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Commit 9175fdba by Mustafa Tekpinar
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Added sstjetormaxtwocomponent as default normweightmode.

parent 7447bfab
Showing with 235 additions and 11 deletions
docs/installation.rst
......@@ -15,12 +15,30 @@ ESGEMME has the following external dependencies:
* java
* naccess: http://www.bioinf.manchester.ac.uk/naccess/
* muscle: https://www.drive5.com/muscle/
* seqinr R package: https://cran.r-project.org/web/packages/seqinr/index.html
* dssp for secondary structure prediction.
After you installed JET2 define a parameter called JET2_PATH inside your .profile file.
You can open .profile as follows:
These tools should be installed to be able to use ESGEMME.
.. code:: bash
gedit ~/.profile
You should add a command like below to the end of that file, save and exit.
.. code:: bash
export JET2_PATH=/home/tekpinar/JET2/
Please, do not forget to replace /home/tekpinar/JET2 with your own file path.
Then, source the saved .profile so that the environment variable will be taken into account:
.. code:: bash
source ~/.profile
JET2 is essential and it should be installed to be able to use ESGEMME.
Preparation of the environment and installation of ESGEMME
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
......@@ -88,16 +106,41 @@ Please note that default dssp in Ubuntu 22.04 is not working properly.
Check the location of hhsuite folder and add it to your path
In my case it was in /home/tekpinar/research/lcqb folder. Therefore, I added the following line
to my .profile file.
PATH="/home/tekpinar/research/lcqb/hhsuite/bin:/home/tekpinar/research/lcqb/hhsuite/scripts:$PATH"
Open .profile file with gedit:
.. code:: bash
Then
source ~/.profile
gedit ~/.profile
Now, add the following line to the end of the file.
.. code:: bash
PATH="/home/tekpinar/research/lcqb/hhsuite/bin:/home/tekpinar/research/lcqb/hhsuite/scripts:$PATH"
Of course, your path will not be /home/tekpinar/research/lcqb/ and you have to modify the path according to
your system. Save the file and exit. Then,
.. code:: bash
source ~/.profile
#
cd ESGEMME
#Download ESGEMME from http://gitlab.lcqb.upmc.fr/tekpinar/ESGEMME repository and go inside the ESGEMME folder.!
You can download the master version using command line as follows:
.. code:: bash
git clone http://gitlab.lcqb.upmc.fr/tekpinar/ESGEMME.git
If you would like the development version:
.. code:: bash
git clone -b development http://gitlab.lcqb.upmc.fr/tekpinar/ESGEMME.git
.. code:: bash
cd ESGEMME
......@@ -115,6 +158,7 @@ file according to your system.
cd ../
#Installing the required R packages
.. code:: bash
sudo Rscript -e 'install.packages("seqinr", repos="http://cran.us.r-project.org", dependencies=TRUE)'
......
esgemme/computePred.R
......@@ -84,9 +84,38 @@ if ((normWeightMode=="max")){
quit(status=-1)
}
}
}else if (normWeightMode=="sstjetormaxtwocomponent"){
print("Using only sstjetormaxtwocomponent")
for (row in 1:nrow(jet)) {
if(sum(colnames(jet)=="sstjetormaxtwocomponent")==1){
trace<-append(trace, jet[row, "sstjetormaxtwocomponent"])
}else{
print("No field called sstjetormaxtwocomponent in the JET output!")
quit(status=-1)
}
}
}else if (normWeightMode=="sstjetormaxthirdchanged"){
print("Using only sstjetormaxthirdchanged")
for (row in 1:nrow(jet)) {
if(sum(colnames(jet)=="sstjetormaxthirdchanged")==1){
trace<-append(trace, jet[row, "sstjetormaxthirdchanged"])
}else{
print("No field called sstjetormaxthirdchanged in the JET output!")
quit(status=-1)
}
}
}else if (normWeightMode=="sstjetormaxthirdpcstar"){
print("Using only sstjetormaxthirdpcstar")
for (row in 1:nrow(jet)) {
if(sum(colnames(jet)=="sstjetormaxthirdpcstar")==1){
trace<-append(trace, jet[row, "sstjetormaxthirdpcstar"])
}else{
print("No field called sstjetormaxthirdpcstar in the JET output!")
