def __init__(self, seq):
self.seq = seq
self.featureSizeEstimators = []
self.sequenceEstimatedSize = 0
self.sequenceDataLength = sum([cu.TAG_LENGTH_ST26['SequenceData'],
len(seq.seqIdNo) + cu.TAG_LENGTH_ST26['sequenceIDNumber'],
cu.TAG_LENGTH_ST26['INSDSeq']])
self.INSDSeq_lengthLength = len(seq.length) + cu.TAG_LENGTH_ST26['INSDSeq_length']
self.INSDSeq_moltypeLength = len('AA' if seq.molType == 'PRT' else seq.molType) + cu.TAG_LENGTH_ST26['INSDSeq_moltype']
self.INSDSeq_divisionLength = len("PAT") + cu.TAG_LENGTH_ST26['INSDSeq_division']
self.INSDSeq_feature_tableLength = cu.TAG_LENGTH_ST26['INSDSeq_feature-table']
sourceFeatureSizeEstimator = self.getSourceFeatureSizeEstimator(seq)
self.featureSizeEstimators.append(sourceFeatureSizeEstimator)
residues = seq.residues_nuc
if seq.molType == 'PRT':
residues = cu.oneLetterCode(seq.residues_prt)
self.INSDSeq_sequenceLength = len(residues) + cu.TAG_LENGTH_ST26['INSDSeq_sequence']
for f in self.seq.features:
if f.key == cu.BLANK_PLACEHOLDER and f.location == cu.BLANK_PLACEHOLDER:
noteQ = {'INSDQualifierLength': cu.TAG_LENGTH_ST26['INSDQualifier'],
'INSDQualifier_nameLength': len('note') + cu.TAG_LENGTH_ST26['INSDQualifier_name'],
'INSDQualifier_valueLength': len(f.description) + cu.TAG_LENGTH_ST26['INSDQualifier_value']
}
sourceFeatureSizeEstimator['qualifiers'].append(noteQ)
else:
self.featureSizeEstimators.append(self.getOtherFeatureSizeEstimator(f))
featuresEstimatedSize = 0
for fse in self.featureSizeEstimators:
qualsSize = sum(sum([q['INSDQualifierLength'],
q['INSDQualifier_nameLength'],
q['INSDQualifier_valueLength']]) for q in fse['qualifiers'])
res = sum([fse['INSDFeatureLength'],
fse['INSDFeature_keyLength'],
fse['INSDFeature_locationLength'],
fse['INSDFeature_qualsLength'],
qualsSize])
featuresEstimatedSize += res
self.sequenceEstimatedSize = sum([self.sequenceDataLength,
self.INSDSeq_lengthLength,
self.INSDSeq_moltypeLength,
self.INSDSeq_divisionLength,
self.INSDSeq_feature_tableLength,
featuresEstimatedSize,
self.INSDSeq_sequenceLength])
def setSequencesSt26(self):
for s25 in self.seql_st25.generateSequence():
residues_st26 = ''
if s25.molType in ('DNA', 'RNA'):
molType_st26 = s25.molType
sourceKey = 'source'
organismQualifierName = 'organism'
noteQualifierName = 'note'
residues_st26 = s25.residues_nuc
else:
molType_st26 = 'AA'
sourceKey = 'SOURCE'
organismQualifierName = 'ORGANISM'
noteQualifierName = 'NOTE'
residues_st26 = converter_util.oneLetterCode(s25.residues_prt)
s26 = Sequence(sequenceListing = self.seql_st26,
sequenceIdNo = s25.seqIdNo,
length = s25.length,
moltype = molType_st26,
division = 'PAT',
# otherSeqId = '-', #optional, so we don't include it in converted sl
residues = residues_st26)
s26.save()
sourceFeature = Feature(sequence=s26,
featureKey = sourceKey,
location = '1..%s' % s26.length)
sourceFeature.save()
organismQualifier = Qualifier(feature=sourceFeature,
qualifierName=organismQualifierName,
qualifierValue=s25.organism)
organismQualifier.save()
for f in s25.features:
currentFeature = Feature(sequence=s26,
featureKey = f.key,
location = f.location)
currentFeature.save()
currentQualifier = Qualifier(feature=currentFeature,
qualifierName=noteQualifierName,
qualifierValue=f.description)
currentQualifier.save()
