Download sequences
Genbank
tmpgb <- tempfile(fileext = '.gb')
tmpfa <- tempfile(fileext = '.fa')
download_genbank(acc='AB115403', format='genbank', outfile=tmpgb)
download_genbank(acc='AB115403', format='fasta', outfile=tmpfa)
readLines(tmpgb)[1:10]## [1] "LOCUS AB115403 561 bp RNA linear VRL 31-JUL-2004"
## [2] "DEFINITION Transmissible gastroenteritis virus ORF 7 gene for protein 7,"
## [3] " complete cds, strain:h-5."
## [4] "ACCESSION AB115403"
## [5] "VERSION AB115403.1"
## [6] "KEYWORDS ."
## [7] "SOURCE Transmissible gastroenteritis virus"
## [8] " ORGANISM Transmissible gastroenteritis virus"
## [9] " Viruses; ssRNA viruses; ssRNA positive-strand viruses, no DNA"
## [10] " stage; Nidovirales; Coronaviridae; Coronavirinae; Alphacoronavirus."## [1] ">AB115403.1 Transmissible gastroenteritis virus ORF 7 gene for protein 7, complete cds, strain:h-5"
## [2] "GTTTGATGACACACAGGTTGAGATAATTGATGAGGTAACGAACTAAACGAGATGCTCGTCCTCCTCCATG"
## [3] "CTGTATTTATTACAGTTTTAATCTTACTACTAATTGGTAGACTCCAATTATTAGAAAGATTATTACTTAA"
## [4] "TCACTCTTTCAATCTTAAAACTGTTAATGATTTTAATATCTTATATAGGAGTTTAGCAGAAATCAGATTA"
## [5] "CTAAAAGTGTTGCTTCGATTAATCTTTCTAGTTTTACTAGGATTTTGCTGCTATAGATTGTTAGTTATAT"
## [6] "TAATGTAAGGCAACCCGATGTCTAAAACTGGTTTTTCCGAGGAATTACTGGTCATCGCGCTGTCTACTCT"
## [7] "TGTACAGAATGGTAAGCACGTGTAATAGGAGGTACAAGCAACCCTATTGCATATTAGGAAGTTTAGATTT"
## [8] "GATTTGGCAATGCTAGATTTAGTAATTTAGAGAAGTTTAAAGATCCGCTACGACGAGCCAACAATGGAAG"
## [9] "AGCTAACGTCTGGATCTAGTGATTGTTTAAAATGTAAAATTGTTTGAAAATTTTCCTTTTGATAGTGATA"
## [10] "C"
## [11] ""File conversion
fasta and phylip conversion
fa_file <- system.file("extdata/HA.fas", package="seqmagick")
## use the small subset to save compilation time of the vignette
fa2 <- tempfile(fileext = '.fa')
fa_read(fa_file) %>% bs_filter('ATGAAAGTAAAA', by='sequence') %>% fa_write(fa2, type='interleaved')
alnfas <- tempfile(fileext = ".fas")
fa_read(fa2) %>% bs_aln(quiet=TRUE) %>% fa_write(alnfas)
## phylip format is only for aligned sequences
tmpphy <- tempfile(fileext = ".phy")
fas2phy(alnfas, tmpphy, type = 'sequential')
readLines(tmpphy)[1:3]## [1] "8 \t 1720"
