def test(gFN):
map = cgSeqMod.loadCodonMap("hg19")
geneSet = cgGenes3.createGeneSetEditing(gFN)
for transcript in geneSet.transcripts:
if "_coding" in transcript.tType:
try:
print transcript.id
print transcript.getMRNA(coding=True)
print cgSeqMod.translateRNA(transcript.getMRNA(coding=True), map)
except:
print "fail"
def test(gFN):
map = cgSeqMod.loadCodonMap('hg19')
geneSet = cgGenes3.createGeneSetEditing(gFN)
for transcript in geneSet.transcripts:
if '_coding' in transcript.tType:
try:
print transcript.id
print transcript.getMRNA(coding=True)
print cgSeqMod.translateRNA(transcript.getMRNA(coding=True),
map)
except:
print 'fail'
def testit(gFN):
geneSet = cgGenes3.createGeneSetEditing(gFN)
map = cgSeqMod.loadCodonMap('hg19')
for gene in geneSet.genes:
for transcript in gene.transcripts:
try:
print ''
mRNA = transcript.getMRNA(coding = True)
i = transcript.getRelativePositionMRNA(35872409)
if i == -1:
continue
print transcript.id
print i
print mRNA[:i], mRNA[i], mRNA[i + 1:]
print cgSeqMod.translateRNA(mRNA, map)
except:
pass
import bioLibCG
import cgSeqMod
map = cgSeqMod.loadCodonMap('hg19')
numN = 0
numS = 0
for codon in map:
bAlter = cgSeqMod.translateRNA(codon, map)
codonList = list(codon)
for i,nt in enumerate(codonList):
if nt == 'A':
codonList[i] = 'G'
newCodon = ''.join(codonList)
newAlter = cgSeqMod.translateRNA(newCodon, map)
if newAlter == bAlter:
print 'SYN', bAlter, newAlter, codon, newCodon
numS += 1
else:
print 'NON', bAlter, newAlter, codon, newCodon
numN += 1
codonList[i] = 'A'
print numN, numS
import bioLibCG
import cgSeqMod
map = cgSeqMod.loadCodonMap('hg19')
numN = 0
numS = 0
for codon in map:
bAlter = cgSeqMod.translateRNA(codon, map)
codonList = list(codon)
for i, nt in enumerate(codonList):
if nt == 'A':
codonList[i] = 'G'
newCodon = ''.join(codonList)
newAlter = cgSeqMod.translateRNA(newCodon, map)
if newAlter == bAlter:
print 'SYN', bAlter, newAlter, codon, newCodon
numS += 1
else:
print 'NON', bAlter, newAlter, codon, newCodon
numN += 1
codonList[i] = 'A'
print numN, numS
def updateSynonomous(eFN, gFN, resultsFN, outFN):
#Load Transcripts and Editing Sites
print 'Loading editing sites'
eSites = cgEdit.loadEditingSites(eFN)
print 'Loading gene set'
geneSet = cgGenes3.createGeneSetEditing(gFN)
codingTID_eID = {}
f = open(resultsFN, 'r')
for line in f:
ls = line.strip().split('\t')
if ls[4] == 'C':
codingTID_eID[ls[2]] = int(ls[0])
#Get coding Transcripts
codingTranscripts = {} #tID : eID ! many:one always!
f = open(resultsFN, 'r')
for line in f:
ls = line.strip().split('\t')
if ls[4] == 'C':
codingTranscripts[ls[2]] = int(ls[0])
eID_eSite = {}
for eSite in eSites:
eID_eSite[eSite.ID] = eSite
tID_transcript = {}
for transcript in geneSet.transcripts:
tID[transcript.id] = transcript
codingT_eSite
for tID in codingTID_eID:
eID = codingTID_eID[tID]
t = tID_transcript[tID]
e = eID_eSite[eID]
print 'Creating scroll dict'
scrollDict = {} # transcript: eSite
for tID in codingTranscripts:
e = eJoint[codingTranscripts[tID]]
try:
t = tJoint[tID]
scrollDict[t] = e
except KeyError:
pass
print 'Deducing synonomous'
map = cgSeqMod.loadCodonMap('hg19')
finalDict = {} # tID: [SYN, AAA, AAB, G, A]
#Figure out if they are synonomous
for t in scrollDict:
eSite = scrollDict[t]
#dumpObj.dumpObj(t)
#dumpObj.dumpObj(eSite)
ePositionInMRNA = t.getRelativePositionMRNA(eSite.coordinate - 1)
if ePositionInMRNA == -1:
print t.id, 'should not be designated coding...'
continue
#grab mRNA and emRNA
mRNA = t.getMRNA(coding=True)
emRNA = t.getMRNA(coding=True)
if mRNA[ePositionInMRNA] != 'A':
print 'wrong position', t.id, '%s:%s' % (
eSite.chromosome, eSite.coordinate), eSite.strand, mRNA[
ePositionInMRNA - 5:ePositionInMRNA -
1], mRNA[ePositionInMRNA], mRNA[ePositionInMRNA +
1:ePositionInMRNA + 5]
#edit the site
emRNA = list(emRNA)
emRNA[ePositionInMRNA] = 'G'
emRNA = ''.join(emRNA)
#Test the protein sequences
pRNA = cgSeqMod.translateRNA(mRNA, map)
epRNA = cgSeqMod.translateRNA(emRNA, map)
#print t.parent, t.id
newString = ['%s ' % x for x in list(pRNA)]
newString = ''.join(newString)
if pRNA[0] != 'M':
print 'Non-canonical Start AA:', pRNA[0:5], mRNA[:10]
if pRNA[-1] != '*':
print 'Non-canonical End AA:', pRNA[-5:], mRNA[-10:]
#compare the codons.
