proper w

/home/abojchevski/anaconda3/bin/python /home/abojchevski/projects/nala/scripts/train.py --test_corpus tmVar_test --model_path_1 /home/abojchevski/Downloads/nala_BIEO_del_None_466744.bin --we
SpacyLemmatizer: INIT START
SpacyLemmatizer: INIT END
word embddings loaded with vocab size: 519819
Running arguments: 
	crf_train_params = None
	cv_fold = None
	cv_n = None
	delete_subclasses = []
	do_train = False
	elastic_net = False
	labeler = BIEO
	model_name = None_BIEO_del_None
	model_name_suffix = 
	model_path_1 = /home/abojchevski/Downloads/nala_BIEO_del_None_466744.bin
	model_path_2 = None
	nl = False
	nl_features = None
	nl_threshold = 0
	nl_window = False
	output_folder = /tmp/tmpmke3wcpu
	pruner = parts
	ps_NL = False
	ps_ST = False
	ps_random = 0.0
	test_corpus = tmVar_test
	training_corpus = None
	use_feat_windows = True
	validation = stratified
	we_additive = 0
	we_model_location = None
	we_multiplicative = 1
	we_params = {'multiplicative': 1, 'location': None, 'additive': 0}
	word_embeddings = True
	write_anndoc = False


None_BIEO_del_None
starting feature generator: <class 'nalaf.features.stemming.SpacyLemmatizer'>
starting feature generator: <class 'nalaf.features.simple.SentenceMarkerFeatureGenerator'>
starting feature generator: <class 'nala.features.tmvar.TmVarFeatureGenerator'>
starting feature generator: <class 'nala.features.tmvar.TmVarDictionaryFeatureGenerator'>
starting feature generator: <class 'nalaf.features.window.WindowFeatureGenerator'>
starting feature generator: <class 'nalaf.features.embeddings.WordEmbeddingsFeatureGenerator'>

	test size: 166
test: 
pred: 
	subclass distribution: Counter({0: 445, 1: 17, 2: 2})

	num sentences: 1755
test: c.737delC || p.Pro246HisfsX13

pred: c.737delC || p.Pro246HisfsX13

test: 
pred: 

test: Ex2+860G>C || S276T || rs2234671 || rs2234671 || rs2234671
pred: S276T || rs2234671 || rs2234671 || rs2234671 at position Ex2+860G>C

test: 
pred: 

test: 3190C>T || Arg987Ter || Arg987Ter
pred: 3190C>T in exon 24 || Arg987Ter || Arg987Ter || replacement of an arginine residue at position 573 by termination codon

overlapping subclasses do not match 0 1
test: 
pred: 

test: 
pred: insertion of A between nucleotides 1900 and 1901, which resulted in a 3-nucleotide change within the Kozak sequence || single nucleotide insertion/deletion

test: 
pred: 

test: c.104delT || p.Val35AlafsX25
pred: c.104delT || p.Val35AlafsX25 || panel of 262,000 single nucleotide polymorphism || premature termination codon

test: 
pred: 

test: rs16754 || rs16754
pred: All exon 7 mutations were frameshift mutations || including the insertion within codon 313 and codon 314 || rs16754 || rs16754 single nucleotide polymorphism was G

test: 
pred: 

test: c.130G>A || c.130G>A || p.V44M
pred: D13S1316 || D13S1316 || D13S175 || D13S175 || c.130G>A || c.130G>A || non-conservative substitution of valine-to-methionine at codon 44 || p.V44M

test: 
pred: 

test: 
pred: 4G/5G || single base pair guanine insertion/deletion polymorphism (4G/5G)

test: 
pred: 13-bp deletion in the 3' untranslated region

test: CD +90 del 13 bp || IVSII-1 (G > A) || IVSII-1 (G > A)
pred: 13-bp deletion || 13-bp deletion at nucleotide 90 downstream of the termination codon || 13-bp deletion in the 3' UTR || 13-bp deletion in the 3' UTR || CD +90 del 13 bp || G > A || G > A

test: 
pred: single base pair substitution activates a 10-base downstream cryptic splice acceptor site in exon 12

