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License: MIT License
Hi all
This package is so great! I was wondering if there is any way to fetch the location
out of the gbk.genes
field. Currently we can get all the fields that start with the /
in the record:
gbk.genes[end]
CDS 47738..47944
/db_xref="GeneID:2703534"
/locus_tag="lambdap79"
/codon_start=1
/transl_table=11
/product="hypothetical protein"
/protein_id="NP_597782.1"
/translation="MNKEQSADDPSVDLIRVKNMLNSTISMSYPDVVIACIEHKVSLE
AFRAIEAALVKHDNNMKDYSLVVD"
/note="Predicted by GeneMark"
I want to be able to get the location qualifier 47738..47944
encoded later as a UnitRange{Int64}
--> 47738:47944
. Is this a feature we can have in GenomicAnnotations
(or already have)?
Best.
Hi, I'm trying to open a .gbff.gz
file and I'm getting the following error:
julia> readgbk(joinpath(DATA_DIR, "genome.gbff.gz"))
ERROR: UndefVarError: GzipDecompressorStream not defined
Stacktrace:
[1] open(#unused#::Type{GenomicAnnotations.GenBank.Reader}, input::String)
@ GenomicAnnotations.GenBank ~/.julia/packages/GenomicAnnotations/aGEUx/src/GenBank/reader.jl:31
[2] readgbk(input::String)
@ GenomicAnnotations ~/.julia/packages/GenomicAnnotations/aGEUx/src/utils.jl:65
[3] top-level scope
@ REPL[5]:1
Any help would be much appreciated. Thanks!
Hi, I'm trying converting a genbank file to a gff with the package, however it fails. For example, one gene is as below:
Input: Screenshot 1; https://www.ncbi.nlm.nih.gov/nuccore/7525012
As shown, the CDS in the gff output doesn't have an intron between the two exons. CDS sequences extracted based on these kinds of coordinates must be wrong. Thank you!
The REQUIRE file could not be found.
cc: @kdyrhage
Hello,
I have downloaded a genebank file from NCBI (https://www.ncbi.nlm.nih.gov/nuccore/NC_022898.1?report=genbank then send to -> file -> GeneBank (full))
I then try to open the file using
gbff = readgbk("sequence.gb")
but get an error:
ERROR: ArgumentError: invalid index: nothing of type Nothing
Stacktrace:
[1] to_index(i::Nothing)
@ Base ~/julia-1.3.1/bin/../share/julia/base/indices.jl:273
[2] to_index(A::Array{SubString{String},1}, i::Nothing)
@ Base ~/julia-1.3.1/bin/../share/julia/base/indices.jl:250
[3] to_indices
@ Base ~/julia-1.3.1/bin/../share/julia/base/indices.jl:301 [inlined]
[4] to_indices
@ Base ~/julia-1.3.1/bin/../share/julia/base/indices.jl:298 [inlined]
[5] getindex
@ ~/julia-1.3.1/bin/../share/julia/base/abstractarray.jl:981 [inlined]
[6] parseheader(header::String)
@ GenomicAnnotations.GenBank ~/.julia/packages/GenomicAnnotations/gigUo/src/GenBank/reader.jl:58
[7] parsechromosome!(stream::TranscodingStreams.TranscodingStream{TranscodingStreams.Noop,IOStream}, record::GenomicAnnotations.Record{Gene})
@ GenomicAnnotations.GenBank ~/.julia/packages/GenomicAnnotations/gigUo/src/GenBank/reader.jl:227
[8] tryread!
@ GenomicAnnotations.GenBank ~/.julia/packages/GenomicAnnotations/gigUo/src/GenBank/reader.jl:49 [inlined]
[9] iterate
@ GenomicAnnotations.GenBank ~/.julia/packages/GenomicAnnotations/gigUo/src/GenBank/reader.jl:42 [inlined]
[10] _collect(cont::UnitRange{Int64}, itr::GenomicAnnotations.GenBank.Reader{TranscodingStreams.TranscodingStream{TranscodingStreams.Noop,IOStream}}, ::Base.HasEltype, isz::Base.SizeUnknown)
@ Base ~/julia-1.3.1/bin/../share/julia/base/array.jl:572
[11] collect
@ Base ~/julia-1.3.1/bin/../share/julia/base/array.jl:560 [inlined]
[12] readgbk(input::String)
@ GenomicAnnotations ~/.julia/packages/GenomicAnnotations/gigUo/src/utils.jl:65
[13] top-level scope
@ REPL[15]:1
It should get noted that if I download the GeneBank file instead (no "(full)"), then I can load it (but there's not much actual content in it).
I'm trying to parse a .gb
file that I exported via Benchling (it shouldn't make a difference), but for some reason readgbk
just keeps running without ever ending. BioPython parses the file, so I assume the file is encoded correctly. I'm attaching the file below. Thanks in advance! Really appreciate the package
LOCUS pAC03_(pQJ6_w/_mOrange 10073 bp ds-DNA circular 17-SEP-2023
DEFINITION .