def getOtherFeatureSizeEstimator(self, feat):
qualsLength = 0
quals = []
if feat.description != cu.BLANK_PLACEHOLDER:
qualsLength = cu.TAG_LENGTH_ST26['INSDFeature_quals']
quals = [{'INSDQualifierLength': cu.TAG_LENGTH_ST26['INSDQualifier'],
'INSDQualifier_nameLength': len('note') + cu.TAG_LENGTH_ST26['INSDQualifier_name'],
'INSDQualifier_valueLength': len(feat.description) + cu.TAG_LENGTH_ST26['INSDQualifier_value']
}]
if feat.key == 'CDS':
qualsLength = cu.TAG_LENGTH_ST26['INSDFeature_quals']
quals = [{'INSDQualifierLength': cu.TAG_LENGTH_ST26['INSDQualifier'],
'INSDQualifier_nameLength': len('translation') + cu.TAG_LENGTH_ST26['INSDQualifier_name'],
'INSDQualifier_valueLength': len(cu.oneLetterCode(feat.translation)) + cu.TAG_LENGTH_ST26['INSDQualifier_value']
}]
return {
'INSDFeatureLength': cu.TAG_LENGTH_ST26['INSDFeature'],
'INSDFeature_keyLength': len(feat.key) + cu.TAG_LENGTH_ST26['INSDFeature_key'],
'INSDFeature_locationLength': len(feat.location) + cu.TAG_LENGTH_ST26['INSDFeature_location'],
'INSDFeature_qualsLength': qualsLength,
'qualifiers': quals
}
def setSequencesSt26(self):
# for s25 in self.seql_st25.sequences:
for s25 in self.seql_st25.generateSequence():
print 'seq', s25.seqIdNo
residues_st26 = ''
if s25.molType in ('DNA', 'RNA'):
molType_st26 = s25.molType
sourceKey = 'source'
organismQualifierName = 'organism'
mol_typeQualifierName = 'mol_type'
mol_typeQualifierValue = 'genomic %s' % s25.molType
noteQualifierName = 'note'
residues_st26 = s25.residues_nuc
else:
molType_st26 = 'AA'
sourceKey = 'SOURCE'
organismQualifierName = 'ORGANISM'
mol_typeQualifierName = 'MOL_TYPE'
mol_typeQualifierValue = 'protein'
noteQualifierName = 'NOTE'
residues_st26 = converter_util.oneLetterCode(s25.residues_prt)
s26 = Sequence(sequenceListing = self.seql_st26,
sequenceIdNo = s25.seqIdNo,
length = s25.length,
moltype = molType_st26,
division = 'PAT',
# otherSeqId = '-', #optional, so we don't include it in converted sl
residues = residues_st26)
s26.save()
sourceFeature = Feature(sequence=s26,
featureKey = sourceKey,
location = '1..%s' % s26.length)
sourceFeature.save()
organismQualifier = Qualifier(feature=sourceFeature,
qualifierName=organismQualifierName,
qualifierValue=s25.organism)
organismQualifier.save()
mol_typeQualifier = Qualifier(feature=sourceFeature,
qualifierName=mol_typeQualifierName,
qualifierValue=mol_typeQualifierValue)
mol_typeQualifier.save()
for f in s25.features:
if f.key == seqlutils.DEFAULT_STRING and f.location == seqlutils.DEFAULT_STRING:
sourceNoteQualifier = Qualifier(feature=sourceFeature,
qualifierName=noteQualifierName,
qualifierValue=f.description)
sourceNoteQualifier.save()
else:
currentFeature = Feature(sequence=s26,
featureKey = f.key,
location = f.location)
currentFeature.save()
if f.description != seqlutils.DEFAULT_STRING:
currentQualifier = Qualifier(feature=currentFeature,
qualifierName=noteQualifierName,
qualifierValue=f.description)
currentQualifier.save()
if f.key == 'CDS':
translationQualifierValue = converter_util.oneLetterCode(f.translation)
translationQualifier = Qualifier(feature=currentFeature,
qualifierName='translation',
qualifierValue=translationQualifierValue)
translationQualifier.save()
self.successful = True
def setSequenceRows(self):
res = []
parsedSequences = []
