def createNS(self, NStype, NSname, NSseq):
"""Create a NamedSequence using raw data and then adding it to the database
as a NamedSequenceDB.
PARAMETERS:
NStype: string type of the named sequence
NSname: string name of the named sequence
NSseq: string sequence of the named sequence
RETURNS:
NSentry: created NamedSequenceDB that is in the database
"""
# type checking
checkType(NStype, "NStype")
# get the nameID
nameID = self.getEntry().getNextNSid()[NStype]
# create it as a NamedSequence
newNS = NamedSequence.makeNew(NStype, NSname, NSseq, nameID)
# add it as a NamedSequenceDB to the database and the user
NSentry = self.addNS(newNS)
return NSentry
def findNamedSequenceNoSeq(self, NStype, NSname):
"""Searches UserDataDB for a NamedSequenceDB; don't need sequence.
PARAMETERS:
NStype: string type of the named sequence
NSname: string name of the named sequence
RETURNS:
found NamedSequenceDB
RAISES:
SequenceNotFoundError: if the named sequence was not found
Exception: if multiple named sequences that fits the requirements were found
"""
# type checking
checkType(NStype, "NStype")
if type(NSname) != str:
raise TypeError("name not a string")
# query database
namedSeqList = (
self.getAllNSQuery().filter_by(elemType=NStype, name=NSname).all()
)
# handle the results from the query
if len(namedSeqList) == 0:
raise e.SequenceNotFoundError("Could not find sequence.")
if len(namedSeqList) > 1:
raise Exception("Multiple sequences found.")
else:
return namedSeqList[0]
def makeNew(cls, NSType, NSName, NSSeq, nameID):
"""Create a new NamedSequence.
PARAMETERS:
NSType: string type of the named sequence
NSName: string name of the named sequence
NSSeq: string sequence of the named sequence
NSnameID: string name ID of the named sequence
RETURNS:
newNS: the new NamedSequence
"""
# type checking
checkType(NSType, "NSType")
if type(NSName) != str:
raise TypeError("NSName not a string")
if type(NSSeq) != str:
raise TypeError("NSSeq not a string")
if type(nameID) != int:
raise TypeError("newID not an int")
# initialize the instance
newNS = cls()
# set instance's variables
newNS.__type = NSType
newNS.__name = NSName
newNS.__seq = NSSeq
newNS.__nameID = nameID
return newNS
def findComponent(self, compType, compName, compPos, compTerminalLetter):
"""Searches UserDataDB for ComponentDB with specifications.
PARAMETERS:
compType: string type of the component's sequence to find
compName: string name of the component's sequence to find
compPos: integer position of the component
compTerminalLetter: string component's terminal letter
RETURNS:
comp: found component that fits the paramters
RAISES:
ComponentNotFoundError: if no component was found that fits the parameters.
"""
# type checking
checkType(compType, "compType")
if type(compName) != str:
raise TypeError("compName not a string")
if type(compPos) != int:
raise TypeError("comPos not an int")
if type(compTerminalLetter) != str:
raise TypeError("compTerminalLetter not a string")
# first search for a NamedSequenceDB that fits the type and name
foundNS = self.findNamedSequenceNoSeq(compType, compName)
# search through the components of foundNS
for comp in foundNS.getAllComponents():
# for each component, check the position and terminal letter
if (comp.getPosition() == compPos) and (
comp.getTerminalLetter() == compTerminalLetter
):
# return if found.
return comp
# did not find it
raise e.ComponentNotFoundError("Could not find component.")
def validateNewNS(newNSType, newNSName, newNSSeq):
"""Validates the input from creating a new NamedSequence on the design page.
PARAMETERS:
newNSType: string type for the named sequence ("Pr", "RBS", "GOI", or "Term")
newNSName: string name for the named sequence
newNSSeq: string sequence for the named sequence
RETURNS:
validInput: boolean. True if all input is valid, False otherwise.
outputStr: HTML string to output to the website so errors are displayed.
"""
validInput = True
outputStr = ""
##### TYPE CHECKING #####
if type(newNSType) != type(newNSName) != type(newNSSeq) != str:
validInput = False
outputStr += "ERROR: input received not all strings.<br>"
try:
checkType(newNSType, "newNSType")
except ValueError:
validInput = False
outputStr += "ERROR: '" + newNSType + "' is not a valid type.<br>"
##### VALIDATE NAME #####
# length
if len(newNSName) < 1 or len(newNSName) > 20:
validInput = False
outputStr += "ERROR: Sequence name must be 1-20 characters.<br>"
# whether it already exists in default:
longNames = {
"Pr": "promoter",
"RBS": "ribosome binding site",
"GOI": "gene",
"Term": "terminator",
}
for elemType in ["Pr", "RBS", "GOI", "Term"]:
try:
defaultUser.findNamedSequenceNoSeq(elemType, newNSName)
validInput = False
outputStr += (
"ERROR: {newNSName} already exists in the default "
"library as a {longName}.<br>"
).format(newNSName=newNSName, longName=longNames[elemType])
break
except SequenceMismatchError:
validInput = False
outputStr += (
"ERROR: {newNSName} already exists in the default "
"library as a {longName}, and with a different sequence.<br>"
).format(newNSName=newNSName, longName=longNames[elemType])
break
except SequenceNotFoundError:
pass
# characters
for special in specialChars:
newNSName = newNSName.replace(special, specialChars[special])
invalidCharactersName = []
for character in newNSName:
if (character not in validCharacters) and (
character not in invalidCharactersName
):
validInput = False
outputStr += (
"ERROR: '" + character + "' is not allowed in a sequence's name.<br>"
)
invalidCharactersName.append(character)
##### VALIDATE SEQUENCE #####
# length
if (
len(newNSSeq) < 1 or len(newNSSeq) > 99999
): # I don't know what limits should be used
validInput = False
outputStr += "ERROR: Sequence must be 1-99999 nucleotides.<br>"
# characters
validNucleotides = "AGTCBDHKMNRSVWY"
invalidCharactersSeq = []
# check special Chars first:
for special in specialChars:
if special in newNSSeq:
validInput = False
outputStr += (
"ERROR: {char} is not allowed in a sequence's name.<br>".format(
char=specialChars[special]
)
)
invalidCharactersSeq.append(specialChars[special])
for character in newNSSeq:
if (character not in validNucleotides) and (
character not in invalidCharactersSeq
):
validInput = False
outputStr += "ERROR: '" + character + "' is not an allowed nucleotide.<br>"
invalidCharactersSeq.append(character)
return (validInput, outputStr)