def add_ion_dnabarcode_set():
'''List from TS-1517 or, file Barcodes_052611.xlsx
Added extra T to start of each sequence'''
blist=[
"TACTCACGATA",
"TCGTGTCGCAC",
"TGATGATTGCC",
"TCGATAATCTT",
"TCTTACACCAC",
"TAGCCAAGTAC",
"TGACATTACTT",
"TGCCTTACCGC",
"TACCGAGGCAC",
"TGCAAGCCTTC",
"TACATTACATC",
"TCAAGCACCGC",
"TAGCTTACCGC",
"TCATGATCAAC",
"TGACCGCATCC",
"TGGTGTAGCAC"]
btype='none'
name='IonSet1'
adapter = 'CTGCTGTACGGCCAAGGCGT'
# Check for barcode set named 'ionSet1' and remove it
# this is slightly different than desired name: 'IonSet1'
allbarcodes = models.dnaBarcode.objects.filter(name='ionSet1')
if allbarcodes:
allbarcodes.all().delete()
# Check for barcode set named 'IonSet1'
allbarcodes = models.dnaBarcode.objects.filter(name=name)
if allbarcodes:
allbarcodes.all().delete()
# Add the IonSet1 default barcodes
index = 1
for i in blist:
kwargs = {
'name':name,
'id_str':'%s_%02d' % (name,index),
'sequence':i,
'type':btype,
'length':len(i),
'floworder':'',
'index':index,
'annotation':'',
'adapter':adapter,
'score_mode':0,
'score_cutoff':0.90,
}
ret = models.dnaBarcode(**kwargs)
ret.save()
index += 1
def add_barcode_set():
kwargs = {'name' : 'single_nuke',
'type' : 'text',
'sequence' : 'T',
'length':1,
'floworder':'TACG'
}
ret = models.dnaBarcode(**kwargs)
ret.save()
kwargs = {
'name' : 'single_nuke',
'type' :'text',
'sequence' : 'A',
'length':1,
'floworder':'TACG'
}
ret = models.dnaBarcode(**kwargs)
ret.save()
kwargs = {
'name' : 'single_nuke',
'type' : 'text',
'sequence' : 'C',
'length':1,
'floworder':'TACG'
}
ret = models.dnaBarcode(**kwargs)
ret.save()
kwargs = {
'name' :'single_nuke',
'type' : 'text',
'sequence' : 'G',
'length':1,
'floworder':'TACG'
}
ret = models.dnaBarcode(**kwargs)
ret.save()
def add_barcode_set():
kwargs = {'name' : 'single_nuke',
'type' : 'text',
'sequence' : 'T',
'length':1,
'floworder':'TACG'
}
ret = models.dnaBarcode(**kwargs)
ret.save()
kwargs = {
'name' : 'single_nuke',
'type' :'text',
'sequence' : 'A',
'length':1,
'floworder':'TACG'
}
ret = models.dnaBarcode(**kwargs)
ret.save()
kwargs = {
'name' : 'single_nuke',
'type' : 'text',
'sequence' : 'C',
'length':1,
'floworder':'TACG'
}
ret = models.dnaBarcode(**kwargs)
ret.save()
kwargs = {
'name' :'single_nuke',
'type' : 'text',
'sequence' : 'G',
'length':1,
'floworder':'TACG'
}
ret = models.dnaBarcode(**kwargs)
ret.save()
def add_ion_xpress_dnabarcode_set():
'''List from jira wiki page:
https://iontorrent.jira.com/wiki/display/MOLBIO/Ion+Xpress+Barcode+Adapters+1-16+Kit+-+Lot+XXX
'''
blist=['CTAAGGTAAC', #1
'TAAGGAGAAC', #2
'AAGAGGATTC', #3
'TACCAAGATC', #4
'CAGAAGGAAC', #5
'CTGCAAGTTC', #6
'TTCGTGATTC', #7
'TTCCGATAAC', #8
'TGAGCGGAAC', #9
'CTGACCGAAC', #10
'TCCTCGAATC', #11
'TAGGTGGTTC', #12
'TCTAACGGAC', #13
'TTGGAGTGTC', #14
'TCTAGAGGTC', #15
'TCTGGATGAC', #16
'TCTATTCGTC', #17
'AGGCAATTGC', #18
'TTAGTCGGAC', #19
'CAGATCCATC', #20
'TCGCAATTAC', #21
'TTCGAGACGC', #22
'TGCCACGAAC', #23
'AACCTCATTC', #24
'CCTGAGATAC', #25
'TTACAACCTC', #26
'AACCATCCGC', #27
'ATCCGGAATC', #28
'TCGACCACTC', #29
'CGAGGTTATC', #30
'TCCAAGCTGC', #31
'TCTTACACAC', #32
]
btype='none'
name='IonXpress'
adapter = 'GAT'
# Attempt to read dnabarcode set named 'IonXpress' from dbase
dnabcs = models.dnaBarcode.objects.filter(name=name)
if len(dnabcs) > 0:
print '%s dnaBarcode Set exists in database' % name
# make sure we have all the sequences we expect
for index,sequence in enumerate(blist,start=1):
# Search for this sequence in the list of barcode records
bc_found = dnabcs.filter(sequence=sequence)
if len(bc_found) > 1:
print "ERROR: More than one entry with sequence %s" % sequence
print "TODO: Fix this situation, Mr. Programmer!"