for s in self.seql.generateSequence():
parsedSequences.append(s)
# TODO: test
if s.molType == 'PRT':
self.seql.quantity_prt += 1
else:
self.seql.quantity_nuc += 1
if s.mixedMode:
self.seql.quantity_mix += 1
for seq in self.seql_raw.raw_sequences:
currentIndex = self.seql_raw.raw_sequences.index(seq)
parsedSequence = parsedSequences[currentIndex]
currentSeqId = parsedSequence.seqIdNo
# ====================== 210 ======================
currentRow_SequenceData = self._getSt25St26Lengths(0, currentSeqId,
'-', '-', 'SequenceData',
'ST.26 specific element')
res.append(currentRow_SequenceData)
currentRow210 = self._getSt25St26Lengths(210, currentSeqId,
seq.seqIdNo, parsedSequence.seqIdNo, 'sequenceIDNumber', '-')
res.append(currentRow210)
currentRow_INSDSeq = self._getSt25St26Lengths(0, currentSeqId,
'-', '-', 'INSDSeq', 'ST.26 specific element')
res.append(currentRow_INSDSeq)
# ====================== 211 ======================
currentRow211 = self._getSt25St26Lengths(211, currentSeqId,
seq.length, parsedSequence.length, 'INSDSeq_length', cu.BLANK_PLACEHOLDER)
res.append(currentRow211)
# ====================== 212 ======================
moltypeValue = 'AA' if parsedSequence.molType == 'PRT' else parsedSequence.molType
currentRow212 = [212, currentSeqId, cu.safeLength(seq.molType),
cu.safeLength(parsedSequence.molType),
cu.TAG_LENGTH_ST26['INSDSeq_moltype'],
cu.safeLength(moltypeValue) + cu.TAG_LENGTH_ST26['INSDSeq_moltype'],
'INSDSeq_moltype',
'PRT replaced by AA for protein raw_sequences' if moltypeValue == 'AA' else cu.BLANK_PLACEHOLDER]
res.append(currentRow212)
# ====================== INSDSeq_division ======================
INSDSeq_division_val = 'PAT'
currentRow_INSDSeq_division = self._getSt25St26Lengths(0, currentSeqId,
'-', INSDSeq_division_val, 'INSDSeq_division',
'ST.26 specific element')
res.append(currentRow_INSDSeq_division)
# ====================== INSDSeq_other-seqids ======================
# optional element, therefore not included in calculations
# ====================== INSDSeq_feature-table ======================
currentRow_INSDSeq_feature_table = self._getSt25St26Lengths(0,
currentSeqId,
'-', '-', 'INSDSeq_feature-table',
'ST.26 specific element')
res.append(currentRow_INSDSeq_feature_table)
# ====================== 213 ======================
# create ST.26 feature source
currentRow_INSDFeature = [0, currentSeqId, 0, 0,
cu.TAG_LENGTH_ST26['INSDFeature'],
cu.TAG_LENGTH_ST26['INSDFeature'],
'INSDFeature',
'ST.26 mandatory feature source']
res.append(currentRow_INSDFeature)
currentRow_INSDFeature_key = [0, currentSeqId, 0, 0,
cu.TAG_LENGTH_ST26['INSDFeature_key'],
len('source') + cu.TAG_LENGTH_ST26['INSDFeature_key'],
'INSDFeature_key',
'ST.26 mandatory feature source']
res.append(currentRow_INSDFeature_key)
sourceLocation = '1..%s' % parsedSequence.length
currentRow_INSDFeature_location = [0, currentSeqId, 0, 0,
cu.TAG_LENGTH_ST26['INSDFeature_location'],
len(sourceLocation) + cu.TAG_LENGTH_ST26['INSDFeature_location'],
'INSDFeature_location',
'ST.26 mandatory feature source']
res.append(currentRow_INSDFeature_location)
def append_INSDFeature_quals(msg):
res.append([0, currentSeqId, 0, 0,
cu.TAG_LENGTH_ST26['INSDFeature_quals'],
cu.TAG_LENGTH_ST26['INSDFeature_quals'],
'INSDFeature_quals',
msg])
