Commit cce7cb89 by Mustafa Tekpinar

Removed Linux grep command calls.

parent 2d117e24
......@@ -21,7 +21,7 @@ ESGEMME requires two files:
One of the fastest ways to obtain both input MSA and a PDB file is to run colabfold:
https://colab.research.google.com/github/sokrypton/ColabFold/blob/main/AlphaFold2.ipynb
Please note that the MSA file produced by colabfold (a3m file) can contain gaps in the query sequence. You have to remove them before using it in ESGEMME.
Please note that the MSA file produced by colabfold (a3m file) can contain gaps in the query sequence. You have to remove them before using it in ESGEMME. You can remove the gaps with pragrams that have a GUI, such as ugene (http://ugene.net/) or jalview (https://www.jalview.org/).
For testing purpose, you can find example input files for BLAT protein in data/ folder of this repository.
......@@ -81,9 +81,12 @@ export ESGEMME_PATH=/path-to-ESGEMME-directory/
#### Installing the dependencies:
ESGEMME has the following external dependencies:
* Joint Evolutionary Trees: http://www.lcqb.upmc.fr/JET2/
* seqinr R package: https://cran.r-project.org/web/packages/seqinr/index.html
* naccess: http://www.bioinf.manchester.ac.uk/naccess/
* Joint Evolutionary Trees: http://www.lcqb.upmc.fr/JET2/ and its dependencies:
- 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
These tools should be installed to be able to use ESGEMME.
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R273S -0.030727435
R273T -0.017076403
R273V -0.039767452
R273W -0.143334305
R273M -0.104095374
Q274E -0.05505396
Q274A 0.021095374
Q274C 0.002516021
Q274D -1.901776732
Q274F -0.114884101
Q274N -0.138912435
Q274H 0.015989086
Q274I -0.035070981
Q274K -0.067261017
Q274L 0.004304036
Q274M -0.0016282929999999
Q274T -0.039528661
Q274P -1.761989201
Q274R -0.067524796
Q274G -0.353408171
Q274V 0.017103224
Q274S -0.036141202
Q274Y -0.092507326
Q274W 0.0223956739999999
I275T -2.361641829
I275C -1.816160071
I275D -2.93899551
I275E -2.747169622
I275F 0.08968222
I275G -2.711967313
I275H -2.541811455
I275V -0.044125186
I275K -2.755343908
I275M -0.220181281
I275N -2.476543529
I275P -3.0192967260000003
I275Q -2.642484156
I275R -2.93873551
I275S -2.732310421
I275A -2.439738277
I275L -0.126616109
I275Y -1.614571656
I275W -2.362077217
A276W -0.913513533
A276Y -0.088587526
A276C -0.299150607
A276D -1.550481094
A276E -0.779277688
A276F -0.088089711
A276G -0.344260545
A276H -0.0692059
A276I -1.478838915
A276K 0.049749611
A276L -0.60293422
A276M -0.06703507
A276N -0.616039405
A276P -2.550635631
A276Q -0.052753796
A276R -0.022418982
A276S -0.055652281
A276T -0.6621733879999999
A276V -0.172800332
E277G -0.146375894
E277W -1.5297713590000002
E277Y -0.677625439
E277A -0.084317277
E277C -0.6154974639999999
E277D -0.061959965
E277F -0.970996006
E277H -0.333711473
E277I -0.01757013
E277K -0.144432723
E277M -0.253701899
E277N -0.077807463
E277P -2.622383871
E277Q -0.046492212
E277R -0.086642792
E277S -0.123684104
E277T -0.1008509019999999
E277L -0.0744075159999999
E277V -0.169901523
I278A -2.41015192
I278C -2.724411475
I278W -2.958656634
I278T -2.2320846430000003
I278S -2.904324884
I278R -2.68954879
I278Q -2.882117157
I278P -2.732630383
I278N -2.518349116
I278Y -2.5746331330000003
I278M -0.522765186
I278K -2.392231202
I278H -2.801357298
I278G -3.270264765
I278F -2.779089453
I278E -2.768557532
I278D -2.7189780810000004
I278L -0.61840592
I278V -0.232038281
G279D -2.457716759
G279Y -2.126980805