FEATURES Location/Qualifiers
primer 596..615
/label="oLAC01"
/note="sequence: GATTCATTAATGCAGCTGGC"
/ApEinfo_revcolor="#d59687"
/ApEinfo_fwdcolor="#d59687"
primer 621..642
/label="oQJ70"
/note="sequence: CGCGTAGCCTGTCAGAAATTGA"
/ApEinfo_revcolor="#faac61"
/ApEinfo_fwdcolor="#faac61"
primer 621..642
/label="oQJ70"
/note="sequence: CGCGTAGCCTGTCAGAAATTGA"
/ApEinfo_revcolor="#f7977a"
/ApEinfo_fwdcolor="#f7977a"
misc_feature 621..1698
/label="lacZ upstream"
/ApEinfo_revcolor="#ffef86"
/ApEinfo_fwdcolor="#ffef86"
3'UTR 672..690
/label="KS1469"
/ApEinfo_revcolor="#b1ff67"
/ApEinfo_fwdcolor="#b1ff67"
primer 801..819
/label="oLAC22"
/note="sequence: AAGTAGCAGTGAAAGCCAA"
/ApEinfo_revcolor="#c7b0e3"
/ApEinfo_fwdcolor="#c7b0e3"
3'UTR 824..849
/label="KS584"
/ApEinfo_revcolor="#b1ff67"
/ApEinfo_fwdcolor="#b1ff67"
misc_feature 824..849
/label="KS584\"
/ApEinfo_revcolor="#faac61"
/ApEinfo_fwdcolor="#faac61"
misc_feature 923..942
/label="KS281\"
/ApEinfo_revcolor="#85dae9"
/ApEinfo_fwdcolor="#85dae9"
primer 951..971
/label="oLAC19"
/note="sequence: AACACATAACCCTGCAGTAAG"
/ApEinfo_revcolor="#faac61"
/ApEinfo_fwdcolor="#faac61"
primer 1033..1053
/label="oLAC09"
/note="sequence: AGTAGCTTCAAGCCATGAATC"
/ApEinfo_revcolor="#d59687"
/ApEinfo_fwdcolor="#d59687"
primer 1196..1213
/label="oLAC23"
/note="sequence: CAACTTGGCTAGAACCGG"
/ApEinfo_revcolor="#b4abac"
/ApEinfo_fwdcolor="#b4abac"
primer 1479..1498
/label="oQY48"
/note="sequence: CACCATTATGATGGCAATCG"
/ApEinfo_revcolor="#85dae9"
/ApEinfo_fwdcolor="#85dae9"
misc_feature 1573..1595
/label="p1"
/ApEinfo_revcolor="#b1ff67"
/ApEinfo_fwdcolor="#b1ff67"
misc_feature complement(1678..1698)
/label="pr"
/ApEinfo_revcolor="#84b0dc"
/ApEinfo_fwdcolor="#84b0dc"
misc_feature 1699..1733
/label="BBa_J23119"
/ApEinfo_revcolor="#75c6a9"
/ApEinfo_fwdcolor="#75c6a9"
misc_feature 1734..1767
/label="FRT"
/ApEinfo_revcolor="#c7b0e3"
/ApEinfo_fwdcolor="#c7b0e3"
misc_feature 1768..1787
/label="pf"
/ApEinfo_revcolor="#f8d3a9"
/ApEinfo_fwdcolor="#f8d3a9"
misc_feature 1785..1819
/label="kanR promoter"
/ApEinfo_revcolor="#b7e6d7"
/ApEinfo_fwdcolor="#b7e6d7"
primer 1815..1840
/label="oLAC30"
/note="sequence: TTTAAATACTGTAGAAAAGAGGAAGG"
/ApEinfo_revcolor="#f58a5e"
/ApEinfo_fwdcolor="#f58a5e"
misc_feature 1834..1839
/label="RBS"
/ApEinfo_revcolor="#c6c9d1"
/ApEinfo_fwdcolor="#c6c9d1"
CDS 1850..2644
/label="KanR"
/ApEinfo_revcolor="#faac61"
/ApEinfo_fwdcolor="#faac61"
misc_feature 2626..2648
/label="KS445\"
/ApEinfo_revcolor="#b4abac"
/ApEinfo_fwdcolor="#b4abac"
misc_feature complement(2627..2644)
/label="ACM205\"
/ApEinfo_revcolor="#ff9ccd"
/ApEinfo_fwdcolor="#ff9ccd"
misc_feature 2657..2678
/label="KS518\"
/ApEinfo_revcolor="#b1ff67"
/ApEinfo_fwdcolor="#b1ff67"
misc_feature complement(2657..2678)
/label="KS464\"
/ApEinfo_revcolor="#85dae9"
/ApEinfo_fwdcolor="#85dae9"
3'UTR 2666..2717
/label="terminator"
/ApEinfo_revcolor="#ff9ccd"
/ApEinfo_fwdcolor="#ff9ccd"
misc_feature 2676..2695
/label="ACM300\"
/ApEinfo_revcolor="#c6c9d1"
/ApEinfo_fwdcolor="#c6c9d1"
misc_feature complement(2720..2739)
/label="KS325\"
/ApEinfo_revcolor="#85dae9"
/ApEinfo_fwdcolor="#85dae9"
misc_feature 2720..2759
/label="KS635\"
/ApEinfo_revcolor="#d6b295"
/ApEinfo_fwdcolor="#d6b295"
misc_feature complement(2720..2759)
/label="KS661\"
/ApEinfo_revcolor="#b7e6d7"
/ApEinfo_fwdcolor="#b7e6d7"
primer 2729..2747
/label="oLAC32"
/note="sequence: CTCTCCTGAGTCCCACAAT"
/ApEinfo_revcolor="#85dae9"
/ApEinfo_fwdcolor="#85dae9"
primer complement(2729..2747)
/label="oLAC31"
/note="sequence: ATTGTGGGACTCAGGAGAG"
/ApEinfo_revcolor="#c7b0e3"
/ApEinfo_fwdcolor="#c7b0e3"
misc_feature 2740..2759
/label="KS644\"
/ApEinfo_revcolor="#75c6a9"
/ApEinfo_fwdcolor="#75c6a9"
misc_feature 2750..2760
/label="ACM325\"
/ApEinfo_revcolor="#ff9ccd"
/ApEinfo_fwdcolor="#ff9ccd"
misc_feature complement(2750..2760)
/label="ACM324\"
/ApEinfo_revcolor="#faac61"
/ApEinfo_fwdcolor="#faac61"
primer 2929..2948
/label="oLAC04"
/note="sequence: CACTCCCGTTCTGGATAATG"
/ApEinfo_revcolor="#c7b0e3"
/ApEinfo_fwdcolor="#c7b0e3"
primer complement(2929..2948)
/label="oLAC33"
/note="sequence: CATTATCCAGAACGGGAGTG"
/ApEinfo_revcolor="#b7e6d7"
/ApEinfo_fwdcolor="#b7e6d7"
misc_feature 3000..3005
/label="-35 box"
/ApEinfo_revcolor="#75c6a9"
/ApEinfo_fwdcolor="#75c6a9"
promoter 3000..3028
/label="tac promoter"
/ApEinfo_revcolor="#75c6a9"
/ApEinfo_fwdcolor="#75c6a9"
misc_feature 3006..3021
/label="Ptac"
/ApEinfo_revcolor="#b4abac"
/ApEinfo_fwdcolor="#b4abac"
misc_feature 3022..3028
/label="-10 box"
/ApEinfo_revcolor="#c6c9d1"
/ApEinfo_fwdcolor="#c6c9d1"
misc_binding 3032..3054
/label="LacO"
/ApEinfo_revcolor="#84b0dc"
/ApEinfo_fwdcolor="#84b0dc"
misc_feature 3094..3127
/label="FRT"
/ApEinfo_revcolor="#c7b0e3"
/ApEinfo_fwdcolor="#c7b0e3"
misc_feature 3170..3175
/label="RBS?"