# add first the parent element INSDFeature_quals
append_INSDFeature_quals('ST.26 mandatory feature source')
def createQualifier(name, msg):
currentRow_INSDQualifier = [0, currentSeqId, 0, 0,
cu.TAG_LENGTH_ST26['INSDQualifier'],
cu.TAG_LENGTH_ST26['INSDQualifier'],
'INSDQualifier',
msg]
res.append(currentRow_INSDQualifier)
currentRow_INSDQualifier_name = [0, currentSeqId, 0, 0,
cu.TAG_LENGTH_ST26['INSDQualifier_name'],
len(name) + cu.TAG_LENGTH_ST26['INSDQualifier_name'],
'INSDQualifier_name',
msg]
res.append(currentRow_INSDQualifier_name)
def createQualifierValue(tag_st25, element_st25, value_st25, msg):
currentRow_INSDQualifier_value = [tag_st25,
currentSeqId, cu.safeLength(element_st25),
cu.safeLength(value_st25),
cu.TAG_LENGTH_ST26['INSDQualifier_value'],
cu.safeLength(value_st25) + cu.TAG_LENGTH_ST26['INSDQualifier_value'],
'INSDQualifier_value',
msg]
res.append(currentRow_INSDQualifier_value)
# qualifier organism
createQualifier('organism', 'ST.26 mandatory qualifier organism')
createQualifierValue(213, seq.organism,
parsedSequence.organism,
'ST.26 mandatory qualifier organism')
# qualifier mol_type
mol_typeValue = 'protein' if parsedSequence.molType == 'PRT' else 'genomic DNA'
createQualifier('mol_type', 'ST.26 mandatory qualifier mol_type')
# createQualifierValue(0, 0, mol_typeValue, 'ST.26 mandatory qualifier mol_type')
res.append([0, currentSeqId, 0, 0,
cu.TAG_LENGTH_ST26['INSDQualifier_value'],
cu.safeLength(mol_typeValue) + cu.TAG_LENGTH_ST26['INSDQualifier_value'],
'INSDQualifier_value',
'ST.26 mandatory qualifier mol_type'])
# end create ST.26 feature source
# ====================== other features ======================
parsedFeatures = parsedSequence.features
for feat in seq.features:
currentFeatureIndex = seq.features.index(feat)
parsedFeature = parsedFeatures[currentFeatureIndex]
isSimpleFeature = False
if parsedFeature.key == cu.BLANK_PLACEHOLDER and parsedFeature.location == cu.BLANK_PLACEHOLDER:
isSimpleFeature = True
if not isSimpleFeature:
# ====================== 220 ======================
currentRow220 = self._getSt25St26Lengths(220, currentSeqId,
feat.featureHeader, parsedFeature.featureHeader,
'INSDFeature', cu.BLANK_PLACEHOLDER)
res.append(currentRow220)
# ====================== 221 ======================
currentRow221 = self._getSt25St26Lengths(221, currentSeqId,
feat.key, parsedFeature.key,
'INSDFeature_key', cu.BLANK_PLACEHOLDER)
res.append(currentRow221)
# ====================== add row for mixed mode translation qualifier ======================
if parsedFeature.key == 'CDS':
createQualifier('translation', 'ST.26 specific element translation')
translationRow = [400, currentSeqId,
0,
cu.safeLength(parsedFeature.translation),
cu.TAG_LENGTH_ST26['INSDQualifier_value'],
(cu.TAG_LENGTH_ST26['INSDQualifier_value'] +
len(cu.oneLetterCode(parsedFeature.translation))),
'INSDQualifier_value', '3-to-1 letter code']
res.append(translationRow)
# ====================== 222 ======================
currentRow222 = self._getSt25St26Lengths(222, currentSeqId,
feat.location, parsedFeature.location,
'INSDFeature_location', cu.BLANK_PLACEHOLDER)
res.append(currentRow222)
# ====================== 223 ======================
if parsedFeature.description != cu.BLANK_PLACEHOLDER: #do not add row if 223 missing!
