def testGetSequence(genomeFilePath):
chrom = 'chr1'
seq = '808984'
seqlen = 1
seqStart = int(seq) - seqlen - 500
seqEnd = seqStart + seqlen + 1000
genome = sequenceutils.loadGenome(genomeFilePath)
seqA = sequenceutils.getSequence(genome,chrom,seqStart,seqEnd)
seqA = seqA.upper()
print seqA
print "~"*50
# get sesion id
print "Getting sesion id ..."
hgsid = genomebrowser.gb_getSessionId()
print hgsid
if hgsid == "":
print "blank hgsid. quitting"
sys.exit(1)
seqB = genomebrowser.gb_getSequence(hgsid)
print seqB
print "~"*50
if seqA == seqB:
print "Sequences match!"
else:
print "Sequences do not match :("
bseqA = sequenceutils.bracketSequence(seqA)
bseqB = sequenceutils.bracketSequence(seqB)
if bseqA != bseqB:
print "Bracketed sequences do not match!"
sys.exit(1)
primerA = webprimer3.getPrimer(bseqA,chrom,int(seq))
primerB = webprimer3.getPrimer(bseqB,chrom,int(seq))
if primerA.fSeq != primerB.fSeq \
or primerA.rSeq != primerB.rSeq \
or primerA.size != primerB.size:
print "Primer mismatch"
print "primerA:"
print primerA
print "primerB:"
print primerB
sys.exit(1)
else:
print "Primer match"
print primerA
primerList = [primerA,primerB]
outfile = "/tmp/"+str(uuid.uuid4())+".csv"
fileutils.primersToCsv(primerList,outfile)
print "Wrote %s"%(outfile)
def testGetSequence(genomeFilePath):
chrom = 'chr1'
seq = '808984'
seqlen = 1
seqStart = int(seq) - seqlen - 500
seqEnd = seqStart + seqlen + 1000
genome = sequenceutils.loadGenome(genomeFilePath)
seqA = sequenceutils.getSequence(genome, chrom, seqStart, seqEnd)
seqA = seqA.upper()
print seqA
print "~" * 50
# get sesion id
print "Getting sesion id ..."
hgsid = genomebrowser.gb_getSessionId()
print hgsid
if hgsid == "":
print "blank hgsid. quitting"
sys.exit(1)
seqB = genomebrowser.gb_getSequence(hgsid)
print seqB
print "~" * 50
if seqA == seqB:
print "Sequences match!"
else:
print "Sequences do not match :("
bseqA = sequenceutils.bracketSequence(seqA)
bseqB = sequenceutils.bracketSequence(seqB)
if bseqA != bseqB:
print "Bracketed sequences do not match!"
sys.exit(1)
primerA = webprimer3.getPrimer(bseqA, chrom, int(seq))
primerB = webprimer3.getPrimer(bseqB, chrom, int(seq))
if primerA.fSeq != primerB.fSeq \
or primerA.rSeq != primerB.rSeq \
or primerA.size != primerB.size:
print "Primer mismatch"
print "primerA:"
print primerA
print "primerB:"
print primerB
sys.exit(1)
else:
print "Primer match"
print primerA
primerList = [primerA, primerB]
outfile = "/tmp/" + str(uuid.uuid4()) + ".csv"
fileutils.primersToCsv(primerList, outfile)
print "Wrote %s" % (outfile)
def processRows(self,
rows,
genomeFile,
db='hg38',
chromcol='#CHROM',
poscol='POS',
refcol='REF',
bracketlen=500,
primerlen='200-500'):
# celery kung fu
self.primers = list()
#self.warnings = list()
warnings = list()
task_id = processRows.request.id
rowCount = len(rows)
for idx, row in enumerate(rows):
logger.info('Processing row %d' % (idx))
warnings.append('Processing row %d' % (idx))