/ApEinfo_revcolor="#f8d3a9"
/ApEinfo_fwdcolor="#f8d3a9"
misc_feature 3181..3891
/label="mTFP"
/ApEinfo_revcolor="#85dae9"
/ApEinfo_fwdcolor="#85dae9"
primer 3805..3824
/label="oLAC05"
/note="sequence: CACGACAAGGACTACAACAA"
/ApEinfo_revcolor="#c6c9d1"
/ApEinfo_fwdcolor="#c6c9d1"
misc_feature 3911..3927
/label="Hairpin - terminator"
/ApEinfo_revcolor="#f8d3a9"
/ApEinfo_fwdcolor="#f8d3a9"
misc_feature 3963..3981
/label="Hairpin (less likely) - terminator"
/ApEinfo_revcolor="#d6b295"
/ApEinfo_fwdcolor="#d6b295"
misc_feature 4068..4196
/label="BBa_B0015"
/ApEinfo_revcolor="#b7e6d7"
/ApEinfo_fwdcolor="#b7e6d7"
misc_feature 4224..4257
/label="FRT"
/ApEinfo_revcolor="#c7b0e3"
/ApEinfo_fwdcolor="#c7b0e3"
misc_feature complement(4263..4280)
/label="pr"
/ApEinfo_revcolor="#b1ff67"
/ApEinfo_fwdcolor="#b1ff67"
primer 4277..4298
/label="oLAC18"
/note="sequence: AGGAcaagagacaggatactag"
/ApEinfo_revcolor="#faac61"
/ApEinfo_fwdcolor="#faac61"
misc_feature 4281..4304
/label="pf"
/ApEinfo_revcolor="#faac61"
/ApEinfo_fwdcolor="#faac61"
misc_feature 4302..4307
/label="RBS"
/ApEinfo_revcolor="#ff9ccd"
/ApEinfo_fwdcolor="#ff9ccd"
CDS 4313..5023
/label="mOrange2"
/ApEinfo_revcolor="#c7b0e3"
/ApEinfo_fwdcolor="#c7b0e3"
/note="product: photostable monomeric orange derivative of DsRed fluorescent protein (Shaner et al., 2008) note: mammalian codon-optimized translation: MVSKGEENNMAIIKEFMRFKVRMEGSVNGHEFEIEGEGEGRPYEGFQTAKLKVTKGGPLPFAWDILSPHFTYGSKAYVKHPADIPDYFKLSFPEGFKWERVMNYEDGGVVTVTQDSSLQDGEFIYKVKLRGTNFPSDGPVMQKKTMGWEASSERMYPEDGALKGKIKMRLKLKDGGHYTSEVKTTYKAKKPVQLPGAYIVDIKLDITSHNEDYTIVEQYERAEGRHSTGGMDELYK"
primer 4505..4523
/label="oLAC13"
/note="sequence: atcctgtcccctcatttca"
/ApEinfo_revcolor="#84b0dc"
/ApEinfo_fwdcolor="#84b0dc"
primer 4731..4750
/label="oLAC11"
/note="sequence: tgatgcagaagaagaccatg"
/ApEinfo_revcolor="#84b0dc"
/ApEinfo_fwdcolor="#84b0dc"
misc_feature complement(5011..5037)
/label="pr"
/ApEinfo_revcolor="#d59687"
/ApEinfo_fwdcolor="#d59687"
primer 5024..5044
/label="oLAC26"
/note="sequence: taattagctgagctCTTCACG"
/ApEinfo_revcolor="#85dae9"
/ApEinfo_fwdcolor="#85dae9"
misc_feature 5058..5085
/label="pf"
/ApEinfo_revcolor="#75c6a9"
/ApEinfo_fwdcolor="#75c6a9"
misc_feature 5065..5070
/label="RBS"
/ApEinfo_revcolor="#c6c9d1"
/ApEinfo_fwdcolor="#c6c9d1"
misc_feature 5070..5075
/label="RBS"
/ApEinfo_revcolor="#f8d3a9"
/ApEinfo_fwdcolor="#f8d3a9"
CDS 5081..5875
/label="KanR"
/ApEinfo_revcolor="#faac61"
/ApEinfo_fwdcolor="#faac61"
misc_feature 5857..5879
/label="KS445\"
/ApEinfo_revcolor="#b4abac"
/ApEinfo_fwdcolor="#b4abac"
misc_feature complement(5858..5875)
/label="ACM205\"
/ApEinfo_revcolor="#ff9ccd"
/ApEinfo_fwdcolor="#ff9ccd"
misc_feature complement(5860..5882)
/label="pr"
/ApEinfo_revcolor="#b4abac"
/ApEinfo_fwdcolor="#b4abac"
primer 5883..5901
/label="oLAC24"
/note="sequence: CAAACTGGGGCACAGATAG"
/ApEinfo_revcolor="#b4abac"
/ApEinfo_fwdcolor="#b4abac"
misc_feature 5883..5903
/label="pf"
/ApEinfo_revcolor="#b7e6d7"