## [2] "KU242635 A/swine/Iowa/A01795851/2015 2015/11/09 4 (HA) ATGAAAGTAAAACTACTGATCCTGTTATGTACATTTACAGCTGCATATGCGGACACAATATGTATAGGATACCATGCCAACAACTCAACCGACACTGTTGACACAGTACTTGAAAGGAATGTGACAGTGACCCACTCTGTCAACCTACTTGAGGACAGTCACAATGGAAAGCTGTGCCTATTAAAGGGAATAGCCCCCCTACAATTGGGTAATTGCAGCGTTGCCGGATGGATATTAGGAAACCCAGAATGCGAATCACTGATTTCCAAGAAATCATGGTCCTACATTGTAGAAGCACCCAATTCTGATAATGGTGCATGTTACCCAGGGCAGTTCGCCGACTATGAGGAGCTAAGGGAGCAATTGAGTTCAGTGTCTTCATTTGAGAGATTCGAGATATTCCCCAGAGAAAGCTCATGGCCCAACCACACCGTAACCGGAGAGTCAGCATCATGCTCCCATAATGGGAAAAGAAGTTTTTACAGAAATCTGATCTGGCTGACAGTGAAAAATGGTTTGTACCCAAACCTGAGCAAGTCCTATGAGAACGACAAAGGGAAAGAAGTCCTTATATTATGGGGTGTTCATCATCCGTCTAACATAGGGGACCAAAGGACCCTCTATCAAACGGAAAATGCTTATGTCTCTGTAATGTCTTCACATTATAGCAGAAGATTCACCCCAGAAATAACCAAAAGGCCCAAAGTAAGAGATCAGGAAGGAAGAATCAACTACTACTGGACTCTGCTGGAGCCCGGAGACACAATAATATTTGAAACAAATGGAAATCTAATAGCTCCATGGTATGCTTTCGCACTGAGTAGGGGCCTTGGATCAGGAATCATCACCTCTAAAGCACCAATGGACGGGTGTGATGCAAAGTGTCAAACACCAAAGGGAGCTATAAACAGCAATCTTCCTTTCCAGAATGTACATCCAGTCACAATAGGAGAATGTCCAAAATATGTCAGGAGTACAAAATTAAGGATGGTAACAGGACTAAGGAATATCCCATCTATTCAATCCAGAGGTTTGTTTGGGGCCATTGCCGGTTTCATTGAAGGGGGATGGACTGGAATGGTAGATGGGTGGTATGGTTATCATCATCAGAATGAGCAAGGAACTGGCTATGCTGCAGATCAAGAAAGCACACAAAATGCCATTAACGGAATTACAAACAAGGTGAATTCCGTAATTGAGAAAATAAACACTCAGTTCACAGCTGTGGGCAAAGAATTCAACAAATTGGAAAGAAGACTGGAAAACTTAAATAAAAAGGTTGATGATGGGTTTCTAGACATTTGGACATACAACGCAGAGTTGTTGGTTCTACTGGAAAATGAAAGAACTTTGGACTTCCACGATTCCAATGTGAAGAGTCTGTACGAGAAAGTAAAAAGCCAATTAAAGAATAATGCTAAAGAAATAGGAAATGGGTGCTTTGAATTCTATCACAAGTGTAACAACGAATGCATGGAGAGTGTTAGAAATGGGACCTATGACTATCCAAAATATTCCGAAGAATCAAAGTTAAACAGGGAAAAAATTGATGGAGTGAAATTGGACTCAATGGGGGTCTATCGGATTCTGTCGATCTACTCAACTGTTGCCAGTTCCCTGGTTCTTTTGGTCTCCCTGGGGGCAATCAGCTTCTGGATGTGTTCCAATGGGTCTTTGCAATGTAGAATATGCATCTAA----------------------"
## [3] "KU877368 A/swine/Indiana/A01731716/2016 2016/02/15 4 (HA) ATGAAAGTAAAACTACTGATCCTGTTATGTACATTTACAGCTGCATATGCGGACACAATATGTATAGGATACCATGCCAACAACTCAACCGACACTGTTGACACAGTACTTGAAAAGAATGTGACAGTGACCCACTCTGTCAATCTACTTGAGGACAGTCACAATGGAAAACTGTGCCTGTTAAAGGGAATAGCCCCCCTACAATTGGGTAATTGCAGCGTTGCCGGATGGATATTAGGAAACCCAGAATGCGAATCACTGATTTCCAAGAAATCATGGTCCTACATTGTAGAAGCACCCAATTCTGATAATGGTGCATGTTACCCAGGGCAGTTTGCCGACTATGAGGAGCTAAGGGAGCAATTGAGTTCAGTGTCTTCATTTGAGAGATTCGAAATATTCCCCAGAGAAAGCTCATGGCCCAACCACACTGTAACCGGAGGGTCAGTATCATGCTCCCATAATGGGGAAGGAAGTTTTTACAGAAATCTGATCTGGCTGACAGTGAAAAATGGTTTGTACCCAAACCTGAGCAAGTCCTATAAGAACGAAAAAGGGAAAGAAGTCCTTATATTATGGGGTGTTCATCATCCGTCTAACATAGGGGACCAAAAGACCCTCTATCACACGGAAAATGCTTATGTATCTGTAATGTCTTCACATTATAGCAGAAGATTCACCCCAGAAATAACCAAAAGGCCCAAAGTAAGAGATCAGGAAGGAAGAATCAACTACTACTGGACTCTGCTGGAGCCCGGAGACACAATAATATTTGAAACAAATGGAAATCTAATAGCTCCATGGTATGCTTTCGCACTGAGTAGAGGCCTTGGATCAGGAATCATCACCTCTAAAGCACCAATGGACGAGTGTGATGCAAAGTGTCAAACACCAAAGGGAGCTATAAACAGCAATCTTCCTTTCCAGAATGTACATCCAGTCACAATAGGAGAATGTCCAAAATATGTCAGGAGTACAAAATTAAGGATGGTAACAGGACTAAGGAATATCCCATCTATTCAATCCAGAGGTTTGTTTGGGGCCATTGCCGGTTTCATTGAAGGGGGGTGGACTGGAATGGTAGATGGGTGGTATGGTTATCATCATCAGAATGAGCAAGGAACTGGCTATGCTGCAGATCAAGAAAGCACACAAAATGCCATTAACGGAATTACAAACAAGGTGAATTCCGTAATTGAGAAAATGAACACTCAATTCACAGCTGTGGGCAAAGAATTCAACAAATTGGAAAGAAGACTGGAAAACTTAAATAAAAAGGTTGATGATGGGTTTCTAGACATTTGGACATACAACGCAGAGTTGTTGGTTCTACTGGAAAATGAAAGAACTTTGGACTTCCACGATTCCAATGTGAAGAGTCTGTACGAGAAAGTAAAAAGCCAATTAAAGAATAATGCTAAAGAAATAGGAAATGGGTGCTTTGAATTCTATCACAAGTGTAACAACGAATGCATGGAGAGTGTTAGAAATGGGACCTATGACTATCCAAAATATTCCGAAGAATCAAAATTAAACAGGGAAAAAATTGATGGAGTGAAATTGGACTCAATGGGGGTCTATCGGATTCTGTCGATCTACTCAACTGTTGCCAGTTCCCTGGTTCTTTTGGTCTCCCTGGGGGCAATCAGCTTCTGGATGTGTTCCAATGGGTCTTTGCAATGTAGAATATGCATCTAA----------------------"seqmagick supports both sequential and interleaved formats, users can specify the format by type parameter.
## [1] ">KU242635 A/swine/Iowa/A01795851/2015 2015/11/09 4 (HA)"
## [2] "ATGAAAGTAAAACTACTGATCCTGTTATGTACATTTACAGCTGCATATGCGGACACAATATGTATAGGATACCATGCCAA"
## [3] "CAACTCAACCGACACTGTTGACACAGTACTTGAAAGGAATGTGACAGTGACCCACTCTGTCAACCTACTTGAGGACAGTC"
## [4] "ACAATGGAAAGCTGTGCCTATTAAAGGGAATAGCCCCCCTACAATTGGGTAATTGCAGCGTTGCCGGATGGATATTAGGA"interleaved and sequential format conversion
## [1] ">KU242635 A/swine/Iowa/A01795851/2015 2015/11/09 4 (HA)"
## [2] "ATGAAAGTAAAACTACTGATCCTGTTATGTACATTTACAGCTGCATATGCGGACACAATATGTATAGGATACCATGCCAA"
## [3] "CAACTCAACCGACACTGTTGACACAGTACTTGAAAGGAATGTGACAGTGACCCACTCTGTCAACCTACTTGAGGACAGTC"
## [4] "ACAATGGAAAGCTGTGCCTATTAAAGGGAATAGCCCCCCTACAATTGGGTAATTGCAGCGTTGCCGGATGGATATTAGGA"
## [5] "AACCCAGAATGCGAATCACTGATTTCCAAGAAATCATGGTCCTACATTGTAGAAGCACCCAATTCTGATAATGGTGCATG"
## [6] "TTACCCAGGGCAGTTCGCCGACTATGAGGAGCTAAGGGAGCAATTGAGTTCAGTGTCTTCATTTGAGAGATTCGAGATAT"
## [7] "TCCCCAGAGAAAGCTCATGGCCCAACCACACCGTAACCGGAGAGTCAGCATCATGCTCCCATAATGGGAAAAGAAGTTTT"
## [8] "TACAGAAATCTGATCTGGCTGACAGTGAAAAATGGTTTGTACCCAAACCTGAGCAAGTCCTATGAGAACGACAAAGGGAA"
## [9] "AGAAGTCCTTATATTATGGGGTGTTCATCATCCGTCTAACATAGGGGACCAAAGGACCCTCTATCAAACGGAAAATGCTT"
## [10] "ATGTCTCTGTAATGTCTTCACATTATAGCAGAAGATTCACCCCAGAAATAACCAAAAGGCCCAAAGTAAGAGATCAGGAA"This is a fasta file in interleaved format. We can convert it to sequential format.
