else:
spliceAcceptorCase = 'SpliceAcceptorIsNotAG'
agCase = None
if "AG" == sequence[1:3] or "AG" == sequence[7:9]:
agCase = 'FoundAGOnSides'
elif sequence[1:3][0] == 'A' or sequence[1:3][1] == 'G' or sequence[
7:9][0] == 'A' or sequence[7:9][1] == 'G':
agCase = 'FoundEitherAOrGOnSides'
if agCase:
nagAnnotationFile.write("\t".join([
records[0]['chromosome'], 'mayur', 'NAGNAG', records[0]
['geneID'], records[0]['geneName'], records[0]['geneType'],
lastTranscriptID, records[0]['transcriptType'], direction,
str(startPosition),
str(endPosition), sequence, lowerPosition, higherPosition,
spliceAcceptorCase, agCase
]) + "\n")
if __name__ == '__main__':
arguments = gencode.getArguments()
nagAnnotationFile = open(
os.path.join(arguments[2], "nagnag_cases_test_ignore.gtf"), "w")
gencode.run(arguments[0], arguments[1], None, transcriptCallback)
nagAnnotationFile.close()
fields = line.split()
RefSeqID = fields[0]
position_to_aTIS = int(fields[4])
annotation = fields[5]
RLTM_RCHX = fields[6]
codon = fields[12]
EnsemblID = RefSeq_Ensembl_dict.get(RefSeqID)
if EnsemblID:
uORF_number = Ensembl_count_dict.get(EnsemblID)
lee_TIS_dict.setdefault((EnsemblID, uORF_number),
(RefSeqID,
position_to_aTIS,
annotation,
RLTM_RCHX,
codon,
uORF_number))
Ensembl_count_dict[EnsemblID] = uORF_number + 1
leeToFritschFile = open("lee_uORF2.bed", "w")
leeToFritschFile.write('#chrom\tchromStart\tchromEnd\tname\tRLTM-RCHX\tstrand\n') # header line
tooFarleeuorfsFile = open("lee_toofar_uORFs.bed", "w")
tooFarleeuorfsFile.write("#These are the bad uorfs that don't match too far from corresponding codons in the GENCODE transcripts\n" +
"#chrom\tchromStart\tchromEnd\tname\tRLTM-RCHX\tstrand\tdistance-from-nearest-GENCODE-codon\n")
gencode.run(sys.argv[1], sys.argv[2], None, transcriptCallback)
leeToFritschFile.close()
tooFarleeuorfsFile.close()
#Coder: Mayur Pawashe
#Program: Writes out five primes
#Dependencies: gencode.py
import os
import gencode
global fivePrimesSequenceFile
global fivePrimesAnnotationFile
def newChromosomeCallback(newChromosome):
fivePrimesSequenceFile.write(">" + newChromosome + "\n")
def transcriptCallback(records, sequenceData, lastTranscriptID, fivePrimeUTRs, fivePrimeContent, cdss, stopCodon, direction):
if fivePrimeContent != "":
fivePrimesSequenceFile.write(">" + str(records[0]['geneID']) + "|" + str(lastTranscriptID) + "|" + str(records[0]["geneName"]) + "\n")
fivePrimesSequenceFile.write(fivePrimeContent + "\n")
for fivePrime in fivePrimeUTRs:
fivePrimesAnnotationFile.write(fivePrime['line'])
if __name__ == '__main__':
arguments = gencode.getArguments()
fivePrimesSequenceFile = open(os.path.join(arguments[2], "five_primes.fa"), "w")
fivePrimesAnnotationFile = open(os.path.join(arguments[2], "five_primes.gtf"), "w")
gencode.run(arguments[0], arguments[1], newChromosomeCallback, transcriptCallback)
fivePrimesSequenceFile.close()
fivePrimesAnnotationFile.close()