if len(bc_found) == 1:
# Make sure floworder field is not 'none'
if bc_found[0].floworder == 'none':
bc_found[0].floworder = ''
# Make sure id string has zero padded index field
bc_found[0].id_str = '%s_%03d' % (name,index)
# Save changes to database
bc_found[0].save()
else: # array length is zero
print "Adding entry for %s" % sequence
kwargs = {
'name':name,
'id_str':'%s_%03d' % (name,index),
'sequence':sequence,
'type':btype,
'length':len(sequence),
'floworder':'',
'index':index,
'annotation':'',
'adapter':adapter,
'score_mode':1,
'score_cutoff':2.0,
}
ret = models.dnaBarcode(**kwargs)
ret.save()
else:
# Add the barcodes because they do not exist.
# NOTE: name for id_str
for index,sequence in enumerate(blist,start=1):
kwargs = {
'name':name,
'id_str':'%s_%03d' % (name,index),
'sequence':sequence,
'type':btype,
'length':len(sequence),
'floworder':'',
'index':index,
'annotation':'',
'adapter':adapter,
'score_mode':1,
'score_cutoff':2.0,
}
ret = models.dnaBarcode(**kwargs)
ret.save()
print '%s dnaBarcode Set added to database' % name
return
def add_or_update_barcode_set(blist,btype,name,adapter):
# Attempt to read dnabarcode set named 'IonXpress' from dbase
dnabcs = models.dnaBarcode.objects.filter(name=name)
if len(dnabcs) > 0:
print '%s dnaBarcode Set exists in database' % name
# make sure we have all the sequences we expect
for index,sequence in enumerate(blist,start=1):
# Search for this sequence in the list of barcode records
bc_found = dnabcs.filter(sequence=sequence)
if len(bc_found) > 1:
print "ERROR: More than one entry with sequence %s" % sequence
print "TODO: Fix this situation, Mr. Programmer!"
if len(bc_found) == 1:
# Make sure floworder field is not 'none'
if bc_found[0].floworder == 'none':
bc_found[0].floworder = ''
# Make sure id string has zero padded index field
bc_found[0].id_str = '%s_%03d' % (name,index)
# Save changes to database
bc_found[0].save()
else: # array length is zero
print "Adding entry for %s" % sequence
kwargs = {
'name':name,
'id_str':'%s_%03d' % (name,index),
'sequence':sequence,
'type':btype,
'length':len(sequence),
'floworder':'',
'index':index,
'annotation':'',
'adapter':adapter,
'score_mode':1,
'score_cutoff':2.0,
}
ret = models.dnaBarcode(**kwargs)
ret.save()
else:
# Add the barcodes because they do not exist.
# NOTE: name for id_str
for index,sequence in enumerate(blist,start=1):
kwargs = {
'name':name,
'id_str':'%s_%03d' % (name,index),
'sequence':sequence,
'type':btype,
'length':len(sequence),
'floworder':'',
'index':index,
'annotation':'',
'adapter':adapter,
'score_mode':1,
'score_cutoff':2.0,
}
ret = models.dnaBarcode(**kwargs)
ret.save()
print '%s dnaBarcode Set added to database' % name