test: c.1706-1715del.ATCTCCTCAG || c.1706-2 A>T || p.(Asp569Valfs*93)
pred: 10-base deletion from the beginning of exon 12 || Asp569Valfs || c.1706-1715del || c.1706-2 A>T || deletion generates a frameshift and a premature termination codon (c.1991-1993

test: Arg399Gln
pred: Arg399Gln

test: Arg399Gln || Arg399Gln || Arg399Gln || Arg399Gln || rs25487
pred: Arg or Arg || Arg versus Arg || Arg versus Arg || Arg399Gln || Arg399Gln || Arg399Gln || Arg399Gln || rs25487

test: 
pred: 

test: 
pred: C35322C || C35322C || C35322T || deletion at 5063 || substitution of C to T at 33468 in exon 8

test: 
pred: 

test: A1762T || E164D || G1764A || G1896A || G1899A || I195M || L180M || L180M || M204V || M204V || V173L || V173L
pred: A1762T || G1764A || G1896A || G1899A || rtL180M || rtL180M + rtM204V || rtM204V || rtV173L || rtV173L || sE164D || sI195M

test: 
pred: 

test: c.263C>T || c.263C>T || p.Ala88Val || p.Ala88Val || p.Asp50Asn
pred: c.263C>T || c.263C>T || leading to a substitution of alanine for valine at position 88 || p.Ala88Val || p.Ala88Val || p.Asp50Asn

test: 
pred: 

test: 
pred: C to T substitution at a polymorphic site 13

test: 
pred: 

test: 
pred: 

test: 
pred: 

test: 
pred: 

test: Arg158 Pro
pred: Arg158 Pro

test: 
pred: G to C at codon 158 of exon 4 || amino acid substitution of arginine residue for the proline residue at position 158 of apoE

test: 
pred: 

test: c.410+5 G/A || c.69delC
pred: c.410+5 G/A || c.69delC

test: 
pred: 

test: 
pred: 

test: 
pred: 

test: G303E || c.908G>A
pred: G303E || c.908G>A within exon 8 || substitution of the amino acid glycine at position 303

test: 
pred: 

test: I597T || T>C
pred: I597T || heterozygous T>C nucleotide substitution on exon 14

overlapping subclasses do not match 0 1
test: 
pred: 

test: -1240 L/S || -521 C/T || -521 C/T || -521C/T || -616C/G
pred: -120 bp duplication, -616C/G

test: 
pred: 

test: 
pred: 

test: delta32
pred: 

test: 
pred: 

test: -1021C/T
pred: 

test: rs1611115 || rs1800587
pred: rs1611115 || rs1800587

test: 
pred: 

test: c.-17T>C || c.171T>C || c.465G>T || c.465G>T || p.Glu155Asp
pred: c.-17T>C || c.171T>C || c.465G>T || c.465G>T || p.Glu155Asp

test: 
pred: 

test: 
pred: 

test: 10034C>T
pred: fibrinogen gamma 10034C>T

test: 10034C>T || 10034C>T || rs2066865
pred: FGG 10034 T || FGG 10034C>T || FGG 10034C>T || rs2066865

test: 
pred: 

test: rs20551 || rs525549 || rs5758222 || rs6589664 || rs6589664 || rs7286979
pred: rs20551 || rs525549 || rs5758222 || rs6589664 || rs6589664 || rs7286979

test: 
pred: 

test: 
pred: lack of CDKN2A

test: 
pred: 

test: c.2554+1G>T
pred: c.2554+1G>T || deletion of amino acids 809-852

test: 
pred: 

test: 
pred: 

test: 
pred: 

test: 
pred: 

test: 
pred: 

test: c.2515_2519delAAGTT
pred: c.2515_2519delAAGTT

test: 
pred: 

test: C119Y || C119Y || c.356G>A || rs13267
pred: C119Y || c.356G>A || leading to amino acid substitution C119Y || rs13267

overlapping subclasses do not match 0 1
test: 
pred: 

test: IVS3 + 18C > T || IVS3 + 18C > T || c.1546_1547insC
pred: IVS3 + 18C > T || c.1546_1547insC || single nucleotide polymorphism (SNP) in intron 3 (IVS3 + 18C > T)