/ApEinfo_fwdcolor="#b7e6d7"
primer complement(5895..5913)
/label="oLAC28"
/note="sequence: GGGATGGGTACCCTATCTG"
/ApEinfo_revcolor="#faac61"
/ApEinfo_fwdcolor="#faac61"
misc_feature 5932..6154
/label="From pJA02"
/ApEinfo_revcolor="#ffef86"
/ApEinfo_fwdcolor="#ffef86"
misc_feature 5993..5993
/label="C->T"
/ApEinfo_revcolor="#ff9ccd"
/ApEinfo_fwdcolor="#ff9ccd"
misc_feature 5999..6127
/label="BBa_B0015"
/ApEinfo_revcolor="#b7e6d7"
/ApEinfo_fwdcolor="#b7e6d7"
misc_feature 6155..7290
/label="lacZ downstream"
/ApEinfo_revcolor="#ff9ccd"
/ApEinfo_fwdcolor="#ff9ccd"
misc_feature complement(6165..6185)
/label="p2"
/ApEinfo_revcolor="#85dae9"
/ApEinfo_fwdcolor="#85dae9"
primer complement(6265..6282)
/label="oLAC27"
/note="sequence: AGTTGGCTCTTGCTTTGG"
/ApEinfo_revcolor="#d59687"
/ApEinfo_fwdcolor="#d59687"
primer 6293..6312
/label="oLAC25"
/note="sequence: TTCTGCCATCAGTTGGATTG"
/ApEinfo_revcolor="#faac61"
/ApEinfo_fwdcolor="#faac61"
primer 6492..6509
/label="oQJ39"
/note="sequence: AGGTTAGTCATCGCCTGT"
/ApEinfo_revcolor="#85dae9"
/ApEinfo_fwdcolor="#85dae9"
primer 6969..6987
/label="oLAC16"
/note="sequence: GGATCAGAAACATCGCTGA"
/ApEinfo_revcolor="#f58a5e"
/ApEinfo_fwdcolor="#f58a5e"
primer complement(7270..7290)
/label="oQJ71"
/note="sequence: TGTTGAACAAGCGTCATGGCT"
/ApEinfo_revcolor="#f7977a"
/ApEinfo_fwdcolor="#f7977a"
primer complement(7270..7290)
/label="oQJ71"
/note="sequence: TGTTGAACAAGCGTCATGGCT"
/ApEinfo_revcolor="#c7b0e3"
/ApEinfo_fwdcolor="#c7b0e3"
misc_feature 7431..8291
/label="AmpR"
/ApEinfo_revcolor="#b7e6d7"
/ApEinfo_fwdcolor="#b7e6d7"
ORIGIN
1 GTTATTTCTT GATGTCTCTG ACCAGACACC CATCAACAGT ATTATTTTCT CCCATGAAGA
61 CGGTACGCGA CTGGGCGTGG AGCATCTGGT CGCATTGGGT CACCAGCAAA TCGCGCTGTT
121 AGCGGGCCCA TTAAGTTCTG TCTCGGCGCG TCTGCGTCTG GCTGGCTGGC ATAAATATCT
181 CACTCGCAAT CAAATTCAGC CGATAGCGGA ACGGGAAGGC GACTGGAGTG CCATGTCCGG
241 TTTTCAACAA ACCATGCAAA TGCTGAATGA GGGCATCGTT CCCACTGCGA TGCTGGTTGC
301 CAACGATCAG ATGGCGCTGG GCGCAATGCG CGCCATTACC GAGTCCGGGC TGCGCGTTGG
361 TGCGGATATC TCGGTAGTGG GATACGACGA TACCGAAGAC AGCTCATGTT ATATCCCGCC
421 GTCAACCACC ATCAAACAGG ATTTTCGCCT GCTGGGGCAA ACCAGCGTGG ACCGCTTGCT
481 GCAACTCTCT CAGGGCCAGG CGGTGAAGGG CAATCAGCTG TTGCCCGTCT CACTGGTGAA
541 AAGAAAAACC ACCCTGGCGC CCAATACGCA AACCGCCTCT CCCCGCGCGT TGGCCGATTC
601 ATTAATGCAG CTGGCACGAC CGCGTAGCCT GTCAGAAATT GATCGGTCGA TAGGCTGTCA
661 CCTAAGGCAT TTTGCAGCAA GGGAAGAACC ACATGACCGC CACCAAACAC TAAGCTTCCT
721 GCTTGGAAGA AATGGCCAAA CAACTCAACC AGCGGTGAGC TTGCAGCCAA GAGCGGCAGC
781 CCGAGTAATA AACTTGCAAA AAGTAGCAGT GAAAGCCAAG AGGGGCTGAA CGTGGTTGTC
841 GAAAATGACT GTTGTGGTGC CAAGCGGGCT TGGCCAACGA AAGCGGCGAT CAGAAGGACC
901 GCAAACTGAG TGATGAGACC GGGAGCTAAC GTAATCGCAA CCGCAGTCAG AACACATAAC
961 CCTGCAGTAA GGCGTTGCTG ACAAAAATTG CGATACATGG TTAAACAAGC ATCGGCCACC
1021 ACTATGATCG CGAGTAGCTT CAAGCCATGA ATCATTTGTT CAAACAGTGG GGTATCAAGG
1081 AGATGGCTGC TTAGCCCCGC GAGCAGCAGC ATGATGAGCA CGGAGGGAAG GGTAAAACCG
1141 AGAAACGCTG CCCAAGCGCC AGCCAGACCA CCACGATGAT AACCAATCGC AAAACCAACT
