Commit 06ff7a4c by Mustafa Tekpinar

Added half-pc+cv option to normweightmode!

parent ba2786df
......@@ -100,7 +100,7 @@ print("running normalization...")
#This part of the code obtains max values of Trace, PC, or CV for weighting the
#normalized results.
trace = c()
if((normWeightMode=="trace+pc") | (normWeightMode=="pc+trace")){
if((normWeightMode=="max-trace-pc") | (normWeightMode=="max-pc-trace")){
print(paste("Using ", normWeightMode))
for (row in 1:nrow(jet)) {
if(sum(colnames(jet)=="traceMax")==1){
......@@ -109,7 +109,7 @@ if((normWeightMode=="trace+pc") | (normWeightMode=="pc+trace")){
trace<-append(trace, max(jet[row, "trace"], jet[row, "pc"]))
}
}
} else if ((normWeightMode=="trace+cv") | (normWeightMode=="cv+trace")){
} else if ((normWeightMode=="max-trace-cv") | (normWeightMode=="max-cv-trace")){
print(paste("Using ", normWeightMode))
for (row in 1:nrow(jet)) {
if(sum(colnames(jet)=="traceMax")==1){
......@@ -118,7 +118,7 @@ if((normWeightMode=="trace+pc") | (normWeightMode=="pc+trace")){
trace<-append(trace, max(jet[row, "trace"], jet[row, "cv"]))
}
}
} else if ((normWeightMode=="trace+pc+cv")|(normWeightMode=="trace+cv+pc")){
} else if ((normWeightMode=="max-trace-pc-cv")|(normWeightMode=="max-trace-cv-pc")){
print(paste("Using ", normWeightMode))
for (row in 1:nrow(jet)) {
if(sum(colnames(jet)=="traceMax")==1){
......@@ -127,6 +127,15 @@ if((normWeightMode=="trace+pc") | (normWeightMode=="pc+trace")){
trace<-append(trace, max(jet[row, "trace"], max(jet[row, "pc"], jet[row, "cv"])))
}
}
} else if ((normWeightMode=="half-cv+pc") | (normWeightMode=="half-pc+cv")){
print(paste("Using ", normWeightMode))
for (row in 1:nrow(jet)) {
if(sum(colnames(jet)=="traceMax")==1){
trace<-append(trace, max(jet[row, "traceMax"], jet[row, "cv"]))
}else{
trace<-append(trace, (jet[row, "pc"]+jet[row, "cv"])/2.0)
}
}
} else if (normWeightMode=="trace"){
print("Using only JET2 traces")
for (row in 1:nrow(jet)) {
......@@ -138,7 +147,7 @@ if((normWeightMode=="trace+pc") | (normWeightMode=="pc+trace")){
}
}else{
print("ERROR: Unknown --normWeightMode selected!")
print("It can only be 'trace', 'trace+pc', 'trace+cv' or 'trace+pc+cv'!")
print("It can only be 'trace', 'max-trace-pc', 'max-trace-cv', 'max-trace-pc-cv' or 'half-cv+pc'!")
}
print(trace)
......
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......@@ -19,6 +19,13 @@ then
cp ../tests/BLAT_jet.res .
python $GEMME_PATH/gemme.py aliBLAT.fasta -r input -f aliBLAT.fasta --jetfile BLAT_jet.res
elif [ "$1" == "withpdb" ]
then
#Please note that CV isa structural feature and it can not be calculated if you don't specify a pdb file.
echo "Using blat-curated.pdb for the structural feature calculations!"
python $GEMME_PATH/gemme.py aliBLAT.fasta -r input -f aliBLAT.fasta --pdbfile blat-curated.pdb --normweightmode max-trace-pc-cv
else
echo "Running GEMME with a user-provided alignment file."
python $GEMME_PATH/gemme.py aliBLAT.fasta -r input -f aliBLAT.fasta
......
......@@ -265,7 +265,7 @@ def parse_command_line():
required=False, default=None)
retMet_args.add_argument('--normweightmode', dest='normweightmode', type=str, \
help="It can be one of these: 'trace', 'trace+pc', 'trace+cv' or 'trace+pc+cv'. Default is 'trace'.",
help="It can be one of these: 'trace', 'max-trace-pc', 'max-trace-cv', 'max-trace-pc-cv' or 'half-cv+pc'. Default is 'trace'.",
required=False, default="trace")
args = parser.parse_args()
......@@ -303,6 +303,18 @@ def doit(inAli,mutFile,retMet,bFile,fFile,n,N, jetfile, pdbfile, normWeightMode)
print("query protein: "+prot)
if( (normWeightMode != 'trace') and \
(normWeightMode != 'max-trace-pc') and \
(normWeightMode != 'max-pc-trace') and \
(normWeightMode != 'max-trace-cv') and \
(normWeightMode != 'max-cv-trace') and \
(normWeightMode != 'max-trace-pc-cv') and \
(normWeightMode != 'max-trace-cv-pc') and \
(normWeightMode != 'half-pc+cv') and \
(normWeightMode != 'half-cv+pc')):
print("ERROR: normWeightMode can only be 'trace', 'max-trace-pc', 'max-trace-cv', 'max-trace-pc-cv' or 'half-cv+pc'!")
sys.exit(-1)
if((jetfile) == None):
#I intend to run JET2 completely externally!!
