def __init__(self):

pass

# Info:TranscriptID|Strand_Direction|Variant_Classification1,Variant_Classification2,...|Shared_EffKey(s)|

# REF_Codon(s);Variant_Position_in_Codon|REF_AA|old_CDS_Position|ALT_Codon(s);Variant_Position_in_Codon|

# ALT_AA|new_CDS_Position|NAVIP_END|<old info field>

# Chr1 12584 . A C 2961.77 PASS AT1G01030.1|REV|SUB|NONE|AAC;2|v|357|CAC;2|v|357|NAVIP_END|

# 0 1 2

##INFO=<ID=ANN,Number=.,Type=String,Description="Functional annotations: 'Allele | Annotation | Annotation_Impact |

# 3 4 5 6 7 8 9 10 11.1 11.2

# Gene_Name | Gene_ID | Feature_Type | Feature_ID | Transcript_BioType | Rank | HGVS.c | HGVS.p | cDNA.pos / cDNA.length |

# 12.1 12.2 13.1 13.2 14 15

# CDS.pos / CDS.length | AA.pos / AA.length | Distance | ERRORS / WARNINGS / INFO' ">

# 0 1 2 3 4 5 6 7 8

# ['C', 'synonymous_variant', 'LOW', 'AT1G01030', 'AT1G01030', 'transcript', 'AT1G01030.1', 'protein_coding', '2/2',

# 9 10 11 12 13 14

# 'c.357T>G', 'p.Val119Val', '970/1905', '357/1077', '119/358', '',

# 0 1 2 3 4 5 6 7 8 9

#ANN=A|upstream_gene_variant|MODIFIER|AT1G01010|AT1G01010|transcript|AT1G01010.1|protein_coding| |c.-3408G>A|

# 10 11 12 13 14 15

# | | | |3279| ,A|upstream_gene_variant|MODIFIER|AT1G01010.1|AT1G01010.1-Protein|transcript|TRANSCRIPT_AT1G01010.1-Protein|

# protein_coding||c.-3408G>A|||||3408|,A|intergenic_region|MODIFIER|CHR_START-AT1G01010|CHR_START-AT1G01010|intergenic_region|

# CHR_START-AT1G01010|||n.352G>A||||||

##INFO=<ID=LOF,Number=.,Type=String,Description="Predicted loss of function effects for this variant. Format: 'Gene_Name | Gene_ID | Number_of_transcripts_in_gene | Percent_of_transcripts_affected'">

##INFO=<ID=NMD,Number=.,Type=String,Description="Predicted nonsense mediated decay effects for this variant. Format: 'Gene_Name | Gene_ID | Number_of_transcripts_in_gene | Percent_of_transcripts_affected'">

@staticmethod

def convert_main(transcript:Transcript, vinfo:Variant_Information_Storage) -> str :

#note to myself: don't forget: info-files are ;-seperated

aminodict = {"Ala": "A", "A": "Ala", "Cys": "C", "C": "Cys", "Asp": "D", "D": "Asp", "Glu": "E", "E": "Glu",

"Phe": "F", "F": "Phe", "Gly": "G", "G": "Gly", "His": "H", "H": "His", "Ile": "I", "I": "Ile",

"Lys": "K", "K": "Lys", "Leu": "L", "L": "Leu", "Met": "M", "M": "Met", "Asn": "N", "N": "Asn",

"Pro": "P", "P": "Pro", "Gln": "Q", "Q": "Gln", "Arg": "R", "R": "Arg", "Ser": "S", "S": "Ser",

"Thr": "T", "T": "Thr", "Val": "V", "V": "Val", "Trp": "W", "W": "Trp", "Tyr": "Y", "Y": "Tyr",

"*": "*", 'X': 'Xaa', 'Xaa': 'X'}

#aminodict["*"] = "stop_gained"

#aminodict["stop_gained"] = "*"

annotation = "" #1

annotation_impact = "" #2

gene_name = transcript.TID.split(".")[0]#3

gene_ID = transcript.TID.split(".")[0] #4

feature_type = "transcript" #5

feature_ID = transcript.TID #6

transcript_bio_type = "protein_coding" #7

rank = "" #8 # ignored

HGVS_C = "" #9 # http://varnomen.hgvs.org/recommendations/DNA/

HGVS_P = "" #10 # http://varnomen.hgvs.org/recommendations/protein/

cDNA_pos = "" #11.1 # cDNA_pos != CDS_pos, I'm using the matured positions only

cDNA_length = "" #11.2 # cDNA_length != CDS_length, I'm using the matured positions only