1201 TGGCTAGAAC CGGGGCCAGG AAGGAACTGG CTCAGTGCCA CAAATTGTGC ATATTCTTGC
1261 TCGCTAACCC AGCGTAATTT CTCAACAAAG GTGTGGCGAA AGTAACCTAT ATGTGCGGCT
1321 GGCCCACCAA AACTCACCCA TCCGAGAGCA AAAAAAGTTC TAAAAATCGT TAGCATAATG
1381 ATCTGAAGTC ATCCGTAATC AATGGAAGGT CAACATCCGT AGGAGCATAG GTTATGGAGA
1441 GTCAAAGCGC AGAACAACTC CGAATGTGTA AAAAATTACA CCATTATGAT GGCAATCGTA
1501 TGAATCGATT CAGAAATAGA AAAATTGGGT CAATATCGAC CTCTATTTAA ATTGTGGAAA
1561 CGTTTACACA ATTGGTGAGT GGTTCACAGA ATCGGTGTTT GAAAGTTTGT TAGACTTTTT
1621 TGCATCTGCA GCATGTCATC ATTCCTATTC AAAGCTGCGA ATCTTATTGA ATGACTTCTT
1681 TACTCCTCGG CTTGAGGGtt gacagctagc tcagtcctag gtataatgct agcgaagttc
1741 ctattctcta gaaagtatag gaacttcCGA AGCTGGGGAT CCGTTTGATT TTTAATGGAT
1801 AATGTGATAT AATCTTTAAA TACTGTAGAA AAGAGGAAGG AAATAATAAA TGGCTAAAAT
1861 GAGAATATCA CCGGAATTGA AAAAACTGAT CGAAAAATAC CGCTGCGTAA AAGATACGGA
1921 AGGAATGTCT CCTGCTAAGG TATATAAGCT GGTGGGAGAA AATGAAAACC TATATTTAAA
1981 AATGACGGAC AGCCGGTATA AAGGGACCAC CTATGATGTG GAACGGGAAA AGGACATGAT
2041 GCTATGGCTG GAAGGAAAGC TGCCTGTTCC AAAGGTCCTG CACTTTGAAC GGCATGATGG
2101 CTGGAGCAAT CTGCTCATGA GTGAGGCCGA TGGCGTCCTT TGCTCGGAAG AGTATGAAGA
2161 TGAACAAAGC CCTGAAAAGA TTATCGAGCT GTATGCGGAG TGCATCAGGC TCTTTCACTC
2221 CATCGACATA TCGGATTGTC CCTATACGAA TAGCTTAGAC AGCCGCTTAG CCGAATTGGA
2281 TTACTTACTG AATAACGATC TGGCCGATGT GGATTGCGAA AACTGGGAAG AAGACACTCC
2341 ATTTAAAGAT CCGCGCGAGC TGTATGATTT TTTAAAGACG GAAAAGCCCG AAGAGGAACT
2401 TGTCTTTTCC CACGGCGACC TGGGAGACAG CAACATCTTT GTGAAAGATG GCAAAGTAAG
2461 TGGCTTTATT GATCTTGGGA GAAGCGGCAG GGCGGACAAG TGGTATGACA TTGCCTTCTG
2521 CGTCCGGTCG ATCAGGGAGG ATATCGGGGA AGAACAGTAT GTCGAGCTAT TTTTTGACTT
2581 ACTGGGGATC AAGCCTGATT GGGAGAAAAT AAAATATTAT ATTTTACTGG ATGAATTGTT
2641 TTAGGACGTC GCCGGCGGCA TCAAATAAAA CGAAAGGCTC AGTCGAAAGA CTGGGCCTTT
2701 CGTTTTATCT GTTGTTTGTC GGTGAACGCT CTCCTGAGTC CCACAATAAG CCAGAGAGCC
2761 GGTGTCAACG TAAATGCATG CCGCTTCGCC TTCGCGCGCG AATTGCAAGC TGATCCGGGC
2821 TTATCGACTG CACGGTGCAC CAATGCTTCT GGCGTCAGGC AGCCATCGGA AGCTGTGGTA
2881 TGGCTGTGCA GGTCGTAAAT CACTGCATAA TTCGTGTCGC TCAAGGCGCA CTCCCGTTCT
2941 GGATAATGTT TTTTGCGCCG ACATCATAAC GGTTCTGGCA AATATTCTGA AATGAGCTGT
3001 TGACAATTAA TCATCGGCTC GTATAATGTG TGGAATTGTG AGCGGATAAC AATTTCACAC
3061 AGGAAACAGC CTCGACAGGC CTAGGAATTC AGGgaagttc ctattctcta gaaagtatag
3121 gaacttcAGT GTGGGGTCTG CCTCGACAGG CCTAGGAATT CAGGAGCTAA GGAAGCTAAA
3181 ATGGTGAGCA AGGGCGAGGA GACCACAATG GGCGTAATCA AGCCCGACAT GAAGATCAAG
3241 CTGAAGATGG AGGGCAACGT GAATGGCCAC GCCTTCGTGA TCGAGGGCGA GGGCGAGGGC
3301 AAGCCCTACG ACGGCACCAA CACCATCAAC CTGGAGGTGA AGGAGGGAGC CCCCCTGCCC
3361 TTCTCCTACG ACATTCTGAC CACCGCGTTC GCCTACGGCA ACAGGGCCTT CACCAAGTAC
3421 CCCGACGACA TCCCCAACTA CTTCAAGCAG TCCTTCCCCG AGGGCTACTC TTGGGAGCGC
3481 ACCATGACCT TCGAGGACAA GGGCATCGTG AAGGTGAAGT CCGACATCTC CATGGAGGAG
3541 GACTCCTTCA TCTACGAGAT ACACCTCAAG GGCGAGAACT TCCCCCCCAA CGGCCCCGTG
3601 ATGCAGAAGA AGACCACCGG CTGGGACGCC TCCACCGAGA GGATGTACGT GCGCGACGGC
3661 GTGCTGAAGG GCGACGTCAA GCACAAGCTG CTGCTGGAGG GCGGCGGCCA CCACCGCGTT