mCodonList = cgSeqMod.getCodonListFromRNA(mRNA)
emCodonList = cgSeqMod.getCodonListFromRNA(emRNA)
compareList = zip(mCodonList, emCodonList)
synFlag = 'SYN'
codonNumber = ePositionInMRNA // 3
codonPair = compareList[codonNumber]
print t.id
print eSite.ID
print mCodonList[:codonNumber]
print mRNA[:ePositionInMRNA]
bCodon = codonPair[0]
aCodon = codonPair[1]
baa = cgSeqMod.translateRNA(bCodon, map)
aaa = cgSeqMod.translateRNA(aCodon, map)
if baa != aaa:
synFlag = 'NON'
bCodonList = list(bCodon)
aCodonList = list(aCodon)
matchedLetters = zip(bCodonList, aCodonList)
for pair in matchedLetters:
if pair[0] != 'A':
if pair[1] == 'G' and pair[0] != 'G':
print 'messed up codon switch', bCodonList, aCodonList
print t.parent, '%s:%s' % (
eSite.chromosome, eSite.coordinate
), eSite.strand, bCodon, aCodon, baa, aaa
else:
synFlag = 'SYN'
finalDict[t.id] = [synFlag, bCodon, aCodon, baa, aaa]
print 'writing to file'
#update line by line
newLines = []
f = open(resultsFN, 'r')
for line in f:
newLine = line.strip()
tID = line.strip().split('\t')[2]
if tID in finalDict:
newLine = newLine + '\t%s\t%s\t%s\t%s\t%s\n' % (
finalDict[tID][0], finalDict[tID][1], finalDict[tID][2],
finalDict[tID][3], finalDict[tID][4])
else:
newLine = newLine + '\tNA\tNA\tNA\tNA\tNA\n'
newLines.append(newLine)
f.close()
#update file
f = open(outFN, 'w')
f.writelines(newLines)
f.close()
def betterSynonymous(eFN, gFN, contextFN, outFN, refBase='A', eBase='G'):
print 'loading e sites'
eSites = cgEdit.loadEditingSites(eFN)
print 'loading geneSet'
geneSet = cgGenes3.createGeneSetEditing(gFN)
contextInfo = {} # eID: tID : [UTR, C]
f = open(contextFN, 'r')
for line in f:
ls = line.strip().split('\t')
eID = int(ls[0])
tID = ls[2]
cInfo = [ls[3], ls[4]]
if eID not in contextInfo:
contextInfo[eID] = {}
contextInfo[eID][tID] = cInfo
else:
contextInfo[eID][tID] = cInfo
eID_tIDs = {}
f = open(contextFN, 'r')
for line in f:
ls = line.strip().split('\t')
eID = int(ls[0])
tID = ls[2]
if tID not in eID_tIDs.setdefault(eID, []): eID_tIDs[eID].append(tID)
eID_eSite = {}
for eSite in eSites:
eID_eSite[eSite.ID] = eSite
tID_transcript = {}
for transcript in geneSet.transcripts:
tID_transcript[transcript.id] = transcript
eSite_transcripts = {}
for eID in eID_tIDs:
eSite = eID_eSite[eID]
tList = []
for tID in eID_tIDs[eID]:
if tID == 'NONE': continue
if tID_transcript.get(tID, None) == None: continue
tList.append(tID_transcript[tID])
eSite_transcripts[eSite] = tList
outF = open(outFN, 'w')
map = cgSeqMod.loadCodonMap('hg19')
for eSite in eSite_transcripts:
for transcript in eSite_transcripts[eSite]:
siteType, codingType = contextInfo[eSite.ID][transcript.id]
if '_noncoding' in transcript.tType:
continue
if codingType != 'C':
continue
ePositionInMRNA = transcript.getRelativePositionMRNA(
eSite.coordinate - 1)
mRNA = transcript.getMRNA(coding=True)
emRNA = transcript.getMRNA(coding=True)
if mRNA[ePositionInMRNA] != refBase:
print 'Editing site was not an A...'
#edit the site
emRNA = list(emRNA)
emRNA[ePositionInMRNA] = eBase
emRNA = ''.join(emRNA)
#Test the protein sequences
pRNA = cgSeqMod.translateRNA(mRNA, map)
epRNA = cgSeqMod.translateRNA(emRNA, map)
if pRNA[0] != 'M':
print 'Non-canonical Start AA:', pRNA[0:5], mRNA[:10]
if pRNA[-1] != '*':
print 'Non-canonical End AA:', pRNA[-5:], mRNA[-10:]
#compare the codons.
mCodonList = cgSeqMod.getCodonListFromRNA(mRNA)
emCodonList = cgSeqMod.getCodonListFromRNA(emRNA)
compareList = zip(mCodonList, emCodonList)
codonNumber = ePositionInMRNA // 3
codonPair = compareList[codonNumber]
bCodon = codonPair[0]
aCodon = codonPair[1]
baa = cgSeqMod.translateRNA(bCodon, map)
aaa = cgSeqMod.translateRNA(aCodon, map)
synFlag = 'SYN'
if baa != aaa:
synFlag = 'NON'
bCodonList = list(bCodon)
aCodonList = list(aCodon)
matchedLetters = zip(bCodonList, aCodonList)
for pair in matchedLetters:
if pair[0] != 'A':
if pair[1] == 'G' and pair[0] != 'G':
print 'messed up codon switch', bCodonList, aCodonList
print t.parent, '%s:%s' % (
eSite.chromosome, eSite.coordinate
), eSite.strand, bCodon, aCodon, baa, aaa
outF.write('\t'.join([
str(eSite.ID), transcript.parent, transcript.id, synFlag,
bCodon, aCodon, baa, aaa
]) + '\n')