quit(status=-1)
}
}
}else if (normWeightMode=="tjetormax"){
print("Using tjetormax with inverse CV")
print("Using tjetormax with inverse")
for (row in 1:nrow(jet)) {
if(sum(colnames(jet)=="traceMax")==1){
trace<-append(trace, max((jet[row, "traceMax"]+jet[row, "pc"])/2.0, max((jet[row, "traceMax"]+1.0-jet[row, "cv"])/2.0, (jet[row, "pc"]+1.0-jet[row, "cv"])/2.0 )))
......
esgemme/esgemme.py
......@@ -936,8 +936,8 @@ def parse_command_line():
parser.add_argument('--normweightmode', dest='normweightmode', type=str, \
help="It can be one of these: 'tjet', 'cv', 'pc',"+\
"max, tjetormax or sstjetormax. Default is 'tjet'.",
required=False, default="tjet")
"max, tjetormax or sstjetormaxtwocomponent. Default is 'tjet'.",
required=False, default="sstjetormaxtwocomponent")
parser.add_argument('--verbose', dest='verbose', type=bool, \
help="This argument controls amount of the output. Default is 'False'."+\
......@@ -1004,6 +1004,9 @@ def doit(inAli,mutFile,retMet,bFile,fFile,n,N, jetfile, pdbfile, normWeightMode,
(normWeightMode != 'pc') and \
(normWeightMode != 'max') and \
(normWeightMode != 'tjetormax') and \
(normWeightMode != 'sstjetormaxtwocomponent') and \
(normWeightMode != 'sstjetormaxthirdchanged') and \
(normWeightMode != 'sstjetormaxthirdpcstar') and \
(normWeightMode != 'sstjetormax')):
print("ERROR: normWeightMode can only be 'tjet', 'cv', 'pc', "+\
"'max', 'tjetormax' or 'sstjetormax'!")
......@@ -1073,6 +1076,154 @@ def doit(inAli,mutFile,retMet,bFile,fFile,n,N, jetfile, pdbfile, normWeightMode,
df.to_csv(prot+"_jet.res", header=True, index=None, sep='\t', mode='w')
#sys.exit(-1)
if((normWeightMode=='sstjetormaxtwocomponent')):
if (pdbfile == None):
print("ERROR: There is not any pdb file.")
sys.exit(-1)
else:
calculateSecondaryStructure(pdbfile)
countCoilSegments(pdbfile+".dssp")
df = pd.read_table(prot+"_jet.res", sep="\s+")
df2 = pd.read_table(pdbfile+".dssp.new", header=None, sep=",")
df2.columns = ['pos', 'ss', 'length']
mergedRes = pd.merge(df, df2, on ='pos', right_index=False)
if(debug):
print(df['pos'])
print(pdbfile+".dssp")
print(os.getcwd())
print(df2)
print(mergedRes)
sstjetormaxList = []
# maxCoilLength = 5
print("WARNING: Max. coil length = {}".format(maxCoilLength))
for index, row in mergedRes.iterrows():
if(row['ss']=='C') and (row['length']>maxCoilLength):
sstjetormaxList.append(row['trace'])
else:
maxVal = max([((row['trace']+row['pc'])/2.0), ((row['trace']+row['cv'])/2.0)])
sstjetormaxList.append(maxVal)
#sstjetormaxList=rankSortProteinData(sstjetormaxList, inverted=False)
df['sstjetormaxtwocomponent'] = sstjetormaxList
df['sstjetormaxtwocomponent'] = df['sstjetormaxtwocomponent'].round(decimals = 4)
df.to_csv(prot+"_jet.res", header=True, index=None, sep='\t', mode='w')
#sys.exit(-1)
if((normWeightMode=='sstjetormaxthirdchanged')):
if (pdbfile == None):
print("ERROR: There is not any pdb file.")