G279E -2.340217753
G279F -2.008497757
G279H -2.631557034
G279I -1.940218459
G279L -1.730182212
G279M -1.7132280009999998
G279C -1.062366435
G279A -0.144679187
G279Q -2.624825223
G279R -2.726890745
G279S -0.343477982
G279T -1.678160555
G279V -1.91550309
G279W -2.295020434
G279P -2.7982254760000003
G279N -2.428784255
G279K -2.47432449
A280Q 0.001830592
A280C -0.4229538439999999
A280D 0.0026237979999999
A280E 0.017609574
A280F -0.02941169
A280G -0.0300744529999999
A280H -0.00561883
A280W -0.063529329
A280I -0.036654566
A280L -0.032356586
A280M 0.037007801
A280N 0.011650471
A280P -2.494082504
A280V 0.001853805
A280R 0.0306794689999999
A280K 0.075160398
A280S -0.015325554
A280Y -0.060442832
A280T -0.043402807
S281E 0.019996552
S281F -0.310771785
S281G -0.975169465
S281H -0.0019367639999999
S281I 0.005375411
S281K 0.039123014
S281L -0.086506977
S281W -1.05525514
S281N 0.131987915
S281P -2.321086677
S281Q 0.020266376
S281R -0.042061968
S281T -0.000301299
S281V 0.013298684
S281A 0.016871306
S281Y -0.098156934
S281M -0.060161433
S281C -0.239623183
S281D -0.313969132
L282A -0.1030010419999999
L282Y -2.60798928
L282W -2.781623897
L282V -0.020573364
L282T -0.231657908
L282S -1.65506219
L282R -2.703589801
L282P -2.427915802
L282N -2.321377818
L282Q -1.722284209
L282K -2.571033681
L282I 0.07867216
L282H -3.0112685480000003
L282G -2.415650406
L282F -0.663794413
L282E -2.95431837
L282D -2.529507892
L282C -0.617685383
L282M 0.01266562
I283H -2.078123175
I283G -2.247811139
I283F -0.123745791
I283A -0.537631351
I283D -2.788857489
I283C -0.657012279
I283E -2.601698129
I283L -0.190349095
I283K -2.249930577
I283N -2.485288831
I283P -2.613881608
I283Q -1.955217642
I283R -1.948248642
I283S -1.487969518
I283T -0.300995366
I283V -0.030749035
I283W -1.71314797
I283M -0.088552239
I283Y -0.082166485
K284C -0.918670018
K284R -0.041719978
K284Y -0.1114722619999999
K284W -0.4498846729999999
K284V -0.261296948
K284T -0.090440961
K284S -0.020231824
K284Q -0.071555783
K284P -2.593265847
K284N -0.074528787
K284A -0.0389621189999999
K284L -0.044259464
K284I -0.514835422
K284H -0.005217661
K284G -0.092461612
K284F -0.286851229
K284E -0.027480766
K284D -0.061476142
K284M -0.107795746
H285N 0.024088321
H285V -0.8257314490000001
H285T -0.113390602
H285S -0.160348785
H285R -0.157191089
H285Q -0.141955412
H285P -2.724870193
H285M -0.226841047
H285A -0.465274388
H285K -0.271887231
H285I -2.723116824
H285G -0.50993699
H285F -0.149276371
H285E -0.3387617089999999
H285D -1.535460946
H285C -0.251095353
H285W -0.076231453
H285L -0.553995627
H285Y -0.094685853
W286Y -0.962360954
W286D -2.859106006
W286V -2.813837323
W286T -2.806421744
W286S -2.967712254
W286R -2.707731259
W286Q -2.699394131
W286P -2.793520382
W286N -2.584006677
W286M -1.6997812630000002
W286L -2.244688275
W286K -2.566351628
W286I -2.429502334
W286H -1.782739799
W286G -3.228429174
W286F -0.780425279
W286E -2.545852462
W286C -2.983761815
W286A -3.178798104
......@@ -19,7 +19,7 @@ import glob
from prody import *
from scipy.stats import rankdata
from Bio import AlignIO
from Bio import AlignIO, SeqIO
import biotite.structure.io as strucio
import biotite.application.dssp as dssp
......@@ -29,11 +29,40 @@ import biotite.structure.io.pdb as pdb
import pandas as pd
def selectMaxFastaSequences(inputMSAfile, outputMSAfile, maxNumSeqs=40001):
"""
Given a multiple sequence alignment file in FASTA format,
select the top maxNumSeqs sequences and write them to outputMSAfile.