test: 
pred: 

test: (G-->A) at nucleotide position 2141
pred: (G-->A) at nucleotide position 2141 (exon 8), which resulted in substitution of arginine by glutamine at amino acid position 714 || replacement of arginine by glutamine at position 714

test: 
pred: 

test: R68C || rs4112788 || rs4112788
pred: R68C || rs4112788 || rs4112788

test: 
pred: 

test: 
pred: 

test: 
pred: 

test: codon 104 G --> A
pred: nondeletional mutation Hb Sallanches (alpha 2 codon 104 G --> A)

test: 
pred: 

test: rs10954213 || rs10954213 || rs10954213 || rs2004640 || rs2070197
pred: rs10954213 || rs10954213 || rs10954213 || rs2004640 || rs2070197

test: 
pred: 

test: p.C152G || p.D157fsX158 || p.E180K || p.R194S || p.S173fsX174
pred: D157fsX158 || p.C152G || p.E180K || p.R194S

test: Ser326Cys
pred: Ser326Cys

test: rs1052133 || rs1052133 || rs1052133
pred: rs1052133 || rs1052133 || rs1052133 || substitution of the amino acid at codon 326 from Ser to Cys

test: 
pred: 

test: c.263 G>C || c.264 C>A
pred: c.263 G>C || c.264 C>A || substitution from cytosine to adenine at position 264 || substitution from guanine to cytosine at position 263 of the nucleotide sequence

test: 
pred: 

test: G>A substitution at nucleotide 893 || R298Q || rs16864880
pred: G>A substitution at nucleotide 893 || R298Q || rs16864880

test: 
pred: 

test: 
pred: 

test: 
pred: 

test: 
pred: 672 insertion sequence 6110

test: 
pred: G 14 bp insertion/deletion polymorphism

test: rs16375
pred: 14 bp insertion/deletion polymorphism || 14 bp insertion/deletion polymorphism || G 14 bp deletion/insertion polymorphism || rs16375

test: 
pred: 

test: rs2236624 || rs35320474 || rs3761422 || rs5751876
pred: rs2236624 || rs35320474 || rs3761422 || rs5751876

test: 
pred: 

test: 
pred: deletion of a termination-codon-containing region

test: 
pred: 

test: 
pred: 

test: 
pred: 

test: c.1558-1559insA || c.507G>T || c.867G>T || c.897G>T || p.E169stop || p.E299stop || p.G289stop || p.S522fs 525stop
pred: c.1558-1559insA || c.507G>T || c.867G>T || c.897G>T || p.E169stop || p.E299stop || p.G289stop || p.S522fs 525stop

test: 
pred: 

test: 
pred: 

test: 
pred: 

test: G-669A || Glu98X || Leu203fsX15 || Ser863Asn
pred: (Glu98X) and a missense single nucleotide substitution in exon 12 (Ser863Asn) || G-669A || Leu203fsX15 || deletion of TG at the nucleotide position 608-609 in exon 5 || nonsense mutation at the nucleotide position 292 in exon 3

overlapping subclasses do not match 0 1
test: 
pred: 

test: 
pred: Deletion/Deletion (DD)

test: 
pred: 

test: 
pred: 

test: 
pred: 

test: A 11666C || A 1166C || A 1166C
pred: A 11666C || A 1166C || A 1166C

test: R58fs
pred: R58fs

test: R58fs || c.342delA || p.Arg58fs || p.R58fs
pred: R58fs || p.Arg58fs || single nucleotide deletion c.342delA, located in exon 3, which resulted in a frameshift at amino acid position 58

overlapping subclasses do not match 0 1
test: 
pred: 

test: 
pred: 

test: 
pred: 

test: 
pred: SRO of deletion (10-Mb or less) at 11q23

test: 
pred: 

test: 
pred: 

test: 
pred: 

test: rs12329760
pred: rs12329760

test: 
pred: 

test: 118-119insA || 125-126insAA || 46delS || A442V || A6V || E359K || E359K || P163S || P407Q || S429T || c.1146+25insA
pred: 118-119insA || 125-126insAA || 46delS || A442V || A6V || E359K || E359K || P163S || P407Q || S429T || c.1146+25insA in exon 6