CDS_pos = vinfo.Unchanged_CDS_Position #12.1 # original in snpeff (?); me original

CDS_length = transcript.uChDNA_length #12.2 # original in snpeff (?); me original

AA_pos = (vinfo.Unchanged_CDS_Position-1)/3 #13.1 # original in snpeff (?); me original

AA_length = transcript.uChAA_length #13.2 # original in snpeff (?); me original

distance = "" #14 # ignored

errors_warnings = "" #15 # maybe ignored

AA_pos_temp = (vinfo.Unchanged_CDS_Position-1)%3

if AA_pos_temp == 0:

AA_pos = (vinfo.Unchanged_CDS_Position-1 +3) / 3 # AA = 0 is the first, not zero

elif AA_pos_temp == 1:

AA_pos = (vinfo.Unchanged_CDS_Position-1 +2) / 3

elif AA_pos_temp == 2:

AA_pos = (vinfo.Unchanged_CDS_Position-1 +1) / 3

AA_pos = int(AA_pos)

new_AA_pos = 0

AA_pos_temp = (vinfo.Changed_CDS_Position - 1) % 3

if AA_pos_temp == 0:

new_AA_pos = (vinfo.Changed_CDS_Position - 1) / 3 + 1 # AA = 0 is the first, not zero

elif AA_pos_temp == 1:

new_AA_pos = (vinfo.Changed_CDS_Position + 1) / 3 + 1

elif AA_pos_temp == 2:

new_AA_pos = vinfo.Changed_CDS_Position / 3 + 1

new_AA_pos = int(new_AA_pos)

AA_to_next_stop = transcript.IV_ChangedTranslation[new_AA_pos:].find('*')

for i,x in enumerate(vinfo.Classification):

if i < len(vinfo.Classification) -1 :

annotation += x.value + ',' # not efficient, but list isn't large

else:

annotation += x.value

if TranscriptEnum.FRAMESHIFT in vinfo.Classification \

or TranscriptEnum.FRAMESHIFT_1 in vinfo.Classification \

or TranscriptEnum.FRAMESHIFT_2 in vinfo.Classification \

or TranscriptEnum.FRAMESHIFT_1_DEL in vinfo.Classification \

or TranscriptEnum.FRAMESHIFT_2_DEL in vinfo.Classification \

or TranscriptEnum.STOP_GAINED in vinfo.Classification \

or TranscriptEnum.STOP_LOST in vinfo.Classification \

or TranscriptEnum.START_LOST in vinfo.Classification:

annotation_impact = "HIGH"

elif TranscriptEnum.DELETION in vinfo.Classification \

or TranscriptEnum.INSERTION in vinfo.Classification \

or TranscriptEnum.AA_CHANGE in vinfo.Classification:

annotation_impact = "MODERATE"

elif TranscriptEnum.STOP_CHANGED in vinfo.Classification\

or TranscriptEnum.AA_CHANGE not in vinfo.Classification:

annotation_impact = "LOW"

else:

print("Impossible case. Error convert_main.")

#annotation_impact = "MODIFIER" # does not exist? upstream/downstream is not noted

#HGVS_C

if TranscriptEnum.SUBSTITUTION in vinfo.Classification:

# NG_012232.1(NM_004006.1):c.93+1G>T

# a substitution of the G nucleotide at c.93+1 (coding DNA reference sequence) by a T

if TranscriptEnum.FORWARD == transcript.ForwardDirection:

HGVS_C = "c." + str(vinfo.Unchanged_CDS_Position) + vinfo.Ref + ">" + vinfo.Alt

else:

HGVS_C = "c." + str(vinfo.Unchanged_CDS_Position) + vinfo.ReverseRef + ">" + vinfo.ReverseAlt

elif TranscriptEnum.INSERTION in vinfo.Classification:

#insertion, duplication, (repeated seq)

