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Commit 12d7708d by Mustafa Tekpinar
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Removed ESGEMME_PATH dependency for alphabets files.

parent 0c7fe1f3
Showing with 18 additions and 8 deletions
Dockerfile
...@@ -9,12 +9,13 @@ ENV ESGEMME_PATH=/home/tekpinar/research/lcqb/ESGEMME ...@@ -9,12 +9,13 @@ ENV ESGEMME_PATH=/home/tekpinar/research/lcqb/ESGEMME
COPY ./JET2/ ./JET2/ COPY ./JET2/ ./JET2/
COPY ./naccess2.1.1 ./naccess2.1.1 COPY ./naccess2.1.1 ./naccess2.1.1
COPY ./ESGEMME/esgemme/esgemme.py ./ESGEMME/esgemme/esgemme.py COPY ./ESGEMME/esgemme/esgemme.py ./ESGEMME/esgemme/esgemme.py
COPY ./ESGEMME/esgemme/alphabets ./ESGEMME/esgemme/alphabets
COPY ./ESGEMME/esgemme/__init__.py ./ESGEMME/esgemme/__init__.py COPY ./ESGEMME/esgemme/__init__.py ./ESGEMME/esgemme/__init__.py
COPY ./ESGEMME/setup.py ./ESGEMME/setup.py COPY ./ESGEMME/setup.py ./ESGEMME/setup.py
COPY ./ESGEMME/requirements.txt ./ESGEMME/requirements.txt COPY ./ESGEMME/requirements.txt ./ESGEMME/requirements.txt
COPY ./ESGEMME/README.md ./ESGEMME/README.md COPY ./ESGEMME/README.md ./ESGEMME/README.md
COPY ./ESGEMME/pred.R ./ESGEMME/pred.R COPY ./ESGEMME/esgemme/pred.R ./ESGEMME/esgemme/pred.R
COPY ./ESGEMME/computePred.R ./ESGEMME/computePred.R COPY ./ESGEMME/esgemme/computePred.R ./ESGEMME/esgemme/computePred.R
COPY ./ESGEMME/esgemme/default.conf ./ESGEMME/esgemme/default.conf COPY ./ESGEMME/esgemme/default.conf ./ESGEMME/esgemme/default.conf
COPY ./ESGEMME/data/ ./ESGEMME/data/ COPY ./ESGEMME/data/ ./ESGEMME/data/
COPY ./ESGEMME/examples/ ./ESGEMME/examples/ COPY ./ESGEMME/examples/ ./ESGEMME/examples/
......
esgemme/esgemme.py
...@@ -323,6 +323,10 @@ def launchPred(prot,inAli,mutFile, normWeightMode, alphabet): ...@@ -323,6 +323,10 @@ def launchPred(prot,inAli,mutFile, normWeightMode, alphabet):
with as_file(source) as esgemme_computePred_R_path: with as_file(source) as esgemme_computePred_R_path:
shutil.copy2(esgemme_computePred_R_path, os.getcwd()) shutil.copy2(esgemme_computePred_R_path, os.getcwd())
source = files('esgemme').joinpath('alphabets/'+alphabet+'.txt')
with as_file(source) as esgemme_alphabet:
shutil.copy2(esgemme_alphabet, os.getcwd())
if (mutFile!=''): if (mutFile!=''):
# rcmd="Rscript --save $ESGEMME_PATH/computePred.R "+prot+" "+inAli+" FALSE "+mutFile+" "+normWeightMode+" "+alphabet # rcmd="Rscript --save $ESGEMME_PATH/computePred.R "+prot+" "+inAli+" FALSE "+mutFile+" "+normWeightMode+" "+alphabet
rcmd="Rscript --save computePred.R "+prot+" "+inAli+" FALSE "+mutFile+" "+normWeightMode+" "+alphabet rcmd="Rscript --save computePred.R "+prot+" "+inAli+" FALSE "+mutFile+" "+normWeightMode+" "+alphabet
......
esgemme/pred.R
...@@ -174,9 +174,11 @@ computeNbSeqs<-function(mat,gap=FALSE){ ...@@ -174,9 +174,11 @@ computeNbSeqs<-function(mat,gap=FALSE){
# } # }
computeNbSeqsAlph<-function(nbSeqs,alphabet){ computeNbSeqsAlph<-function(nbSeqs,alphabet){
path=paste(Sys.getenv("ESGEMME_PATH"),"/data/alphabets/",sep="") # path=paste(Sys.getenv("ESGEMME_PATH"),"/data/alphabets/",sep="")
AA = read.table(paste(path,alphabet,".txt",sep=""))$V1 # AA = read.table(paste(path,alphabet,".txt",sep=""))$V1
facAA = rep(NA,20) AA = read.table(paste(alphabet,".txt",sep=""))$V1
facAA = rep(NA,20)
for(Let in AA){ for(Let in AA){
Let = toString(Let) Let = toString(Let)
lets = strsplit(Let,"")[[1]] lets = strsplit(Let,"")[[1]]
...@@ -210,8 +212,9 @@ readMut<-function(fname){ ...@@ -210,8 +212,9 @@ readMut<-function(fname){
} }
which.class<-function(a,alphabet){ which.class<-function(a,alphabet){
path=paste(Sys.getenv("ESGEMME_PATH"),"/data/alphabets/",sep="") # path=paste(Sys.getenv("ESGEMME_PATH"),"/data/alphabets/",sep="")
AA = read.table(paste(path,alphabet,".txt",sep=""))$V1 # AA = read.table(paste(path,alphabet,".txt",sep=""))$V1
AA = read.table(paste(alphabet,".txt",sep=""))$V1
for(Let in AA){ for(Let in AA){
Let = toString(Let) Let = toString(Let)
lets = tolower(strsplit(Let,"")[[1]]) lets = tolower(strsplit(Let,"")[[1]])
......
examples/example-esgemme-script.sh
...@@ -8,6 +8,8 @@ then ...@@ -8,6 +8,8 @@ then
# rm -rf BLAT.pdb # rm -rf BLAT.pdb
# rm -rf BLAT.fasta # rm -rf BLAT.fasta
rm -rf BLAT* rm -rf BLAT*
rm -rf *.R
rm -rf *.txt
rm -f default.conf caracTest.dat rm -f default.conf caracTest.dat
rm -rf bin*.fasta rm -rf bin*.fasta
rm -rf ../data/blat-af2.pdb.dssp ../data/blat-af2.pdb.dssp.new rm -rf ../data/blat-af2.pdb.dssp ../data/blat-af2.pdb.dssp.new
......
setup.py
...@@ -64,5 +64,5 @@ setup(name='esgemme', ...@@ -64,5 +64,5 @@ setup(name='esgemme',
] ]
}, },
include_package_data=True, include_package_data=True,
package_data={'esgemme':['default.conf', 'computePred.R', 'pred.R']}, package_data={'esgemme':['default.conf', 'computePred.R', 'pred.R', 'alphabets/*']},
) )
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