sys.exit(-1)
else:
calculateSecondaryStructure(pdbfile)
countCoilSegments(pdbfile+".dssp")
df = pd.read_table(prot+"_jet.res", sep="\s+")
df2 = pd.read_table(pdbfile+".dssp.new", header=None, sep=",")
df2.columns = ['pos', 'ss', 'length']
mergedRes = pd.merge(df, df2, on ='pos', right_index=False)
if(debug):
print(df['pos'])
print(pdbfile+".dssp")
print(os.getcwd())
print(df2)
print(mergedRes)
sstjetormaxList = []
# maxCoilLength = 5
print("WARNING: Max. coil length = {}".format(maxCoilLength))
for index, row in mergedRes.iterrows():
if(row['ss']=='C') and (row['length']>maxCoilLength):
sstjetormaxList.append(row['trace'])
else:
maxVal = max([((row['trace']+row['pc'])/2.0), ((row['trace']+row['cv'])/2.0), ((row['trace']))])
sstjetormaxList.append(maxVal)
#sstjetormaxList=rankSortProteinData(sstjetormaxList, inverted=False)
df['sstjetormaxthirdchanged'] = sstjetormaxList
df['sstjetormaxthirdchanged'] = df['sstjetormaxthirdchanged'].round(decimals = 4)
df.to_csv(prot+"_jet.res", header=True, index=None, sep='\t', mode='w')
if((normWeightMode=='sstjetormaxthirdpcstar')):
if (pdbfile == None):
print("ERROR: There is not any pdb file.")
sys.exit(-1)
else:
from collections import OrderedDict
pcStar = OrderedDict()
pcStar={'A':0.38,
'V':0.54,
'L':0.45,
'I':0.60,
'P':0.18,
'F':0.50,
'W':0.27,
'M':0.40,
'G':0.36,
'S':0.23,
'T':0.24,
'C':0.45,
'Y':0.15,
'N':0.13,
'Q':0.07,
'D':0.15,
'E':0.18,
'K':0.04,
'R':0.02,
'H':0.17}
oneLetter2ThreeLetters = {'C': 'CYS', 'D': 'ASP', 'S': 'SER', 'Q': 'GLN', 'K': 'LYS',
'I': 'ILE', 'P': 'PRO', 'T': 'THR', 'F': 'PHE', 'N': 'ASN',
'G': 'GLY', 'H': 'HIS', 'L': 'LEU', 'R': 'ARG', 'W': 'TRP',
'A': 'ALA', 'V': 'VAL', 'E': 'GLU', 'Y': 'TYR', 'M': 'MET'}
threeLetters2oneLetter = {v: k for k, v in oneLetter2ThreeLetters.items()}
calculateSecondaryStructure(pdbfile)
countCoilSegments(pdbfile+".dssp")
df = pd.read_table(prot+"_jet.res", sep="\s+")
pcstarList = []
for index, row in df.iterrows():
print(row['pos'], row['AA'])
singleLetterCode = threeLetters2oneLetter[row['AA']]
pcstarList.append(pcStar[singleLetterCode])
import numpy as np
df['pcstar'] = list(np.array(pcstarList)/(np.array(pcstarList).max()))
print(df)
df2 = pd.read_table(pdbfile+".dssp.new", header=None, sep=",")
df2.columns = ['pos', 'ss', 'length']
mergedRes = pd.merge(df, df2, on ='pos', right_index=False)
if(debug):
print(df['pos'])
print(pdbfile+".dssp")
print(os.getcwd())
print(df2)
print(mergedRes)
sstjetormaxList = []
# maxCoilLength = 5
print("WARNING: Max. coil length = {}".format(maxCoilLength))
for index, row in mergedRes.iterrows():
if(row['ss']=='C') and (row['length']>maxCoilLength):
sstjetormaxList.append(row['trace'])
else:
maxVal = max([((row['trace']+row['pc'])/2.0), ((row['trace']+row['cv'])/2.0), ( (row['cv']+row['pcstar'])/2.0 )])
sstjetormaxList.append(maxVal)
#sstjetormaxList=rankSortProteinData(sstjetormaxList, inverted=False)
df['sstjetormaxthirdpcstar'] = sstjetormaxList
df['sstjetormaxthirdpcstar'] = df['sstjetormaxthirdpcstar'].round(decimals = 4)
df.to_csv(prot+"_jet.res", header=True, index=None, sep='\t', mode='w')
#sys.exit(-1)
# #If a real pdb file is given, calculate dfi for the residues.
# if(((normWeightMode=='tracemovingaverage'))):
# print("Calculating trace moving average per residue!")
......
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