#It is too much buggy and it has too many dependencies.
......@@ -325,7 +337,7 @@ def doit(inAli,mutFile,retMet,bFile,fFile,n,N, jetfile, pdbfile, normWeightMode)
#Do Python plotting here
#TODO: Eventually, I will do the map plotting with a completely independent
# module and call the module here!
# module and call the module here! demust module was created!
#TODO: Mark the original (wildtype) residue locations with a dot or something
# special to show the original amino acid.
#TODO: You can even put letters on the top line like in EVmutation output.
......
File added
>BLAT
HPETLVKVKDAEDQLGARVGYIELDLNSGKILESFRPEERFPMMSTFKVL
LCGAVLSRVDAGQEQLGRRIHYSQNDLVEYSPVTEKHLTDGMTVRELCSA
AITMSDNTAANLLLTTIGGPKELTAFLHNMGDHVTRLDRWEPELNEAIPN
DERDTTMPAAMATTLRKLLTGELLTLASRQQLIDWMEADKVAGPLLRSAL
PAGWFIADKSGAGERGSRGIIAALGPDGKPSRIVVIYTTGSQATMDERNR
QIAEIGASLIKHW
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*****************************************
>BLAT:A
size 263 size of the sequence
numAli 43 Number of sequences in alignment
numMulti 43 Number of multiple alignment
partition 498;498;456;446 partition of sequences after PSI-BLAST+filtering
*****************************************
>SequenceRetrieving
method input change this parameter with -r option of JET. See usage of JET to obtain description of this parameter
format fasta fasta: fasta input file, fasta: fasta input file
*****************************************
>QBlast
eValue 1.0E-5 psiblast maximum expected value threshold
results 20000 maximum number of results
url http://www.ncbi.nlm.nih.gov/BLAST/Blast.cgi BlastQ server URL
database nr database used
matrix blosum62 matrix used to fetch homologs
gap_existence 11 BLOSUM62=11, PAM30=9, BLOSUM45=15, PAM70=BLOSUM80=10
gap_extension 1 BLOSUM62=1, PAM30=1, BLOSUM45=2, PAM70=BLOSUM80=1
max_iter 3 number of iteration for psi-blast
****************************************
>PDB
url http://www.rcsb.org/pdb/downloadFile.do URL of PDB server
*****************************************
>Filter
min_identity 0.20 min sequence identity
max_identity 0.98 max sequence identity
*****************************************
>Sample
length_cutoff 0.8 minimum sequence length expressed in number of residues
*****************************************
>Software
clustalW /usr/local/bin/clustalw2 clustalW system dependent command
muscle /usr/bin/muscle muscle system dependent command
naccess /home/tekpinar/research/carbone-lab-software/naccess2.1.1/naccess naccess system dependent command
psiblast /usr/bin/psiblast psiblast system dependent command
*****************************************
>Data
substMatrix /home/tekpinar/research/carbone-lab-software/JET2/matrix directory location of matrices used in JET (Blosum62, gonnet and hsdm)
blastDatabases /opt/blastdb directory location of databases used for local blast (nr{0-7})
*****************************************
>ET
coverage 0.95 maximum coverage percentage of trace
freq_cutoff 0.0 minimum frequency of trace residue
msaNumber -1 number of alignments (trees), -1 for JET computting
seqNumber -1 number of sequences in alignments, -1 for JET computting
*****************************************
>Access
probe_radius 1.4 radius of probe used for accessible surface detection
res_cutoff 0.05 minimum percentage accessible surface of a residu
atom_cutoff 0.01 minimum accessible surface of an atom
accessType chain change this parameter with -d option of JET. See usage of JET to obtain description of this parameter
*****************************************
>CV
max_dist 20.0 max distance
*****************************************
>Interface
cutoff 0 minimum percentage accessible surface variation of an interface residu
ligand no (yes|no) keep contact of ligand (SUBSTRATE, PRODUCT and COFACTOR of database ENZYME) to compute interface of protein
enzymeCpd /home/tekpinar/research/carbone-lab-software/JET2/jet/data/enzyme.txt location of file containing database ENZYME
homologousPDB no (yes|no) add interface residues of homologous structures (find in pdb database clustered at 95% of identities) to interface of protein
clusteredPDB /home/tekpinar/research/carbone-lab-software/JET2/jet/data/clusters95.txt location of pdb database clustered at 95% of identities
*****************************************
>Cluster
max_dist 5.0 max distance between atoms to aggregate
analysis 2 change this parameter with -a option of JET. See usage of JET to obtain description of this parameter
namePcCol pc name of the column in results file containing the phisical-chemical score of residues (do not change this parameter)
namePcLCol pcL name of the column in results file containing the residues propensities to be found at prot-lig interfaces (do not change this parameter)
nameTraceCol trace name of the column in results file containing the conservation score of residues (do not change this parameter)
coverage -1 change this parameter with -s option of JET. See usage of JET to obtain description of this parameter
#!/bin/bash
python $GEMME_PATH/gemme.py aliBLAT.fasta -r input -f aliBLAT.fasta
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