#check for duplication

if vinfo.Unchanged_CDS_Position >= len(vinfo.Alt) -1: # check if insertion is long enough to be a duplicate

if transcript.ForwardDirection == TranscriptEnum.FORWARD:

insert = vinfo.Alt[1:] # first base == refstart, always > 0

else:

insert = vinfo.ReverseAlt[:len(vinfo.ReverseAlt)-1]

if len(transcript.uChDNAsequence) >= len(transcript.Complete_CDS):

refpart = transcript.uChDNAsequence[vinfo.Unchanged_CDS_Position - len(insert):vinfo.Unchanged_CDS_Position +1]

#print(str(transcript.TID) + "\t" + insert + "\t" + refpart)

#print("testa1:\t" + vinfo.Alt + "\t" + transcript.uChDNAsequence[vinfo.Unchanged_CDS_Position-1])

#print("testa2:\t" + vinfo.Alt + "\t" + refpart)

#print("testa1:\t" + vinfo.ReverseAlt + "\t" + transcript.uChDNAsequence[vinfo.Unchanged_CDS_Position - 1])

#print("testa2:\t" + vinfo.ReverseAlt + "\t" + refpart)

"""

else:

if TranscriptEnum.FORWARD == transcript.ForwardDirection:

refpart = transcript.Complete_CDS[vinfo.Unchanged_CDS_Position + 1 - len(insert):vinfo.Unchanged_CDS_Position + 1]

#print(str(transcript.TID) + "\t" + insert + "\t" + refpart)

#print("testb1:\t" + vinfo.Alt + "\t" + transcript.Complete_CDS[vinfo.Unchanged_CDS_Position - 1])

#print("testb2:\t" + vinfo.Alt + "\t" + refpart)

else:

refpart = transcript.Rev_CDS[vinfo.Unchanged_CDS_Position + 1 - len(insert):vinfo.Unchanged_CDS_Position + 1]

#print(str(transcript.TID) + "\t" + insert + "\t" + refpart)

#print("testc1:\t" + vinfo.Alt + "\t" + transcript.Rev_CDS[vinfo.Unchanged_CDS_Position - 1])

#print("testc2:\t" + vinfo.Alt + "\t" + refpart)

HGVS_C = "c."

if insert == refpart:

#Format: “prefix”“position(s)_duplicated”“dup”, e.g. g.123_345dup

vinfo.Classification.append(HGVS_DNA.DUP)

HGVS_C += str(vinfo.Unchanged_CDS_Position - len(insert))

if len(insert) == 1:

HGVS_C += 'dup' + insert

else:

HGVS_C += '_' + str(vinfo.Unchanged_CDS_Position) + 'dup' + insert

else:

#Format: “prefix”“positions_flanking”“ins”“inserted_sequence”, e.g. g.123_124insAGC

HGVS_C += str(vinfo.Unchanged_CDS_Position -1) + '_' + str(vinfo.Unchanged_CDS_Position) + 'ins' + insert

#print(HGVS_C)

elif TranscriptEnum.DELETION in vinfo.Classification:

#Format: “prefix”“position(s)_deleted”“del”, e.g. g.123_127del

HGVS_C = "c."

if len(vinfo.Ref) == 2: #del of 1 base

#one nucleotide - NG_012232.1:g.19del

# a deletion of the T at position g.19 in the sequence AGAATCACA to AGAA_CACA

# NOTE: it is allowed to describe the variant as NG_012232.1:g.19delT

HGVS_C += str(vinfo.Unchanged_CDS_Position +1) + 'del' + vinfo.Ref[1]

else:

#NG_012232.1:g.19_21del

#a deletion of nucleotides g.19 to g.21 in the sequence AGAATCACA to AGAA___CA

#NOTE: it is allowed to describe the variant as NG_012232.1:g.19_21delTCA

HGVS_C += str(vinfo.Unchanged_CDS_Position +1) + '_' + str(vinfo.Unchanged_CDS_Position + len(vinfo.Ref)) + 'del' + vinfo.Ref[1:]

#print(HGVS_C)

else:

LogOrganizer.addToLog(LogEnums.CONVERTER_LOG,"No Classification in: " + str(transcript.TID) + "\t" + str(vinfo.ChrPosition))

#HGVS_P

HGVS_P = "p."

new_amino = ''

old_amino= ''

for AA in vinfo.NewAmino:

new_amino += aminodict[AA.upper()]

for AA in vinfo.OrigAmino:

old_amino += aminodict[AA.upper()]

if TranscriptEnum.STOP_LOST in vinfo.Classification:

# Format (C-terminal): “prefix”“Ter_position”“new_amino_acid”“ext”“position_new_termination_site”, e.g. p.Ter110Glnext*17

# extension, sub, del, ins

# sub first, because it's easy

if AA_to_next_stop != -1:

ext = 'ext*' + str(AA_to_next_stop)

else:

ext = 'ext*?'