overlapping subclasses do not match 0 1
test: 
pred: 

test: 
pred: 

test: 
pred: 

test: R1858X || Y1854X || Y1854X
pred: C to G transversion (Y1854X) || R1858X || Y1854X

overlapping subclasses do not match 0 1
test: 
pred: 

test: 
pred: 

test: 
pred: 

test: c.2068-4T>A
pred: 7-bp deletion in exon 21 and a base insertion in exon 26 || c.2068-4T>A || nonsense mutation in exon 19 || nonsense mutation in exon 24

test: L1503R
pred: L1503R

test: L1503Q || L1503R || L1503R || L1503R || T-->G transversion at nucleotide 4508
pred: L1503Q || L1503R || L1503R || heterozygous T-->G transversion at nucleotide 4508 || substitution of L1503R

overlapping subclasses do not match 0 1
test: 
pred: 

test: c.1570+2T>C || c.360+1G>C || c.360+1G>C || c.520delC || c.681dupA || c.899+1G>T || c.956delC || p.Arg153X
pred: 956delC || c.1570+2T>C || c.360+1G>C || c.360+1G>C || c.520delC || c.681dupA || c.899+1G>T || p.Arg153X

test: 
pred: 

test: 
pred: deletion of 13q14 || deletion of 13q14 || deletion of ATM (11q22) || deletion of TP53

test: 
pred: 

test: 
pred: 

test: 
pred: 

test: A/G transition -1,071 bp || D541E || D541E || K294E || R462Q || R462Q
pred: 20 bp insertion/deletion polymorphism 1,109 bp upstream of the initiation codon || D541E || D541E || G transition -1,071 bp from the transcriptional start site || K294E || R462Q || R462Q

test: 
pred: 

test: M200V || P29S
pred: M200V || P29S || replacement of a non-polar amino acid (proline) with a polar amino acid (serine) at position 29

test: 
pred: 

test: 25*G>A || Ala88Thr || Ser424Ser || Tyr428Tyr || c.1272C>T || c.1284T>C || c.262G>A || c.97GCC[9]+[10]
pred: Ala88Thr || G>A substitution in the 3'-untranslated region || Ser424Ser || Tyr428Tyr || c.1272C>T || c.1284T>C || c.262G>A || duplication of GCC (c.97GCC[9]+[10]) || extra alanine within exon 1

overlapping subclasses do not match 0 1
overlapping subclasses do not match 0 1
test: 
pred: 

test: -1082(G/A) || G/A
pred: polymorphic nucleotide A at position -1082

test: IVS1-1G>C
pred: IVS1-1G>C

test: G > C || IVS1-1G > A || IVS1-1G > C || IVS1-1G > C || IVS1-1G > C
pred: G > C || IVS1-1G > A || IVS1-1G > C || IVS1-1G > C substitution || IVS1-1G > C substitution of exon 1

overlapping subclasses do not match 0 2
overlapping subclasses do not match 0 1
test: 
pred: 

test: g.ORF15 + 652-653delAG || g.ORF15 + 652-653delAG
pred: -653delAG || -653delAG || heterozygous AG-deletion at nucleotide 652 and 653

test: 
pred: 

test: Delta32 || Delta32 || Delta32 || Delta32
pred: 

test: 
pred: 

test: 
pred: 

test: 
pred: 

test: rs2648875 || rs2720709 || rs2720709
pred: rs2648875 || rs2720709 || rs2720709

test: V175M
pred: V175M

test: Val175Met || Val175Met || Val175Met || Val175Met || Val175Met || Val175Met || Val175Met
pred: Val175Met || Val175Met || Val175Met || Val175Met || Val175Met || Val175Met || Val175Met

test: 
pred: 

test: A149P || A174D || N334K
pred: A149P || A174D || Delta4E4 || N334K

test: 
pred: 

test: 
pred: 

test: 
pred: 

test: 6bINS || 6bINS || 6bINS || 6bINS || 6bINS
pred: 6bINS || 6bINS || 6bINS || 6bINS || 6bINS