append_INSDFeature_quals('ST.26 mandatory element')
createQualifier('note', cu.BLANK_PLACEHOLDER)
createQualifierValue(223, feat.description,
parsedFeature.description,
cu.BLANK_PLACEHOLDER)
# ====================== 400 ======================
if parsedSequence.molType == 'PRT':
parsedResidues = parsedSequence.residues_prt
currentRow400 = [400, currentSeqId,
cu.safeLength(seq.residues),
cu.safeLength(parsedResidues),
cu.TAG_LENGTH_ST26['INSDSeq_sequence'],
(cu.TAG_LENGTH_ST26['INSDSeq_sequence'] +
len(cu.oneLetterCode(parsedResidues))),
'INSDSeq_sequence', '3-to-1 letter code']
else:
parsedResidues = parsedSequence.residues_nuc
currentRow400 = self._getSt25St26Lengths(400, currentSeqId,
seq.residues, parsedResidues,
'INSDSeq_sequence', cu.BLANK_PLACEHOLDER)
res.append(currentRow400)
return res
def setSequencesSt26(self):
# for s25 in self.seql_st25.sequences:
for s25 in self.seql_st25.generateSequence():
print 'seq', s25.seqIdNo
residues_st26 = ''
if s25.molType in ('DNA', 'RNA'):
molType_st26 = s25.molType
sourceKey = 'source'
organismQualifierName = 'organism'
mol_typeQualifierName = 'mol_type'
mol_typeQualifierValue = 'genomic %s' % s25.molType
noteQualifierName = 'note'
residues_st26 = s25.residues_nuc
else:
molType_st26 = 'AA'
sourceKey = 'SOURCE'
organismQualifierName = 'ORGANISM'
mol_typeQualifierName = 'MOL_TYPE'
mol_typeQualifierValue = 'protein'
noteQualifierName = 'NOTE'
residues_st26 = converter_util.oneLetterCode(s25.residues_prt)
s26 = Sequence(
sequenceListing=self.seql_st26,
sequenceIdNo=s25.seqIdNo,
length=s25.length,
moltype=molType_st26,
division='PAT',
# otherSeqId = '-', #optional, so we don't include it in converted sl
residues=residues_st26)
s26.save()
sourceFeature = Feature(sequence=s26,
featureKey=sourceKey,
location='1..%s' % s26.length)
sourceFeature.save()
organismQualifier = Qualifier(feature=sourceFeature,
qualifierName=organismQualifierName,
qualifierValue=s25.organism)
organismQualifier.save()
mol_typeQualifier = Qualifier(
feature=sourceFeature,
qualifierName=mol_typeQualifierName,
qualifierValue=mol_typeQualifierValue)
mol_typeQualifier.save()
for f in s25.features:
if f.key == seqlutils.DEFAULT_STRING and f.location == seqlutils.DEFAULT_STRING:
sourceNoteQualifier = Qualifier(
feature=sourceFeature,
qualifierName=noteQualifierName,
qualifierValue=f.description)
sourceNoteQualifier.save()
else:
currentFeature = Feature(sequence=s26,
featureKey=f.key,
location=f.location)
currentFeature.save()
if f.description != seqlutils.DEFAULT_STRING:
currentQualifier = Qualifier(
feature=currentFeature,
qualifierName=noteQualifierName,
qualifierValue=f.description)
currentQualifier.save()
if f.key == 'CDS':
translationQualifierValue = converter_util.oneLetterCode(
f.translation)
translationQualifier = Qualifier(
feature=currentFeature,
qualifierName='translation',
qualifierValue=translationQualifierValue)
translationQualifier.save()
self.successful = True
def setSequenceRows(self):
res = []
parsedSequences = []
for s in self.seql.generateSequence():
parsedSequences.append(s)
# TODO: test
if s.molType == 'PRT':
self.seql.quantity_prt += 1
else:
self.seql.quantity_nuc += 1
if s.mixedMode:
self.seql.quantity_mix += 1
