Moved extractQuerySeq from gemmeAnal.py to sgemme.py.

gemmeAnal.py

@@ -133,7 +133,9 @@ def launchJET(prot, retMet, bFile, fFile, pdbfile, chains, n, N, nl):
 
 	chainID = chains[0]
 	
+	#TODO: Remove Bash dependency here. Make the copying process in Python
 	subprocess.call("cp $SGEMME_PATH/default.conf .",shell=True)
+	
 	if retMet=="input":
 		if bFile!='':
 			#TODO: I think these two lines must be here as well but I am not sure. 

sgemme.py

@@ -22,6 +22,30 @@ from gemmeAnal import *
 
 import pandas as pd
 
+def extractQuerySeq(filename):
+	"""
+		# Extract the query sequence from the input alignment
+	"""
+
+	fIN = open(filename,"r")
+	lines = fIN.readlines()
+	fIN.close()
+
+	if lines[0][0]!=">":
+		raise Exception('bad FASTA format')
+	else:
+		prot = re.compile("[^A-Z0-9a-z]").split(lines[0][1:])[0]
+		fOUT = open(prot+".fasta","w")
+		fOUT.write(">"+prot+"\n")
+		seq=""
+		i = 1
+		while lines[i][0]!=">":
+			seq = seq + lines[i].strip().strip(".").strip("-")
+			fOUT.write(lines[i])
+			i = i + 1
+	fOUT.close()
+	return prot,seq,i-1
+
 def rankSortProteinData(dataArray, inverted=True):
     """
         This function ranksorts protein data and converts it

tests/BLAT.fasta

->BLAT
-HPETLVKVKDAEDQLGARVGYIELDLNSGKILESFRPEERFPMMSTFKVL
-LCGAVLSRVDAGQEQLGRRIHYSQNDLVEYSPVTEKHLTDGMTVRELCSA
-AITMSDNTAANLLLTTIGGPKELTAFLHNMGDHVTRLDRWEPELNEAIPN
-DERDTTMPAAMATTLRKLLTGELLTLASRQQLIDWMEADKVAGPLLRSAL
-PAGWFIADKSGAGERGSRGIIAALGPDGKPSRIVVIYTTGSQATMDERNR
-QIAEIGASLIKHW

tests/caracTest.dat

-*****************************************
->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

tests/default.conf

-*****************************************
->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
-	

tests/example-gemme-run.sh

 #!/bin/bash
 
-python $GEMME_PATH/gemme.py aliBLAT.fasta -r input -f aliBLAT.fasta
+python $SGEMME_PATH/sgemme.py ../example/aliBLAT.fasta -r input -f ../example/aliBLAT.fasta