test: 
pred: 

test: 
pred: 

test: 
pred: 

test: 
pred: in-frame deletion

test: 
pred: 

test: -1282G>A || -2084G>C
pred: -1282G>A || -2084G>C

test: 
pred: 

test: 
pred: p53 codon 72 || p53 codon 72 genotype

test: 
pred: 

test: c.2633+1G>C || c.2633+1G>C || p.Ser555Leu || r.2521_2634del
pred: 1 skipping the entire exon 22 || c.2633+1G>C || c.2633+1G>C || p.Ser555Leu || r.2521_2634del || substitution of serine by leucine at amino acid position 555

test: 
pred: 

test: c.2406C-->A
pred: c.2406C-->A

test: 
pred: 

test: 1858C/T || 1858C/T || 2250G/C
pred: premature termination codon after exon 17

test: 
pred: 

test: 
pred: C-to-T || C-to-T single nucleotide substitution

test: 
pred: 

test: -863C > A || -863C > A || C > A substitution at position -863
pred: C > A substitution at position -863 || allele of the TNFA-863C > A

overlapping subclasses do not match 0 1
test: Tyr1306Cys
pred: Tyr1306Cys

test: Tyr1306Cys || Tyr1306Cys
pred: Tyr1306Cys || Tyr1306Cys

test: G1103R
pred: G1103R

test: G1103R
pred: G1103R

test: 
pred: 

test: 
pred: 

test: 
pred: 

test: Arg260His || Ser263Phe || Ser290/Ala291fs || Ser413Leu || Tyr547fs || Tyr69X || Val414Phe || c.1642_1644dupA || c.2045-1G > A || c.210T > G || c.791C > T || c.892_895dupG
pred: (c.1642_1644dupA) and at codonTyr547fs || (c.892_895dupG) at codons Ser290/Ala291fs || Arg260His || Ser263Phe || Ser413Leu || Tyr69X || Val414Phe || c.2045-1G > A || c.210T > G || c.791C > T || single base 'G' duplication

overlapping subclasses do not match 0 1
overlapping subclasses do not match 0 2
test: 
pred: 

test: 
pred: 30-bp deletion || codon: 346-355

test: 
pred: deletion of cDNA nucleotide 81

test: 
pred: nt 81G deletion

test: 
pred: 

test: 
pred: 

test: 
pred: 

test: 
pred: single-nucleotide insertion or deletion

test: 
pred: 

test: 
pred: 

test: 
pred: 

test: 
pred: 

test: 
pred: 

test: 
pred: deletion of chromosome 14q32.33

test: 
pred: 

test: EX6-96A>G || F302fsX39 || G346R || I38fsX19 || IVS12+4A>G || IVS12+6T>A || IVS4+3G>C || L367L || Q267E || Q267H || R111X || R157I || R157K || R243Q || R400K || R413P || S349A || T200fsX6 || Y154H || Y356X
pred: EX6-96A>G || F302fsX39 || G346R || I38fsX19 || IVS12+4A>G || IVS12+6T>A || IVS4+3G>C || L367L || Q267E || Q267H || R111X || R157I || R157K || R243Q || R400K || R413P || S349A || T200fsX6 || Y154H || Y356X

test: 
pred: 

test: A --> G transition at 127 position || Asn --> Ser substitution at codon 127 || Asn127Ser || G --> A transition at 1032 position || Gly --> Asp change at codon 322 || Gly322Asp || Gly322Asp || Gly322Asp
pred: A --> G transition at 127 position producing an Asn --> Ser substitution at codon 127 (the Asn127Ser || G --> A transition at 1032 position || Gly --> Asp change at codon 322 || Gly/Gly phenotype of the Gly322Asp || Gly322Asp || the Gly322Asp polymorphism

overlapping subclasses do not match 0 1
overlapping subclasses do not match 0 1
overlapping subclasses do not match 0 1
test: 
pred: 

test: K386T || S482X
pred: 15-bp deletion in exon 7 || 15-bp deletion that included the 3' splice site for exon 7 || K386T || S482X || deletion mutation in exon 7

test: 
pred: 