for seq in self.seql_raw.raw_sequences:
currentIndex = self.seql_raw.raw_sequences.index(seq)
parsedSequence = parsedSequences[currentIndex]
currentSeqId = parsedSequence.seqIdNo
# ====================== 210 ======================
currentRow_SequenceData = self._getSt25St26Lengths(
0, currentSeqId, '-', '-', 'SequenceData',
'ST.26 specific element')
res.append(currentRow_SequenceData)
currentRow210 = self._getSt25St26Lengths(210, currentSeqId,
seq.seqIdNo,
parsedSequence.seqIdNo,
'sequenceIDNumber', '-')
res.append(currentRow210)
currentRow_INSDSeq = self._getSt25St26Lengths(
0, currentSeqId, '-', '-', 'INSDSeq', 'ST.26 specific element')
res.append(currentRow_INSDSeq)
# ====================== 211 ======================
currentRow211 = self._getSt25St26Lengths(211, currentSeqId,
seq.length,
parsedSequence.length,
'INSDSeq_length',
cu.BLANK_PLACEHOLDER)
res.append(currentRow211)
# ====================== 212 ======================
moltypeValue = 'AA' if parsedSequence.molType == 'PRT' else parsedSequence.molType
currentRow212 = [
212, currentSeqId,
cu.safeLength(seq.molType),
cu.safeLength(parsedSequence.molType),
cu.TAG_LENGTH_ST26['INSDSeq_moltype'],
cu.safeLength(moltypeValue) +
cu.TAG_LENGTH_ST26['INSDSeq_moltype'], 'INSDSeq_moltype',
'PRT replaced by AA for protein raw_sequences'
if moltypeValue == 'AA' else cu.BLANK_PLACEHOLDER
]
res.append(currentRow212)
# ====================== INSDSeq_division ======================
INSDSeq_division_val = 'PAT'
currentRow_INSDSeq_division = self._getSt25St26Lengths(
0, currentSeqId, '-', INSDSeq_division_val, 'INSDSeq_division',
'ST.26 specific element')
res.append(currentRow_INSDSeq_division)
# ====================== INSDSeq_other-seqids ======================
# optional element, therefore not included in calculations
# ====================== INSDSeq_feature-table ======================
currentRow_INSDSeq_feature_table = self._getSt25St26Lengths(
0, currentSeqId, '-', '-', 'INSDSeq_feature-table',
'ST.26 specific element')
res.append(currentRow_INSDSeq_feature_table)
# ====================== 213 ======================
# create ST.26 feature source
currentRow_INSDFeature = [
0, currentSeqId, 0, 0, cu.TAG_LENGTH_ST26['INSDFeature'],
cu.TAG_LENGTH_ST26['INSDFeature'], 'INSDFeature',
'ST.26 mandatory feature source'
]
res.append(currentRow_INSDFeature)
currentRow_INSDFeature_key = [
0, currentSeqId, 0, 0, cu.TAG_LENGTH_ST26['INSDFeature_key'],
len('source') + cu.TAG_LENGTH_ST26['INSDFeature_key'],
'INSDFeature_key', 'ST.26 mandatory feature source'
]
res.append(currentRow_INSDFeature_key)
sourceLocation = '1..%s' % parsedSequence.length
currentRow_INSDFeature_location = [
0, currentSeqId, 0, 0,
cu.TAG_LENGTH_ST26['INSDFeature_location'],
len(sourceLocation) +
cu.TAG_LENGTH_ST26['INSDFeature_location'],
'INSDFeature_location', 'ST.26 mandatory feature source'
]
res.append(currentRow_INSDFeature_location)
def append_INSDFeature_quals(msg):
res.append([
0, currentSeqId, 0, 0,
cu.TAG_LENGTH_ST26['INSDFeature_quals'],
cu.TAG_LENGTH_ST26['INSDFeature_quals'],
'INSDFeature_quals', msg
])
# add first the parent element INSDFeature_quals
append_INSDFeature_quals('ST.26 mandatory feature source')