3721 GACTTCAAGA CCATCTACAG GGCCAAGAAG GCGGTGAAGC TGCCCGACTA TCACTTTGTG
3781 GACCACCGCA TCGAGATCCT GAACCACGAC AAGGACTACA ACAAGGTGAC CGTTTACGAG
3841 AGCGCCGTGG CCCGCAACTC CACCGACGGC ATGGACGAGC TGTACAAGTA AGGATCCGGT
3901 GATTGATTGA GCAAGCTTTA TGCTTGTAAA CCGTTTTGTG AAAAAATTTT TAAAATAAAA
3961 AAGGGGACCT CTAGGGTCCC CAATTACTAG CCAGCGGCCG GCTGTTTTGG CGGATGAGAG
4021 AAGATTTTCA GCCTGATACA GATTAAATCA GAACGCAGAA GCGGTCTcca ggcatcaaat
4081 aaaacgaaag gctcagtcga aagactgggc ctttcgtttt atctgttgtt tgtcggtgaa
4141 cgctctctac tagagtcaca ctggctcacc ttcgggtggg cctttctgcg tttataGATA
4201 AAACAGAATT TGCCTGGCGG CAGgaagttc ctattctcta gaaagtatag gaacttcAAA
4261 CAGCCTCGAC AGGCCTAGGA caagagacag gatactagtg gaggaagaaa aaatggtgag
4321 caagggcgag gagaataaca tggccatcat caaggagttc atgcgcttca aggtgcgcat
4381 ggagggctcc gtgaacggcc acgagttcga gatcgagggc gagggcgagg gccgccccta
4441 cgagggcttt cagaccgcta agctgaaggt gaccaagggt ggccccctgc ccttcgcctg
4501 ggacatcctg tcccctcatt tcacctacgg ctccaaggcc tacgtgaagc accccgccga
4561 catccccgac tacttcaagc tgtccttccc cgagggcttc aagtgggagc gcgtgatgaa
4621 ctacgaggac ggcggcgtgg tgaccgtgac ccaggactcc tccctgcagg acggcgagtt
4681 catctacaag gtgaagctgc gcggcaccaa cttcccctcc gacggccccg tgatgcagaa
4741 gaagaccatg ggctgggagg cctcctccga gcggatgtac cccgaggacg gtgccctgaa
4801 gggcaagatc aagatgaggc tgaagctgaa ggacggcggc cactacacct ccgaggtcaa
4861 gaccacctac aaggccaaga agcccgtgca gctgcccggc gcctacatcg tcgacatcaa
4921 gttggacatc acctcccaca acgaggacta caccatcgtg gaacagtacg aacgcgccga
4981 gggccgccac tccaccggcg gcatggacga gctgtacaag taataattag ctgagctCTT
5041 CACGTGAGAC GTCAACCAGA AAAGAGGAAG GAAATAATAA ATGGCTAAAA TGAGAATATC
5101 ACCGGAATTG AAAAAACTGA TCGAAAAATA CCGCTGCGTA AAAGATACGG AAGGAATGTC
5161 TCCTGCTAAG GTATATAAGC TGGTGGGAGA AAATGAAAAC CTATATTTAA AAATGACGGA
5221 CAGCCGGTAT AAAGGGACCA CCTATGATGT GGAACGGGAA AAGGACATGA TGCTATGGCT
5281 GGAAGGAAAG CTGCCTGTTC CAAAGGTCCT GCACTTTGAA CGGCATGATG GCTGGAGCAA
5341 TCTGCTCATG AGTGAGGCCG ATGGCGTCCT TTGCTCGGAA GAGTATGAAG ATGAACAAAG
5401 CCCTGAAAAG ATTATCGAGC TGTATGCGGA GTGCATCAGG CTCTTTCACT CCATCGACAT
5461 ATCGGATTGT CCCTATACGA ATAGCTTAGA CAGCCGCTTA GCCGAATTGG ATTACTTACT
5521 GAATAACGAT CTGGCCGATG TGGATTGCGA AAACTGGGAA GAAGACACTC CATTTAAAGA
5581 TCCGCGCGAG CTGTATGATT TTTTAAAGAC GGAAAAGCCC GAAGAGGAAC TTGTCTTTTC
5641 CCACGGCGAC CTGGGAGACA GCAACATCTT TGTGAAAGAT GGCAAAGTAA GTGGCTTTAT
5701 TGATCTTGGG AGAAGCGGCA GGGCGGACAA GTGGTATGAC ATTGCCTTCT GCGTCCGGTC
5761 GATCAGGGAG GATATCGGGG AAGAACAGTA TGTCGAGCTA TTTTTTGACT TACTGGGGAT
5821 CAAGCCTGAT TGGGAGAAAA TAAAATATTA TATTTTACTG GATGAATTGT TTTAGGACGT
5881 CGCAAACTGG GGCACAGATA GGGTACCCAT CCCTCAAGCC GAGCCCCATG CGCTGTTTTG
5941 GCGGATGAGA GAAGATTTTC AGCCTGATAC AGATTAAATC AGAACGCAGA AGCGGTCTcc
6001 aggcatcaaa taaaacgaaa ggctcagtcg aaagactggg cctttcgttt tatctgttgt
6061 ttgtcggtga acgctctcta ctagagtcac actggctcac cttcgggtgg gcctttctgc
6121 gtttataGAT AAAACAGAAT TTGCCTGGCG GCAGCCCACA ATAAGCCAGA GAGCCTTAAG
6181 GCTCTCTTTT TTGTGCCACG CTGTCGCGGC GAACGATGGT GGGCGAAAAG ATCATCGGAT
