doit
(
inAli
,
mutFile
,
retMet
,
bFile
,
fFile
,
n
,
N
,
jetfile
,
pdbfile
,
normWeightMode
,
alphabet
):
"""
"""
Perfect explanation for a function: typing the function call exactly!
Perfect explanation for a function: typing the function call exactly!
doit is basically the main function in disguise!
doit is basically the main function in disguise!
...
@@ -468,7 +472,7 @@ def doit(inAli,mutFile,retMet,bFile,fFile,n,N, jetfile, pdbfile, normWeightMode)
...
@@ -468,7 +472,7 @@ def doit(inAli,mutFile,retMet,bFile,fFile,n,N, jetfile, pdbfile, normWeightMode)
print
(
df
)
print
(
df
)
launchPred
(
prot
,
inAli
,
mutFile
,
normWeightMode
)
launchPred
(
prot
,
inAli
,
mutFile
,
normWeightMode
,
alphabet
)
#Do Python plotting here
#Do Python plotting here
#TODO: Eventually, I will do the map plotting with a completely independent
#TODO: Eventually, I will do the map plotting with a completely independent
...
@@ -514,7 +518,8 @@ def doit(inAli,mutFile,retMet,bFile,fFile,n,N, jetfile, pdbfile, normWeightMode)
...
@@ -514,7 +518,8 @@ def doit(inAli,mutFile,retMet,bFile,fFile,n,N, jetfile, pdbfile, normWeightMode)
def
main
():
def
main
():
args
=
parse_command_line
()
args
=
parse_command_line
()
doit
(
args
.
input
,
args
.
mutations
,
args
.
retrievingMethod
,
args
.
blastFile
,
\
doit
(
args
.
input
,
args
.
mutations
,
args
.
retrievingMethod
,
args
.
blastFile
,
\
args
.
fastaFile
,
args
.
nIter
,
args
.
NSeqs
,
args
.
jetfile
,
args
.
pdbfile
,
args
.
normweightmode
)
args
.
fastaFile
,
args
.
nIter
,
args
.
NSeqs
,
args
.
jetfile
,
args
.
pdbfile
,
\
args
.
normweightmode
,
args
.
alphabet
)
if
(
__name__
==
'__main__'
):
if
(
__name__
==
'__main__'
):
main
()
main
()
...
...
gemmeAnal.py
View file @
2eef3ef9
...
@@ -172,12 +172,12 @@ def launchJET(prot, retMet, bFile, fFile, pdbfile, chains, n, N, nl):
...
@@ -172,12 +172,12 @@ def launchJET(prot, retMet, bFile, fFile, pdbfile, chains, n, N, nl):
return
(
reCode
)
return
(
reCode
)
# Run Rscript to compute predictions
# Run Rscript to compute predictions
def
launchPred
(
prot
,
inAli
,
mutFile
,
normWeightMode
):
def
launchPred
(
prot
,
inAli
,
mutFile
,
normWeightMode
,
alphabet
):
if
mutFile
!=
''
:
if
mutFile
!=
''
:
rcmd
=
"Rscript --save $GEMME_PATH/computePred.R "
+
prot
+
" "
+
inAli
+
" FALSE "
+
mutFile
+
" "
+
normWeightMode
rcmd
=
"Rscript --save $GEMME_PATH/computePred.R "
+
prot
+
" "
+
inAli
+
" FALSE "
+
mutFile
+
" "
+
normWeightMode
+
" "
+
alphabet
else
:
else
:
rcmd
=
"Rscript --save $GEMME_PATH/computePred.R "
+
prot
+
" "
+
inAli
+
" TRUE none "
+
normWeightMode
rcmd
=
"Rscript --save $GEMME_PATH/computePred.R "
+
prot
+
" "
+
inAli
+
" TRUE none "
+
normWeightMode
+
" "
+
alphabet
print
(
"
\n
Running:
\n
"
+
rcmd
)
print
(
"
\n
Running:
\n
"
+
rcmd
)
reCode
=
subprocess
.
call
(
rcmd
,
shell
=
True
)
reCode
=
subprocess
.
call
(
rcmd
,
shell
=
True
)
...
...
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