def createQualifier(name, msg):
currentRow_INSDQualifier = [
0, currentSeqId, 0, 0, cu.TAG_LENGTH_ST26['INSDQualifier'],
cu.TAG_LENGTH_ST26['INSDQualifier'], 'INSDQualifier', msg
]
res.append(currentRow_INSDQualifier)
currentRow_INSDQualifier_name = [
0, currentSeqId, 0, 0,
cu.TAG_LENGTH_ST26['INSDQualifier_name'],
len(name) + cu.TAG_LENGTH_ST26['INSDQualifier_name'],
'INSDQualifier_name', msg
]
res.append(currentRow_INSDQualifier_name)
def createQualifierValue(tag_st25, element_st25, value_st25, msg):
currentRow_INSDQualifier_value = [
tag_st25, currentSeqId,
cu.safeLength(element_st25),
cu.safeLength(value_st25),
cu.TAG_LENGTH_ST26['INSDQualifier_value'],
cu.safeLength(value_st25) +
cu.TAG_LENGTH_ST26['INSDQualifier_value'],
'INSDQualifier_value', msg
]
res.append(currentRow_INSDQualifier_value)
# qualifier organism
createQualifier('organism', 'ST.26 mandatory qualifier organism')
createQualifierValue(213, seq.organism, parsedSequence.organism,
'ST.26 mandatory qualifier organism')
# qualifier mol_type
mol_typeValue = 'protein' if parsedSequence.molType == 'PRT' else 'genomic DNA'
createQualifier('mol_type', 'ST.26 mandatory qualifier mol_type')
# createQualifierValue(0, 0, mol_typeValue, 'ST.26 mandatory qualifier mol_type')
res.append([
0, currentSeqId, 0, 0,
cu.TAG_LENGTH_ST26['INSDQualifier_value'],
cu.safeLength(mol_typeValue) +
cu.TAG_LENGTH_ST26['INSDQualifier_value'],
'INSDQualifier_value', 'ST.26 mandatory qualifier mol_type'
])
# end create ST.26 feature source
# ====================== other features ======================
parsedFeatures = parsedSequence.features
for feat in seq.features:
currentFeatureIndex = seq.features.index(feat)
parsedFeature = parsedFeatures[currentFeatureIndex]
isSimpleFeature = False
if parsedFeature.key == cu.BLANK_PLACEHOLDER and parsedFeature.location == cu.BLANK_PLACEHOLDER:
isSimpleFeature = True
if not isSimpleFeature:
# ====================== 220 ======================
currentRow220 = self._getSt25St26Lengths(
220, currentSeqId, feat.featureHeader,
parsedFeature.featureHeader, 'INSDFeature',
cu.BLANK_PLACEHOLDER)
res.append(currentRow220)
# ====================== 221 ======================
currentRow221 = self._getSt25St26Lengths(
221, currentSeqId, feat.key, parsedFeature.key,
'INSDFeature_key', cu.BLANK_PLACEHOLDER)
res.append(currentRow221)
# ====================== add row for mixed mode translation qualifier ======================
if parsedFeature.key == 'CDS':
createQualifier('translation',
'ST.26 specific element translation')
translationRow = [
400, currentSeqId, 0,
cu.safeLength(parsedFeature.translation),
cu.TAG_LENGTH_ST26['INSDQualifier_value'],
(cu.TAG_LENGTH_ST26['INSDQualifier_value'] +
len(cu.oneLetterCode(parsedFeature.translation))),
'INSDQualifier_value', '3-to-1 letter code'
]
res.append(translationRow)
# ====================== 222 ======================
currentRow222 = self._getSt25St26Lengths(
222, currentSeqId, feat.location,
parsedFeature.location, 'INSDFeature_location',
cu.BLANK_PLACEHOLDER)
res.append(currentRow222)
# ====================== 223 ======================
if parsedFeature.description != cu.BLANK_PLACEHOLDER: #do not add row if 223 missing!