test: A467T || A467T || A467T || A467T || A467T || E873-TAG || E873stop || E873stop || E873stop || E873stop
pred: A467T || A467T || A467T || A467T || A467T || E873-TAG || E873stop || E873stop || E873stop || E873stop || premature termination codon (TAG) in exon 17 || threonine to alanine substitution at a highly conserved site in exon 7

test: 
pred: 

test: IVS2-58_55insT
pred: IVS2-58_55insT || insertion in IVS2

test: 
pred: 

test: Arg792Gly || Arg792Gly
pred: A to G transition at nucleotide +79 of exon 41 || Arg792Gly || Arg792Gly substitution is located at the Y-position of Gly-X-Y || converted the codon for arginine at amino acid 792 to a codon for glycine

overlapping subclasses do not match 0 1
test: 
pred: 

test: V175M || V175M || V175M || V175M
pred: Met/Met at residue 175 || V175M || V175M || V175M || V175M

test: 
pred: 

test: C-->T
pred: heterozygous C-->T single-nucleotide substitution, 16 nt upstream of the putative translation initiation site

overlapping subclasses do not match 0 1
test: 
pred: 

test: rs5393
pred: rs5393

test: 
pred: 

test: 
pred: deletion of about 1.4 kb including exon 3

test: 
pred: 

test: 
pred: 

test: 
pred: 

test: c.1044_1049delTTCTGGinsACACT || c.113-1G>A || c.345_372del28 || c.360_363delCAAA || c.532T>C || c.612T>G || c.799+2T>A || c.841_842delAC || c.851T>C || c.865delC || p.A150P || p.A175D || p.C178R || p.L284P || p.N335K || p.R60X || p.Y204X || p.Y204X
pred: c.1044_1049delTTCTGGinsACACT || c.113-1G>A || c.345_372del28 || c.360_363delCAAA || c.532T>C || c.612T>G || c.799+2T>A || c.841_842delAC || c.851T>C || c.865delC || p.A150P || p.A175D || p.C178R || p.L284P || p.N335K || p.R60X || p.Y204X || p.Y204X

test: 
pred: 

test: 157delMTTTVP || 157delMTTTVP || rs2277025
pred: 1 insertion/deletion polymorphism || 157delMTTTVP || 157delMTTTVP || rs2277025

test: 
pred: 

test: A1053G || C3026T || C934A || G1915T/A || G529A || T2005C/A
pred: A1053G || C3026T || C934A || G1915T/A || G529A || T2005C/A

test: 
pred: 

test: rs1639679
pred: rs1639679

test: 
pred: 

test: ACG-->AAG substitution in codon 420 || GAT-->GAG
pred: GAT-->GAG substitution replaces aspartic acid by glutamic acid in codon 416; and ACG-->AAG substitution in codon 420 leads to an exchange of threonine for lysine

overlapping subclasses do not match 0 1
overlapping subclasses do not match 1 0
test: 
pred: 

test: 
pred: 

test: 
pred: 

test: 217_218insC || 217_218insC || A207D || A207D || A49T || A49T || G158R || G158R || G183S || G183S || G196S || G196S || IVS3+1G>A || IVS3+1G>A || Q126R || Q126R || Q126R || R246W || R266W || V89L || del418T || del642T || del642T
pred: 217_218insC plus the A49T || A207D || A207D || A49T || G158R || G158R || G183S || G183S || G196S || G196S || IVS3+1G>A || IVS3+1G>A || Q126R || Q126R || Q126R || R246W || R266W || V89L || and the insertion of a cytosine (217_218insC) || del418T || del642T || del642T || single nucleotide deletion

overlapping subclasses do not match 0 2
overlapping subclasses do not match 0 1
test: 
pred: 

test: 
pred: 

test: 
pred: 

test: 222insT || 835del18 || 912delTA || D418D || GAC/GAT || L89R || P291A || Q536X || R171Q
pred: 222insT || D418D || L89R || P291A || Q536X, exon 10 || R171Q || one frameshift deletion (912delTA, exon 5), one in-frame deletion (835del18, exon 4)

overlapping subclasses do not match 0 1
test: L490R || V561X
pred: L490R || V561X