6241 CATTTTCACG CGGTGCATCG GTTGCCAAAG CAAGAGCCAA CTGAGTGGCT TTTTCTGCCA
6301 TCAGTTGGAT TGGGTAACGC ACGGTCGTCA GGCGTGGGCG TAAGTAGCGC GAAATCAGGG
6361 CATCGTCAAA ACCAATCACT GAGACATGTT CAGGAACCGA ATGCCCATTT TCCTCAAGTA
6421 CCAACAGGGC TCCAGCGGCC ATATTGTCGT TGTAAGCGAC CACTGCGGTA AAAGGCAGTG
6481 ATTTCACCAG TAGGTTAGTC ATCGCCTGTT CGCCGCCTTC ACTGTCTGGG CTGGCTTTTT
6541 CAATATAGCT GCTGCTTAGG GTGATGCCAT GTTCGTTCAA GGCTTGTTGA TAGCCCGCAA
6601 TACGCTGATC GGCATCCTCA ATTTGATGAG AGGAGCTGAT GCAAGCAATG TTTCTATGTC
6661 CTTGACGGAT GAGAAAATCG GTTGCTAAAT AAGCACCTTT CTGGTTGTCG AGTGAAATAC
6721 AGCGATCGGC GAGCTGAGGA ATATGGCGAT TGATCAACAC CAGCGTTTTT ACCTCGTTGG
6781 CGTACTCAAT CAGCTCTTCA TTGGGAAGCG CTTTGGAGTG GATGACCAGT GCATCACAGC
6841 GGCTGTTGAT GAGCAGTTCC AGCGCGCGGC GCTCTTCTTC CGCTCGGTGG TAGCCGTTGC
6901 CGATCAGCAA ATGTTTTCCT TCGCGGTGGG CGACAGTGTC GACGGCTTTG ACTAAAGTTC
6961 CAAAGAAGGG ATCAGAAACA TCGCTGACCA AGACCCCTAT GGTATTGGTG CTTTGATTGA
7021 CTAAAGCGCG AGCCGCGGCG TTCGGACGAT AGCCGAGTTT GTGCATCGCA CTGGTCACCG
7081 TATCAATCGA GGCTTGGCTG GCTTTCGGGG ATTTGTTGAT GACGCGTGAA ACCGTTGCCA
7141 CAGATACACC GGCTTCACGT GCTACGTCTT TTATGGTTGC CATAAGATTC CTTCTCTATC
7201 ACAGGCGCAA TAGTAGCGCT CCCTGTGAAA ACAGCGCAAT TGTAACTGAG TACATAAGAG
7261 TGAATTGTGA GCCATGACGC TTGTTCAACA CAGAAGGCCA TCCTGACGGA TGGCCTTTTT
7321 GCGTTTCTAC AAACTCTTTT TGTTTATTTT TCTAAATACA TTCAAATATG TATCCGCTCA
7381 TGAGACAATA ACCCTGATAA ATGCTTCAAT AATATTGAAA AAGGAAGAGT ATGAGTATTC
7441 AACATTTCCG TGTCGCCCTT ATTCCCTTTT TTGCGGCATT TTGCCTTCCT GTTTTTGCTC
7501 ACCCAGAAAC GCTGGTGAAA GTAAAAGATG CTGAAGATCA GTTGGGTGCA CGAGTGGGTT
7561 ACATCGAACT GGATCTCAAC AGCGGTAAGA TCCTTGAGAG TTTTCGCCCC GAAGAACGTT
7621 TTCCAATGAT GAGCACTTTT AAAGTTCTGC TATGTGGCGC GGTATTATCC CGTGTTGACG
7681 CCGGGCAAGA GCAACTCGGT CGCCGCATAC ACTATTCTCA GAATGACTTG GTTGAGTACT
7741 CACCAGTCAC AGAAAAGCAT CTTACGGATG GCATGACAGT AAGAGAATTA TGCAGTGCTG
7801 CCATAACCAT GAGTGATAAC ACTGCGGCCA ACTTACTTCT GACAACGATC GGAGGACCGA
7861 AGGAGCTAAC CGCTTTTTTG CACAACATGG GGGATCATGT AACTCGCCTT GATCGTTGGG
7921 AACCGGAGCT GAATGAAGCC ATACCAAACG ACGAGCGTGA CACCACGATG CCTACAGCAA
7981 TGGCAACAAC GTTGCGCAAA CTATTAACTG GCGAACTACT TACTCTAGCT TCCCGGCAAC
8041 AATTAATAGA CTGGATGGAG GCGGATAAAG TTGCAGGACC ACTTCTGCGC TCGGCCCTTC
8101 CGGCTGGCTG GTTTATTGCT GATAAATCTG GAGCCGGTGA GCGTGGGTCT CGCGGTATCA
8161 TTGCAGCACT GGGGCCAGAT GGTAAGCCCT CCCGTATCGT AGTTATCTAC ACGACGGGGA
8221 GTCAGGCAAC TATGGATGAA CGAAATAGAC AGATCGCTGA GATAGGTGCC TCACTGATTA
8281 AGCATTGGTA ACTGTCAGAC CAAGTTTACT CATATATACT TTAGATTGAT TTAAAACTTC
8341 ATTTTTAATT TAAAAGGATC TAGGTGAAGA TCCTTTTTGA TAATCTCATG ACCAAAATCC
8401 CTTAACGTGA GTTTTCGTTC CACTGAGCGT CAGACCCCGT AGAAAAGATC AAAGGATCTT
8461 CTTGAGATCC TTTTTTTCTG CGCGTAATCT GCTGCTTGCA AACAAAAAAA CCACCGCTAC
8521 CAGCGGTGGT TTGTTTGCCG GATCAAGAGC TACCAACTCT TTTTCCGAAG GTAACTGGCT
8581 TCAGCAGAGC GCAGATACCA AATACTGTCC TTCTAGTGTA GCCGTAGTTA GGCCACCACT
8641 TCAAGAACTC TGTAGCACCG CCTACATACC TCGCTCTGCT AATCCTGTTA CCAGTGGCTG
