def bSite(path, params):
"""Aligns binding site residues of GPCRs and kinases."""
import queryDevice
import parse
import needle
ksAccFile = params['ksAccFile']
gsAccFile = params['gsAccFile']
ksAliFile = params['ksAliFile']
gsAliFile = params['gsAliFile']
sitePositions = params['sitePositions']
kinaseAcc = parseAcc(ksAccFile)
gpcrAcc = parseAcc(gsAccFile)
kinaseAli = parseKSAli(ksAliFile)
gpcrAli = parseGSAli(gsAliFile)
kinaseDict = sliceBS(kinaseAcc, kinaseAli, sitePositions['kinase'])
gpcrDict = sliceBS(gpcrAcc, gpcrAli, sitePositions['gpcr'])
# Processing the table of homologous pairs.
inFile = open( path, 'r')
lines = inFile.readlines()
inFile.close()
out = open(path ,'w')
out.write("%s\tbs_seq_id\tbs_seq_sim\n"%lines[0].rstrip('\n'))
seqIdDict = {}
for line in lines[1:]:
elements = line.split('\t')
proteinAcc_1 = elements[0]
proteinAcc_2 = elements[1]
pairName = ('_').join([proteinAcc_1, proteinAcc_2])
try:
(seqSim, seqId) = seqIdDict[pairName]
out.write("%s\t%s\t%s\n"%(line.rstrip('\n'), seqId, seqSim))
continue
except KeyError:
pass
if proteinAcc_1 in kinaseDict or proteinAcc_2 in kinaseDict:
(seq_1, seq_2) = (kinaseDict[proteinAcc_1], kinaseDict[proteinAcc_2])
elif proteinAcc_1 in gpcrDict and proteinAcc_2 in gpcrDict:
(seq_1, seq_2) = (gpcrDict[proteinAcc_1], gpcrDict[proteinAcc_2])
else:
out.write("%s\t%s\t%s\n"%(line.rstrip('\n'), None, None))
continue
################################################
# Align the sequences using needle from EMBOSS.
needleReport = needle.ungapped_needle(params['needlepath'], seq_1, seq_2)
################################################
(seqSim, seqId) = needle.parseNeedle(needleReport)
seqIdDict[pairName]=(seqSim, seqId)
out.write("%s\t%s\t%s\n"%(line.rstrip('\n'), seqId, seqSim))
out.close()
def fullSeq(path, params):
import pickle
import queryDevice
import needle
import random
inFile = open( path, 'r')
lines = inFile.readlines()
inFile.close()
out = open(path ,'w')
out.write("%s\tseq_id\tseq_sim\n"%lines[0].rstrip('\n'))
seqIdDict = {}
for line in lines[1:]:
elements = line.split('\t')
proteinAcc_1 = elements[0]
proteinAcc_2 = elements[1]
pairName = ('_').join([proteinAcc_1, proteinAcc_2])
try:
(seqSim, seqId) = seqIdDict[pairName]
out.write("%s\t%s\t%s\n"%(line.rstrip('\n'), seqId, seqSim))
continue
except KeyError:
#print "aligning sequences of: %s\t%s"%(proteinAcc_1, proteinAcc_2)
pass
data = queryDevice.queryDevice("SELECT td.protein_sequence, td.protein_accession FROM target_dictionary td WHERE td.protein_accession IN ('%s')"% "','".join([proteinAcc_1, proteinAcc_2]), params)
lkp = {}
for entry in data:
lkp[entry[1]] = entry[0]
try:
seq_1 = lkp[proteinAcc_1]
seq_2 = lkp[proteinAcc_2]
except KeyError:
seqIdDict[pairName] = (None, None)
out.write("%s\t%s\t%s\n"%(line.rstrip('\n'), None, None))
continue
################################################
# Align the sequences using needle from EMBOSS.
needleReport = needle.needle(params['needlepath'], seq_1, seq_2)
# Parse the output of the alignment
(seqSim, seqId) = needle.parseNeedle(needleReport)
seqIdDict[pairName] = (seqSim, seqId)
out.write("%s\t%s\t%s\n"%(line.rstrip('\n'), seqId, seqSim))
out.close()
def pfam_a(path, params):
import queryDevice
import needle
inFile = open( path, 'r')
lines = inFile.readlines()
inFile.close()
out = open(path ,'w')
out.write("%s\tdom_seq_id\tdom_seq_sim\tpfam_1\tpfam_2\n"%lines[0].rstrip('\n'))
seqIdDict = {}
for line in lines[1:]:
elements = line.split('\t')
proteinAcc_1 = elements[0]
proteinAcc_2 = elements[1]
pairName = ('_').join([proteinAcc_1, proteinAcc_2])
try:
(seqSim, seqId, pfam_1, pfam_2) = seqIdDict[pairName]
out.write("%s\t%s\t%s\t%s\t%s\n"%(line.rstrip('\n'), seqId, seqSim, pfam_1, pfam_2))
continue
except KeyError:
#print "aligning bs_containing domains of: %s\t%s"%(proteinAcc_1, proteinAcc_2)
pass
data_1 = queryDevice.queryDevice("""SELECT DISTINCT mp.pfam_a,
pd.start, pd.end, td.protein_sequence, td.protein_accession
FROM map_pfam mp
JOIN pfam_domains pd
ON mp.pfam_a = pd.pfam_a
JOIN target_dictionary td
ON td.protein_accession = mp.protein_accession
WHERE mp.protein_accession = '%s'
AND pd.protein_accession = '%s' """ % (proteinAcc_1, proteinAcc_1), params)
data_2 = queryDevice.queryDevice("""SELECT DISTINCT mp.pfam_a,
pd.start, pd.end, td.protein_sequence, td.protein_accession
FROM map_pfam mp
JOIN pfam_domains pd
ON mp.pfam_a = pd.pfam_a
JOIN target_dictionary td
ON td.protein_accession = mp.protein_accession
WHERE mp.protein_accession = '%s'
AND pd.protein_accession = '%s' """ % (proteinAcc_2, proteinAcc_2),params)
lkp = {}
for entry in data_1 + data_2:
(pfam, start, end, fullSeq, acc) = (entry[0], entry[1], entry[2], entry[3], entry[4])
seq = fullSeq[start:end]
lkp[acc] = (seq, pfam)
try:
seq_1 = lkp[proteinAcc_1][0]
pfam_1 =lkp[proteinAcc_1][1]
seq_2 = lkp[proteinAcc_2][0]
pfam_2 = lkp[proteinAcc_2][1]
except KeyError:
out.write("%s\t%s\t%s\t%s\t%s\n"%(line.rstrip('\n'), None, None, None, None))
continue
################################################
# Align the sequences using needle from EMBOSS.
needleReport = needle.needle(params['needlepath'], seq_1, seq_2)
################################################
# Parse the output of the alignment
(seqSim, seqId) = needle.parseNeedle(needleReport)
seqIdDict[pairName] = (seqSim, seqId, pfam_1, pfam_2)
out.write("%s\t%s\t%s\t%s\t%s\n"%(line.rstrip('\n'), seqId, seqSim, pfam_1, pfam_2))
out.close()