if chromcol not in row or \
poscol not in row or \
refcol not in row:
print "~" * 20 + " MISSING COL IN ROW " + "~" * 20
print row
warn = ("Error! Row %d could not be parsed. Skipping." % (idx + 1))
warnings.append(warn)
self.primers.append(Primer('ERROR', -1, 'ERROR', 'ERROR', -1))
continue
pos = row[poscol]
ref = row[refcol]
pos_int = 0
ref_char = ''
chrom = "chr%s" % (row[chromcol])
warn = ("Error! Found '%s' in %s column of row %d; expected "
"1-22, X, or Y. Skipping." %
(row[chromcol], chromcol, idx + 1))
# assume that chrom is 1-22, X or Y
try:
chrom_int = int(row[chromcol])
if chrom_int < 1 or chrom_int > 22:
logging.warning(warn)
warnings.append(warn)
self.primers.append(Primer('ERROR', -1, 'ERROR', 'ERROR', -1))
continue
except:
chrom_str = row[chromcol].lower()
if chrom_str != 'x' and chrom_str != 'y':
logging.warning(warn)
warnings.append(warn)
self.primers.append(Primer('ERROR', -1, 'ERROR', 'ERROR', -1))
continue
# test that pos is an int
try:
pos_int = int(pos)
except:
warn = ("Error! Found '%s' in %s column of row %d; expected "
"an integer. Skipping." % (pos, poscol, idx + 1))
logging.warning(warn)
warnings.append(warn)
self.primers.append(Primer('ERROR', -1, 'ERROR', 'ERROR', -1))
continue
# test that ref is a single character in A,C,T,G
lowerRef = ref.lower()
if len(lowerRef) > 1 or \
(lowerRef!='a' and lowerRef!='c'
and lowerRef!='t' and lowerRef!='g'):
warn = ("Error! Found '%s' in %s column of row %d; expected "
"A, C, T, or G. Skipping." % (ref, refcol, idx + 1))
logging.warning(warn)
warnings.append(warn)
self.primers.append(Primer('ERROR', -1, 'ERROR', 'ERROR', -1))
continue
hgsid = ''
if app.config['GB'] == 'UCSC':
hgsid = genomebrowser.gb_getSessionId()
genomeRef = genomebrowser.gb_getSequence(hgsid,
db=db,
chrom=chrom,
left=(int(pos) - 1),
right=(int(pos)),
leftPad=0,
rightPad=0)
else:
genome = sequenceutils.loadGenome(genomeFile)
genomeRef = sequenceutils.getSequence(genome, chrom,
int(pos) - 1, int(pos))
if genomeRef != ref:
warn = ("Warning! Reference '%s' for chromosome %s, "
"position %s was found to be '%s' in the genome file." %
(ref, chrom, pos, genomeRef))
logging.warning(warn)
warnings.append(warn)
seqStart = int(pos) - bracketlen - 1
seqEnd = seqStart + bracketlen + bracketlen + 1
# UCSC defaults to all upper case
if app.config['GB'] == 'UCSC':
seq = genomebrowser.gb_getSequence(hgsid,
db=db,
chrom=chrom,
left=(int(pos) - 1),
right=(int(pos)),
leftPad=500,
rightPad=500)
else:
seq = sequenceutils.getSequence(genome, chrom, seqStart, seqEnd)
bseq = sequenceutils.bracketSequence(seq).upper()
primer = webprimer3.getPrimer(bseq, chrom, int(pos), primerlen)
if primer == None:
logging.warning('getPrimer returned None')
self.primers.append(primer)
logger.debug('Updating state for task id %s' % (str(task_id)))
self.update_state(state='PROGRESS',
meta={
'current': idx,
'total': rowCount,
'warnings': warnings
})
logger.debug('Creating output file ...')