8701 CTGCCAGTGG CGATAAGTCG TGTCTTACCG GGTTGGACTC AAGACGATAG TTACCGGATA
8761 AGGCGCAGCG GTCGGGCTGA ACGGGGGGTT CGTGCACACA GCCCAGCTTG GAGCGAACGA
8821 CCTACACCGA ACTGAGATAC CTACAGCGTG AGCTATGAGA AAGCGCCACG CTTCCCGAAG
8881 GGAGAAAGGC GGACAGGTAT CCGGTAAGCG GCAGGGTCGG AACAGGAGAG CGCACGAGGG
8941 AGCTTCCAGG GGGAAACGCC TGGTATCTTT ATAGTCCTGT CGGGTTTCGC CACCTCTGAC
9001 TTGAGCGTCG ATTTTTGTGA TGCTCGTCAG GGGGGCGGAG CCTATGGAAA AACGCCAGCA
9061 ACGCGGCCTT TTTACGGTTC CTGGCCTTTT GCTGGCCTTT TGCTCACATG TTCTTTCCTG
9121 CGTTATCCCC TGATTCTGTG GATAACCGTA TTACCGCCTT TGAGTGAGCT GATACCGCTC
9181 GCCGCAGCCG AACGACCGAG CGCAGCGAGT CAGTGAGCGA GGAAGCGGAA GAGCGCCTGA
9241 TGCGGTATTT TCTCCTTACG CATCTGTGCG GTATTTCACA CCGCATATGG TGCACTCTCA
9301 GTACAATCTG CTCTGATGCC GCATAGTTAA GCCAGTATAC ACTCCGCTAT CGCTACGTGA
9361 CTGGGTCATG GCTGCGCCCC GACACCCGCC AACACCCGCT GACGCGCCCT GACGGGCTTG
9421 TCTGCTCCCG GCATCCGCTT ACAGACAAGC TGTGACCGTC TCCGGGAGCT GCATGTGTCA
9481 GAGGTTTTCA CCGTCATCAC CGAAACGCGC GAGGCAGCAG ATCAATTCGC GCGCGAAGGC
9541 GAAGCGGCAT GCATTTACGT TGACACCATC GAATGGTGCA AAACCTTTCG CGGTATGGCA
9601 TGATAGCGCC CGGAAGAGAG TCAATTCAGG GTGGTGAATG TGAAACCAGT AACGTTATAC
9661 GATGTCGCAG AGTATGCCGG TGTCTCTTAT CAGACCGTTT CCCGCGTGGT GAACCAGGCC
9721 AGCCACGTTT CTGCGAAAAC GCGGGAAAAA GTGGAAGCGG CGATGGCGGA GCTGAATTAC
9781 ATTCCCAACC GCGTGGCACA ACAACTGGCG GGCAAACAGT CGTTGCTGAT TGGCGTTGCC
9841 ACCTCCAGTC TGGCCCTGCA CGCGCCGTCG CAAATTGTCG CGGCGATTAA ATCTCGCGCC
9901 GATCAACTGG GTGCCAGCGT GGTGGTGTCG ATGGTAGAAC GAAGCGGCGT CGAAGCCTGT
9961 AAAGCGGCGG TGCACAATCT TCTCGCGCAA CGCGTCAGTG GGCTGATCAT TAACTATCCG
10021 CTGGATGACC AGGATGCCAT TGCTGTGGAA GCTGCCTGCA CTAATGTTCC GGC
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Thank you for your hard work on this package!
However, I have noticed that the current version does not support the basic format of GTF, while it already supports GFF3. Would it be possible to add support for GTF in the future?
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A declarative, efficient, and flexible JavaScript library for building user interfaces.
๐ Vue.js is a progressive, incrementally-adoptable JavaScript framework for building UI on the web.
TypeScript is a superset of JavaScript that compiles to clean JavaScript output.
An Open Source Machine Learning Framework for Everyone
The Web framework for perfectionists with deadlines.
A PHP framework for web artisans
Bring data to life with SVG, Canvas and HTML. ๐๐๐
JavaScript (JS) is a lightweight interpreted programming language with first-class functions.
Some thing interesting about web. New door for the world.
A server is a program made to process requests and deliver data to clients.
Machine learning is a way of modeling and interpreting data that allows a piece of software to respond intelligently.
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Open source projects and samples from Microsoft.
Google โค๏ธ Open Source for everyone.
Alibaba Open Source for everyone
Data-Driven Documents codes.
China tencent open source team.