HGVS_P += '*' + str(AA_pos) + new_amino + ext

#if TranscriptEnum.SUBSTITUTION in vinfo.Classification:

# HGVS_P += '*' + str(AA_pos) + vinfo.NewAmino + ext

#elif TranscriptEnum.INSERTION in vinfo.Classification:

# HGVS_P += '*' + str(AA_pos) + vinfo.NewAmino + ext

#elif TranscriptEnum.DELETION in vinfo.Classification:

# HGVS_P += '*' + str(AA_pos) + vinfo.NewAmino + ext

elif TranscriptEnum.STOP_CHANGED in vinfo.Classification and TranscriptEnum.INSERTION in vinfo.Classification and vinfo.NewAmino[0] != '*':

# insertion in the stop codon, but still a stop codon exist -> extension, but only if the first AA

# is not a stop codon

# extension check

if AA_to_next_stop != -1:

ext = 'ext*' + str(AA_to_next_stop)

else:

ext = 'ext*?'

HGVS_P += '*' + str(AA_pos) + new_amino + ext

elif TranscriptEnum.SUBSTITUTION in vinfo.Classification or new_amino == '*':

# missense -> AA-Change #LRG_199p1:p.Trp24Cys

# nonsense -> stop gained #LRG_199p1:p.Trp24Ter (p.Trp24*)

# silent -> AA is not changed #NP_003997.1:p.Cys188=

if vinfo.OrigAmino == vinfo.NewAmino: #silent

HGVS_P += old_amino + str(AA_pos) + old_amino

else: #missense and nonsense

HGVS_P += old_amino + str(AA_pos) + new_amino

elif TranscriptEnum.FRAMESHIFT_1 in vinfo.Classification \

or TranscriptEnum.FRAMESHIFT_2 in vinfo.Classification \

or TranscriptEnum.FRAMESHIFT_1_DEL in vinfo.Classification \

or TranscriptEnum.FRAMESHIFT_2_DEL in vinfo.Classification:

"""

if new_amino == '*': # counts as SUB, len == 1

"""

HGVS_P += old_amino + str(AA_pos) + '*'

#elif '*' in new_amino: #no idea what this is, but not always a frameshift

# pass

else:

#first changed AA has to be the first AA here

if vinfo.OrigAmino[0] != vinfo.NewAmino[0]:

if vinfo.STOP_CAUSED_IN == -1:

HGVS_P += old_amino + str(AA_pos) + new_amino + '*' + '?'

else:

HGVS_P += old_amino + str(AA_pos) + new_amino + '*' + str(vinfo.STOP_CAUSED_IN)

else:

#find first changed AA....

# test every AA, if they are equal, from the variant_position

i = 0

# python can't do that:

#for old_AA,new_AA in transcript.uChAAsequence[AA_pos:], transcript.IV_ChangedTranslation[new_AA_pos:]:

# if old_AA == "":

# print("should not happen")

# elif new_AA == '*':

# HGVS_P += old_amino + str(AA_pos + i) + '*'

# break

# elif old_AA == new_AA:

# i +=1

# continue

# else:

# if vinfo.STOP_CAUSED_IN == -1:

# HGVS_P += old_AA + str(AA_pos + i) + new_AA + '*?'

# else:

# HGVS_P += old_AA + str(AA_pos + i) + new_AA + '*' + str(vinfo.STOP_CAUSED_IN - i)

# break

for j, old_AA in enumerate (transcript.uChAAsequence[AA_pos-1:]):

new_AA = transcript.IV_ChangedTranslation[new_AA_pos-1 + j]

if old_AA == "":

print("should not happen")

elif new_AA == '*':

HGVS_P += old_amino + str(AA_pos + i) + '*'

break

elif old_AA == new_AA:

i +=1

continue

else:

#find better names, here it is to switch single AA-code to 3 letter AA-code

abc1 = ""

abc2 = ""

for abcabc in new_AA:

abc1 += aminodict[abcabc.upper()]

for abcabc in old_AA:

abc2 += aminodict[abcabc.upper()]

if vinfo.STOP_CAUSED_IN == -1:

HGVS_P += abc2 + str(AA_pos + i) + abc1 + '*?'

else:

HGVS_P += abc2 + str(AA_pos + i) + abc1 + '*' + str(vinfo.STOP_CAUSED_IN - i)

break

elif TranscriptEnum.INSERTION in vinfo.Classification:

# extension is already checked ->

# frameshift, too

# first duplication check

# second and last is the normal insertion

if ((len (vinfo.Alt) -1) % 3) != 0:

print('how`?') # well, it should not be a frameshift -> multiple of 3

else:

#dup check

if (len(vinfo.Alt) -1) % 3 != 0:

print("how2?")

if len(transcript.uChAAsequence) >= len(transcript.IV_OriginalTranslation):

if (len(vinfo.Alt) -1) / 3 == len(vinfo.NewAmino):

#Insertion of complete AA without interfering with other AA

refpartAA = transcript.uChAAsequence[AA_pos-1 - len(vinfo.NewAmino):AA_pos]

else:

#Insertion with interfering with other AA

# -> the original AA is in vinfo.NewAmino

# -> do not compare it with itself

if len(vinfo.NewAmino) == 1:

print('how?3')

refpartAA = transcript.uChAAsequence[AA_pos-1 - (len(vinfo.NewAmino) -1) :AA_pos]

else:

if (len(vinfo.Alt) -1) / 3 == len(vinfo.NewAmino):

#Insertion of complete AA without interfering with other AA

refpartAA = transcript.IV_OriginalTranslation[AA_pos-1 - len(vinfo.NewAmino):AA_pos]

else:

#Insertion with interfering with other AA

# -> the original AA is in vinfo.NewAmino

# -> do not compare it with itself

if len(vinfo.NewAmino) == 1:

print('how?3')

refpartAA = transcript.IV_OriginalTranslation[AA_pos-1 - (len(vinfo.NewAmino) -1 ):AA_pos ]

#print(vinfo.NewAmino + "\t" + refpartAA)

#print(transcript.IV_OriginalTranslation[AA_pos - (len(vinfo.NewAmino) -3 ):AA_pos + 3])

if len(vinfo.NewAmino) == len(refpartAA):

dup = True

#print(refpartAA, vinfo.NewAmino)

#print(type(refpartAA))

for i, oa in enumerate(refpartAA):

if vinfo.NewAmino[i] == oa:

continue

else:

dup = False

if dup:

if (len(vinfo.Alt) -1) / 3 == len(vinfo.NewAmino):

# Insertion of complete AA without interfering with other AA

if len(vinfo.NewAmino) == 1: # one AA

"""

HGVS_P += aminodict[vinfo.OrigAmino[0].upper()] + str(AA_pos) + 'dup'

else: # multiple AA

"""

HGVS_P += aminodict[refpartAA[0].upper()] + str(AA_pos - (len(vinfo.NewAmino) -1 )) + '_' \

+ aminodict[vinfo.OrigAmino[0].upper()] + str(AA_pos) + 'dup'

else:

# Insertion with interfering with other AA

if len(vinfo.NewAmino) == 2: # one new AA, first AA not changed, because it's a dup

# so it looks like, this can only happen, if vinfo.NewAmino[0] == vinfo.NewAmino[1]

"""

HGVS_P += aminodict[vinfo.OrigAmino[0].upper()] + str(AA_pos) + 'dup'

else: # multiple AA

"""

#print(refpartAA[0] + str(AA_pos - (len(vinfo.NewAmino) - 1)) + '_' + vinfo.OrigAmino + str(AA_pos) + 'dup' )

#print(refpartAA + str(AA_pos - (len(vinfo.NewAmino) - 1)) + '_' + vinfo.OrigAmino + str(AA_pos) + 'dup')

#print(vinfo.ChrPosition)

HGVS_P += aminodict[refpartAA[0].upper()] + str(AA_pos - (len(vinfo.NewAmino) - 1)) + '_' + \

aminodict[vinfo.OrigAmino[0].upper()] + str(AA_pos) + 'dup'

else:

# no dup, but insertion without frameshift

# delins are possible

if (len(vinfo.Alt) -1) / 3 == len(vinfo.NewAmino):

# Insertion of complete AA without interfering with other AA

"""

#if len(vinfo.NewAmino) == 1: # one AA

HGVS_P += aminodict[vinfo.OrigAmino[0].upper()] + str(AA_pos) + '_' + aminodict[refpartAA[1].upper()] \

+ str(AA_pos+1) + 'ins' + new_amino

#else: # multiple AA

# HGVS_P += vinfo.OrigAmino[0] + str(AA_pos) + '_' + refpartAA[AA_pos + 1] \

# + str(AA_pos + 1) + 'ins' + vinfo.NewAmino

else:

# looks like, if the first AA is changed -> delin, the ref AA, when the variation is interfering

# with another AA

"""

if vinfo.OrigAmino[0] == vinfo.NewAmino[0]: # no delin

#print(vinfo.ChrPosition)

#print(vinfo.OrigAmino[0] + str(AA_pos) + '_')

#print(refpartAA)

#print(transcript.IV_OriginalTranslation[AA_pos:])

HGVS_P += aminodict[vinfo.OrigAmino[0].upper()] + str(AA_pos) + '_' + aminodict[refpartAA[1].upper()] \

+ str(AA_pos + 1) + 'ins' + new_amino

else:

HGVS_P += aminodict[vinfo.OrigAmino[0].upper()] + str(AA_pos) + 'delins' + new_amino

else:

# reasons for a variation to be in this else:

# insertion in the beginning of the transcript -> insert to long, no complete refAA existent

# -> example: insert 5 AA, but it's in the start codon

if len(vinfo.NewAmino) >= AA_pos:

# no duplication/ refAA possible, because insertion is too big

"""

if vinfo.OrigRaster == 2:

#insertion without interfering with first origAA

"""

if len(vinfo.NewAmino) > 1:

HGVS_P += aminodict[vinfo.OrigAmino[0].upper()] + str(AA_pos) + 'ins' + new_amino[1:]

else:

print("curios effect")

HGVS_P += aminodict[vinfo.OrigAmino[0].upper()] + str(AA_pos) + 'ins' + new_amino

else:

#insertion with interfering with first origAA

if vinfo.OrigAmino[0] == vinfo.NewAmino[0]:

#first AA not changed -> insertion after

HGVS_P += aminodict[vinfo.OrigAmino[0].upper()] + str(AA_pos) + 'ins' + new_amino

else:

#first AA changed -> SUB or DELINS

if len(vinfo.NewAmino) == 1 and vinfo.NewAmino == '*':

#SUB

#LRG_199p1:p.Trp24Ter (p.Trp24*)

HGVS_P += aminodict[vinfo.OrigAmino[0].upper()] + str(AA_pos) + new_amino

else:

#DELINS

"""

HGVS_P += aminodict[vinfo.OrigAmino[0].upper()] + str(AA_pos) + 'delins' + new_amino

else:

# stop codon + stuff at the end of the transcript

if vinfo.NewAmino == vinfo.OrigAmino:

#if vinfo.NewAmino[0] == vinfo.OrigAmino[0] and len (vinfo.NewAmino) == 1 and len(vinfo.OrigAmino) == 1:

# silent sub

"""

b = ""

for AA in vinfo.OrigAmino:

b += aminodict[AA.upper()]

HGVS_P += b + str(AA_pos) + b

else:

"""

if vinfo.NewAmino[0] == vinfo.OrigAmino[0]:

# no sub, possible here

if len(vinfo.NewAmino) > 1 and len(vinfo.OrigAmino) > 1:

#delins

b = ""

for AA in vinfo.OrigAmino:

b += aminodict[AA.upper()]

HGVS_P += b + str(AA_pos +1) + 'delins' + new_amino[1:]

elif len(vinfo.OrigAmino) == 1 and len(vinfo.NewAmino) > 1:

# here, if the AA 2+ are not identical with the original AA

HGVS_P += aminodict[vinfo.OrigAmino[0].upper()] + str(AA_pos) + 'delins' + new_amino

else: # orig > 1 and new_amino == 1 () impossible?

print('Impossible case triggered.')

else:

b = ""

for AA in vinfo.OrigAmino:

b += aminodict[AA.upper()]