filename = str(task_id) + '.csv'
path = os.path.join(app.config['UPLOAD_FOLDER'], filename)
logger.debug('Filename: %s' % (filename))
logger.debug('Path: %s' % (path))
fileutils.primersToCsv(self.primers, path)
logger.debug('Done writing to file')
logger.info('Returning result')
return {'current': rowCount, 'total': rowCount, 'warnings': warnings}
def processRows(self,rows,genomeFile,
db='hg38',
chromcol='#CHROM',poscol='POS',refcol='REF',
bracketlen=500,primerlen='200-500'):
# celery kung fu
self.primers = list()
#self.warnings = list()
warnings = list()
task_id = processRows.request.id
rowCount = len(rows)
for idx,row in enumerate(rows):
logger.info('Processing row %d'%(idx))
warnings.append('Processing row %d'%(idx))
if chromcol not in row or \
poscol not in row or \
refcol not in row:
print "~"*20+" MISSING COL IN ROW "+"~"*20
print row
warn = ("Error! Row %d could not be parsed. Skipping."%(idx+1))
warnings.append(warn)
self.primers.append(Primer('ERROR',-1,'ERROR','ERROR',-1))
continue
pos = row[poscol]
ref = row[refcol]
pos_int = 0
ref_char = ''
chrom = "chr%s"%(row[chromcol])
warn = ("Error! Found '%s' in %s column of row %d; expected "
"1-22, X, or Y. Skipping."%(row[chromcol],chromcol,idx+1))
# assume that chrom is 1-22, X or Y
try:
chrom_int = int(row[chromcol])
if chrom_int < 1 or chrom_int > 22:
logging.warning(warn)
warnings.append(warn)
self.primers.append(
Primer('ERROR',-1,'ERROR','ERROR',-1))
continue
except:
chrom_str = row[chromcol].lower()
if chrom_str!='x' and chrom_str!='y':
logging.warning(warn)
warnings.append(warn)
self.primers.append(
Primer('ERROR',-1,'ERROR','ERROR',-1))
continue
# test that pos is an int
try:
pos_int = int(pos)
except:
warn = ("Error! Found '%s' in %s column of row %d; expected "
"an integer. Skipping."%(pos,poscol,idx+1))
logging.warning(warn)
warnings.append(warn)
self.primers.append(
Primer('ERROR',-1,'ERROR','ERROR',-1))
continue
# test that ref is a single character in A,C,T,G
lowerRef = ref.lower()
if len(lowerRef) > 1 or \
(lowerRef!='a' and lowerRef!='c'
and lowerRef!='t' and lowerRef!='g'):
warn = ("Error! Found '%s' in %s column of row %d; expected "
"A, C, T, or G. Skipping."%(ref,refcol,idx+1))
logging.warning(warn)
warnings.append(warn)
self.primers.append(
Primer('ERROR',-1,'ERROR','ERROR',-1))
continue
hgsid = ''
if app.config['GB'] == 'UCSC':
hgsid = genomebrowser.gb_getSessionId()
genomeRef = genomebrowser.gb_getSequence(hgsid, db=db, chrom=chrom,
left=(int(pos)-1),
right=(int(pos)),
leftPad=0,
rightPad=0)
else:
genome = sequenceutils.loadGenome(genomeFile)
genomeRef = sequenceutils.getSequence(genome, chrom,
int(pos)-1, int(pos))
if genomeRef != ref:
warn = ("Warning! Reference '%s' for chromosome %s, "
"position %s was found to be '%s' in the genome file."
%(ref,chrom,pos,genomeRef))
logging.warning(warn)
warnings.append(warn)
seqStart = int(pos) - bracketlen - 1
seqEnd = seqStart + bracketlen + bracketlen + 1
# UCSC defaults to all upper case
if app.config['GB'] == 'UCSC':
seq = genomebrowser.gb_getSequence(hgsid, db=db, chrom=chrom,
left=(int(pos)-1),
right=(int(pos)),
leftPad=500,
rightPad=500)
else:
seq = sequenceutils.getSequence(genome, chrom, seqStart, seqEnd)
bseq = sequenceutils.bracketSequence(seq).upper()
primer = webprimer3.getPrimer(bseq, chrom, int(pos), primerlen)
if primer == None:
logging.warning('getPrimer returned None')
self.primers.append(primer)
logger.debug('Updating state for task id %s'%(str(task_id)))
self.update_state(state='PROGRESS', meta={'current':idx, 'total': rowCount, 'warnings': warnings})
logger.debug('Creating output file ...')
filename = str(task_id) + '.csv'
path = os.path.join(app.config['UPLOAD_FOLDER'],filename)
logger.debug('Filename: %s'%(filename))
logger.debug('Path: %s'%(path))
fileutils.primersToCsv(self.primers,path)
logger.debug('Done writing to file')
logger.info('Returning result')
return {'current': rowCount, 'total': rowCount, 'warnings': warnings }