test: 1469T->G || 1665delC || C282Y || I238M || I238M || L490R || L490R || L490R || V561X || V561X
pred: 1469T->G || 1665delC || 594-597 deletion || 714C-> || C282Y || I238M || I238M || L490R || L490R || L490R || V561X || V561X

test: 
pred: 

test: 
pred: 

test: 
pred: 

test: 
pred: 

test: A>G polymorphism at position -670
pred: single nucleotide A>G polymorphism at position -670

test: 
pred: ) to guanine (G) substitution at position -670

test: 
pred: 

test: 203G > A || N372H || N372H || N372H || N372H || N372H
pred: 203G > A || N372H || N372H || N372H || N372H || nonconservative amino acid substitution polymorphism N372H

overlapping subclasses do not match 0 1
test: 
pred: 

test: E29K || E29K || Glu29 to Lys || g.3907G >A
pred: E29K || E29K || F7 gene deletion || codon for Glu29 to Lys || g.3907G >A

overlapping subclasses do not match 2 1
test: 
pred: 

test: 
pred: A guanine insertion (2G) polymorphism at nucleotide -1607

test: 
pred: 

test: 
pred: T to C substitution at position 1833 || all males were heterozygous in nucleotides 1678, 1694, 1699, 1708 and 1825 || exon 12

test: 
pred: 

test: 
pred: 

test: 
pred: 

test: IVS10 + 4G
pred: A to G substitution denoted IVS10 + 4G

overlapping subclasses do not match 0 1
test: 
pred: 

test: 
pred: 

test: 
pred: 

test: G-->A substitution at codon 1763 || I1762A || V1763M || V1764M
pred: G-->A substitution at codon 1763, which changed a valine (GTG) to a methionine (ATG) || I1762A || V1763M || V1764M

test: 
pred: 

test: 1188-A/C
pred: bp insertion/deletion

test: 
pred: 

test: Delta30 || Delta30 || Delta30 || Delta30 || Delta30 || Delta30 || Delta30 || Delta30 || Delta30
pred: Delta30 || rDEN2Delta30-4995 || rDEN2Delta30-4995

test: 
pred: 

test: 
pred: 

test: 
pred: 

test: 1091 C > T || G71R || G71R || G71R || G71R || P229Q || P364L || P364L || P364L || Y486D || Y486D || Y486D
pred: 1091 C > T || G71R || G71R || G71R || G71R || P229Q || P364L || P364L || P364L || Y486D || Y486D || Y486D

test: 
pred: 

test: Tyr246X
pred: Tyr246X || premature stop codon at the 246 residue || substitution of cytosine (C) for guanine (G) at codon 246 in exon 6

test: 
pred: 

test: 
pred: 

test: 
pred: 

test: 
pred: resulting from the loss of repeat units 7

test: 
pred: 

test: 5504delA || 5504delA || 6573 + 1G > C || 6573 + 1G > C
pred: 5504delA || 5504delA || 6573 + 1G > C || 6573 + 1G > C || deletion mutation || intron 81 || single-nucleotide deletion within exon 64

test: 
pred: 

test: 
pred: 

test: 
pred: 

test: C435G || del 329C
pred: C435G || del 329C || single-nucleotide deletion at position 329

test: 
pred: 

test: 1242G>T || 1780C>A || 1780C>A || 2068G>C || 2068G>C || 2084G>A || 9 +1G>T
pred: 1242G>T || 1780C>A || 1780C>A || 2068G>C in exon 11 || 2084G>A || C insertion in exon 14 between positions 2505-2511 || GGCC insertion at exon 8 (1277) and a nucleotide substitution in exon 11 (2068G>C) || homozygous GGCC insertion at exon 8 || intron 9 +1G>T

overlapping subclasses do not match 0 1
overlapping subclasses do not match 0 1
overlapping subclasses do not match 0 2
test: 
pred: 

test: 
pred: 

test: 
pred: 

test: 
pred: D16S2622 || D16S475 || D16S523

test: 
pred: 

test: 
pred: 

test: 
pred: 

test: 
pred: 