Parameters
----------
inputMSAfile: string
Name of the input multiple sequence alignment file in FASTA format.
outputMSAfile: string
Name of the output multiple sequence alignment file in FASTA format.
maxNumSeqs: int
Maximum number of sequences to be selected from the input MSA file.
Default is 40000 + 1 (for query sequence) .
Returns
-------
Nothing
"""
alignment = AlignIO.read(inputMSAfile, 'fasta')
# print(alignment[0].seq)
numSeqInMSA = len(alignment)
# print("Number of sequences read: "+str(numSeqInMSA))
with open(outputMSAfile, "w") as handle:
SeqIO.write(alignment[0:maxNumSeqs], handle, "fasta")
#############The following part between # signs is moved from gemmeAnal.py to
# make the code more simple.
def extractQuerySeq(filename):
"""
# Extract the query sequence from the input alignment
Extract the query sequence from the input alignment
"""
fIN = open(filename,"r")
......@@ -209,13 +238,17 @@ def launchJET(prot, retMet, bFile, fFile, pdbfile, chains, n, N, nl):
shutil.copy2(fFile, fFile+".orig")
#I think this subprocess call causes overwriting of the fasta file.
#subprocess.call("cp "+fFile+" "+prot+"_"+chainID+".fasta",shell=True)
grpcmd="grep -m "+str(int(N)+1)+" -A "+str(nl)+" '^>' "+fFile+".orig > "+prot+"_"+chainID+".fasta"
# grpcmd="grep -m "+str(int(N)+1)+" -A "+str(nl)+" '^>' "+fFile+".orig > "+prot+"_"+chainID+".fasta"
# print("\nRunning:\n"+grpcmd)
# subprocess.call(grpcmd,shell=True)
selectMaxFastaSequences(fFile+".orig", prot+"_"+chainID+".fasta", maxNumSeqs=(int(N)+1))
else:
#subprocess.call("cp "+fFile+" "+prot+"_"+chainID+".fasta",shell=True)
grpcmd="grep -m "+str(int(N)+1)+" -A "+str(nl)+" '^>' "+fFile+" > "+prot+"_"+chainID+".fasta"
#grpcmd="grep -m "+str(int(N)+1)+" -A "+str(nl)+" '^>' "+fFile+" > "+prot+"_"+chainID+".fasta"
print("\nRunning:\n"+grpcmd)
subprocess.call(grpcmd,shell=True)
#print("\nRunning:\n"+grpcmd)
#subprocess.call(grpcmd,shell=True)
selectMaxFastaSequences(fFile, prot+"_"+chainID+".fasta", maxNumSeqs=(int(N)+1))
if(pdbfile == None):
jetcmd = "java -Xmx4096m -cp $JET2_PATH:$JET2_PATH/jet/extLibs/vecmath.jar jet.JET -c default.conf -i "+\
prot+".pdb -o `pwd` -p J -r input -f "+prot+"_"+chainID+".fasta -d chain -n "+n+" > "+prot+".out"
......
......@@ -48,7 +48,7 @@ then
python $ESGEMME_PATH/esgemme.py ../data/aliBLAT.fasta -r input -f ../data/aliBLAT.fasta \
--pdbfile ../data/blat-af2.pdb --normweightmode sstjetormax \
-m ../data/Stiffler_2015_BLAT_ECOLX.mut
#demust compare -i ../data/BLAT_ECOLX_Stiffler_2015_experimental.dat --itype singleline -j BLAT_normPred_evolCombi.txt --jtype singleline
else
echo "Running EGEMME with a user-provided alignment file."
echo "Since a pdb file is not provided, only evolutionary information will be used!"
......
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