append_INSDFeature_quals('ST.26 mandatory element')
createQualifier('note', cu.BLANK_PLACEHOLDER)
createQualifierValue(223, feat.description,
parsedFeature.description,
cu.BLANK_PLACEHOLDER)
# ====================== 400 ======================
if parsedSequence.molType == 'PRT':
parsedResidues = parsedSequence.residues_prt
currentRow400 = [
400, currentSeqId,
cu.safeLength(seq.residues),
cu.safeLength(parsedResidues),
cu.TAG_LENGTH_ST26['INSDSeq_sequence'],
(cu.TAG_LENGTH_ST26['INSDSeq_sequence'] +
len(cu.oneLetterCode(parsedResidues))),
'INSDSeq_sequence', '3-to-1 letter code'
]
else:
parsedResidues = parsedSequence.residues_nuc
currentRow400 = self._getSt25St26Lengths(
400, currentSeqId, seq.residues, parsedResidues,
'INSDSeq_sequence', cu.BLANK_PLACEHOLDER)
res.append(currentRow400)
return res
def test_setSequencesSt26(self):
sequences = self.sc1.seql_st26.sequence_set.all()
self.assertEqual(4, sequences.count())
s2 = sequences.get(sequenceIdNo=2)
s4 = sequences.get(sequenceIdNo=4)
self.assertEqual('DNA', s2.moltype)
self.assertEqual('AA', s4.moltype)
self.assertEqual('ttgaccaagctggggaccccggtcccttgggaccagtggcagaggagtc', s2.residues)
features_s2 = s2.feature_set.all()
self.assertEqual("3'clip", features_s2[1].featureKey)
self.assertEqual("1..30", features_s2[1].location)
sequences_1004 = self.sc1004.seql_st26.sequence_set.all()
sequence_1004_1 = sequences_1004.get(sequenceIdNo=1)
sequence_1004_7 = sequences_1004.get(sequenceIdNo=7)
self.assertEqual(903, sequence_1004_1.length)
features_1004_1 = sequence_1004_1.feature_set.all()
self.assertEqual("CDS", features_1004_1[1].featureKey)
self.assertEqual("(1)..(903)", features_1004_1[1].location)
# test that feature description missing is not converted to empty element
s1 = sequences.get(sequenceIdNo=1)
features_s1 = s1.feature_set.all()
for f in features_s1:
qualifiers = f.qualifier_set.all()
for q in qualifiers:
self.assertFalse(q.qualifierName in ['note', "NOTE"])
features_s4 = s4.feature_set.all()
for f in features_s4:
qualifiers = f.qualifier_set.all()
for q in qualifiers:
if q.qualifierName == 'NOTE':
exp = 'influenza virus A hemagglutinin subtype H9'
self.assertEqual(exp, q.qualifierValue)
# ============== tests for mixed mode ==================================
translQualifier_seq1 = features_1004_1[1].qualifier_set.all()[0]
self.assertEqual("translation", translQualifier_seq1.qualifierName)
translQualValue_exp = converter_util.oneLetterCode(self.sc1004_seql_st25_sequences[0].residues_prt)
self.assertEqual(translQualValue_exp, translQualifier_seq1.qualifierValue)
features_1004_7 = sequence_1004_7.feature_set.all()
self.assertEqual("CDS", features_1004_7[1].featureKey)
self.assertEqual("(1)..(84)", features_1004_7[1].location)
translQualifier7_1 = features_1004_7[1].qualifier_set.all()[0]
self.assertEqual("translation", translQualifier7_1.qualifierName)
translQualifier7_2 = features_1004_7[2].qualifier_set.all()[0]
self.assertEqual("translation", translQualifier7_2.qualifierName)
translation1 = converter_util.oneLetterCode('MetLysLysSerLeuValLeuLysAlaSerValAlaValAlaThrLeuValProMetLeuSerPheAlaAlaGluGlyGluPhe')
translation2 = converter_util.oneLetterCode('AspProAlaLysAlaAlaPheAspSerLeuGlnAlaSerAlaThrGluTyrIleGlyTyrAlaTrpAlaMetValValValIleValGlyAlaThrIleGlyIleLysLeuPheLysLysPheThrSerLysAlaSer')
self.assertEqual(translation1, translQualifier7_1.qualifierValue)
self.assertEqual(translation2, translQualifier7_2.qualifierValue)
# ============== tests for simple feature conversion ==================================
sourceFeature_1004_7 = features_1004_7[0]
noteQual = sourceFeature_1004_7.qualifier_set.get(qualifierName='note')
self.assertEqual('pc89 major coat protein PVIII', noteQual.qualifierValue)