test: C270T
pred: C270T

test: C270T
pred: C270T

test: 
pred: 

test: +142C/G || +142C/G || +355G/T || +355G/T || -1001C/T || -1001C/T || -1001C/T || -13C/T || -13C/T || -13C/T || -263G/A || -263G/A || -263G/A
pred: G-C-C-G of -1001C/T, -263G

overlapping subclasses do not match 0 1
test: 
pred: 

test: 
pred: 

test: 
pred: 

test: A/C1166 || A/C1166 || A/C1166 || T/C-344 || T/C-344 || T/C-344 || T/C704 || T/C704 || T/C704
pred: A/C1166 || A/C1166 || C allele of AGT T/C704, the A allele of AT1 A/C1166 || T/C-344 || T/C-344 || T/C-344 || T/C704 || T/C704

overlapping subclasses do not match 0 1
test: 
pred: 

test: 
pred: 

test: 
pred: 

test: 620-621del in cDNA || C877T in cDNA
pred: C877T || deletion (620-621del

test: 
pred: 

test: 
pred: 

test: 
pred: 

test: -866 promoter (G/A) || A55V || Ala55Val
pred: nonsynonymous (Ala55Val or A55V) single-nucleotide polymorphism in exon 4

overlapping subclasses do not match 0 1
test: c.399_402del AGAG
pred: c.399_402del AGAG

test: c.399_402delAGAG || c.399_402delAGAG || c.399_402delAGAG || c.399_402delAGAG || c.399_402delAGAG
pred: 4-bp deletion in exon 3 || c.399_402delAGAG || c.399_402delAGAG || c.399_402delAGAG || c.399_402delAGAG || c.399_402delAGAG

test: C-174G || G-308A
pred: C-174G || G-308A

test: C-174G || G-308A || G-308A
pred: C-174C || C-174C || C-174G || G-308A || G-308A || G-308G

test: 
pred: 

test: 
pred: G to C substitution at position -174

test: 
pred: 

test: 
pred: deletion of KLF5

test: 3020insC
pred: 3020insC frameshift mutation

test: 3020insC || 3020insC || 3020insC || 3020insC
pred: 3020insC || 3020insC || 3020insC || 3020insC || cytosine insertion at position 3020 of exon 11

test: 
pred: 

test: 
pred: 

	crf_train_params = None
	cv_fold = None
	cv_n = None
	delete_subclasses = []
	do_train = False
	elastic_net = False
	labeler = BIEO
	model_name = None_BIEO_del_None
	model_name_suffix = 
	model_path_1 = /home/abojchevski/Downloads/nala_BIEO_del_None_466744.bin
	model_path_2 = None
	nl = False
	nl_features = None
	nl_threshold = 0
	nl_window = False
	output_folder = /tmp/tmpmke3wcpu
	pruner = parts
	ps_NL = False
	ps_ST = False
	ps_random = 0.0
	test_corpus = tmVar_test
	training_corpus = None
	use_feat_windows = True
	validation = stratified
	we_additive = 0
	we_model_location = None
	we_multiplicative = 1
	we_params = {'multiplicative': 1, 'location': None, 'additive': 0}
	word_embeddings = True
	write_anndoc = False

# class	tp	fp	fn	fp_ov	fn_ov	match	P	P_SE	R	R_SE	F	F_SE	match	P	P_SE	R	R_SE	F	F_SE
0	338	81	107	58	69	e	0.8067	0.0024	0.7596	0.0033	0.7824	0.0027	o	0.9529	0.0012	0.9245	0.0021	0.9384	0.0013
1	7	93	10	8	10	e	0.0700	0.0025	0.4118	0.0111	0.1197	0.0048	o	0.2273	0.0044	1.0000	0.0000	0.3704	0.0051
2	0	14	2	2	2	e	0.0000	0.0000	0.0000	0.0000	   nan	   nan	o	0.2500	0.0098	1.0000	0.0000	0.4000	0.0220
TOTAL	345	188	119	68	81	e	0.6473	0.0026	0.7435	0.0029	0.6921	0.0025	o	0.8046	0.0021	0.9286	0.0020	0.8621	0.0016

Process finished with exit code 0