HGVS_P += b + str(AA_pos) + 'delins' + new_amino

elif TranscriptEnum.DELETION in vinfo.Classification:

# deletion stuff, no frameshifts possible anymore -> codon-position should always be 2 ???? nope

# len(vinfo.NewAmino) > 1: true

if vinfo.OrigRaster == 2:

#deletion of complete AA, without interfering of another AA (start position +1 (dna))

if len(vinfo.OrigAmino) == 2:

#complete deletion of the second AA

"""

HGVS_P += aminodict[vinfo.OrigAmino[1].upper()] + str(AA_pos +1 ) + 'del'

elif len(vinfo.OrigAmino) == 1:

#impossible case (or something went wrong with the transcript)

if vinfo.OrigAmino == vinfo.NewAmino:

#sub

#NP_003997.1:p.Cys188=

HGVS_P += old_amino + str(AA_pos) + old_amino

else:

try:

HGVS_P += old_amino + str(AA_pos) + aminodict[vinfo.NewAmino[0].upper(9)]

except IndexError:

print("Variant error: " + str(vinfo.ChrPosition))

HGVS_P += 'old_amino' + str(AA_pos) + 'Xaa'

else:

"""

HGVS_P += aminodict[vinfo.OrigAmino[1].upper()] + str(AA_pos + 1) + '_' + \

aminodict[vinfo.OrigAmino[len(vinfo.OrigAmino)-1].upper()] + str(AA_pos +1 + len(vinfo.OrigAmino) -1) + 'del'

else :

if vinfo.OrigAmino == "":

print("Variant error: " + str(vinfo.ChrPosition))

elif len(vinfo.OrigAmino) == 1:

#this should not happen here, but who knows

if vinfo.OrigAmino == vinfo.NewAmino:

#sub

#NP_003997.1:p.Cys188=

HGVS_P += old_amino + str(AA_pos) + old_amino

else:

HGVS_P += old_amino + str(AA_pos) + aminodict[vinfo.NewAmino.upper()]

elif TranscriptEnum.STOP_GAINED in vinfo.Classification:

"""

HGVS_P += aminodict[vinfo.OrigAmino[0].upper()] + str(AA_pos) + aminodict[vinfo.NewAmino.upper()]

else:

# always deletions, starting inside the codon, always multiple of 3 bp deleted

# stop lost, stop changed and stop gained is handled to this point

# --> only delins (?)

"""

HGVS_P += aminodict[vinfo.OrigAmino[0].upper()] + str(AA_pos) + "_" + aminodict[vinfo.OrigAmino[len(vinfo.OrigAmino)-1].upper()] + str(AA_pos + len(vinfo.OrigAmino)) + 'delins'

elif TranscriptEnum.UNKNOWN_AMINOACID in vinfo.Classification :

# this here should be a substitution of X into X (because bad chromosome data)

HGVS_P += old_amino + str(AA_pos) + new_amino

else:

LogOrganizer.addToLog(LogEnums.CONVERTER_LOG,"No Classification in: " + str(transcript.TID) + "\t" + str(vinfo.ChrPosition))

snpeff_like_info_string = 'NAV2=' + vinfo.Alt + '|' \

+ annotation + "|" \

+ annotation_impact + "|" \

+ gene_name + "|" \

+ gene_ID + "|" \

+ feature_type + "|" \

+ feature_ID + "|" \

+ transcript_bio_type + "|" \

+ rank + "|" \

+ HGVS_C + "|" \

+ HGVS_P + "|" \

+ str(cDNA_pos) + "/" \

+ str(cDNA_length) + "|" \

+ str(CDS_pos) + "/" \

+ str(CDS_length) + "|" \

+ str(AA_pos) + "/" \

+ str(AA_length) + "|" \

+ distance + "|" \

+ errors_warnings + ";"

SUB = "Substitution"

DEL = "Deletion"

DUP = "Duplication"

INS = "Insertion"

INV = "Inversion"

CON = "Conversion"

DELIN = "Deletion-Insertion"

ALL = "Alleles"

REP = "Repeated sequences"

SUB = "Substitution"

DEL = "Deletion"

DUP = "Duplication"

INS = "Insertion"

DELIN = "Deletion-Insertion"

ALL = "Alleles"

REP = "Repeated sequences"

FS = "Frame shift"