tmpfas <- tempfile(fileext='.fa')
fa_read(fa2) %>% fa_write(tmpfas, type="sequential")
readLines(tmpfas)[1:4]## [1] "> KU242635 A/swine/Iowa/A01795851/2015 2015/11/09 4 (HA)"
## [2] "ATGAAAGTAAAACTACTGATCCTGTTATGTACATTTACAGCTGCATATGCGGACACAATATGTATAGGATACCATGCCAACAACTCAACCGACACTGTTGACACAGTACTTGAAAGGAATGTGACAGTGACCCACTCTGTCAACCTACTTGAGGACAGTCACAATGGAAAGCTGTGCCTATTAAAGGGAATAGCCCCCCTACAATTGGGTAATTGCAGCGTTGCCGGATGGATATTAGGAAACCCAGAATGCGAATCACTGATTTCCAAGAAATCATGGTCCTACATTGTAGAAGCACCCAATTCTGATAATGGTGCATGTTACCCAGGGCAGTTCGCCGACTATGAGGAGCTAAGGGAGCAATTGAGTTCAGTGTCTTCATTTGAGAGATTCGAGATATTCCCCAGAGAAAGCTCATGGCCCAACCACACCGTAACCGGAGAGTCAGCATCATGCTCCCATAATGGGAAAAGAAGTTTTTACAGAAATCTGATCTGGCTGACAGTGAAAAATGGTTTGTACCCAAACCTGAGCAAGTCCTATGAGAACGACAAAGGGAAAGAAGTCCTTATATTATGGGGTGTTCATCATCCGTCTAACATAGGGGACCAAAGGACCCTCTATCAAACGGAAAATGCTTATGTCTCTGTAATGTCTTCACATTATAGCAGAAGATTCACCCCAGAAATAACCAAAAGGCCCAAAGTAAGAGATCAGGAAGGAAGAATCAACTACTACTGGACTCTGCTGGAGCCCGGAGACACAATAATATTTGAAACAAATGGAAATCTAATAGCTCCATGGTATGCTTTCGCACTGAGTAGGGGCCTTGGATCAGGAATCATCACCTCTAAAGCACCAATGGACGGGTGTGATGCAAAGTGTCAAACACCAAAGGGAGCTATAAACAGCAATCTTCCTTTCCAGAATGTACATCCAGTCACAATAGGAGAATGTCCAAAATATGTCAGGAGTACAAAATTAAGGATGGTAACAGGACTAAGGAATATCCCATCTATTCAATCCAGAGGTTTGTTTGGGGCCATTGCCGGTTTCATTGAAGGGGGATGGACTGGAATGGTAGATGGGTGGTATGGTTATCATCATCAGAATGAGCAAGGAACTGGCTATGCTGCAGATCAAGAAAGCACACAAAATGCCATTAACGGAATTACAAACAAGGTGAATTCCGTAATTGAGAAAATAAACACTCAGTTCACAGCTGTGGGCAAAGAATTCAACAAATTGGAAAGAAGACTGGAAAACTTAAATAAAAAGGTTGATGATGGGTTTCTAGACATTTGGACATACAACGCAGAGTTGTTGGTTCTACTGGAAAATGAAAGAACTTTGGACTTCCACGATTCCAATGTGAAGAGTCTGTACGAGAAAGTAAAAAGCCAATTAAAGAATAATGCTAAAGAAATAGGAAATGGGTGCTTTGAATTCTATCACAAGTGTAACAACGAATGCATGGAGAGTGTTAGAAATGGGACCTATGACTATCCAAAATATTCCGAAGAATCAAAGTTAAACAGGGAAAAAATTGATGGAGTGAAATTGGACTCAATGGGGGTCTATCGGATTCTGTCGATCTACTCAACTGTTGCCAGTTCCCTGGTTCTTTTGGTCTCCCTGGGGGCAATCAGCTTCTGGATGTGTTCCAATGGGTCTTTGCAATGTAGAATATGCATCTAA"
## [3] "> KU877368 A/swine/Indiana/A01731716/2016 2016/02/15 4 (HA)"
## [4] "ATGAAAGTAAAACTACTGATCCTGTTATGTACATTTACAGCTGCATATGCGGACACAATATGTATAGGATACCATGCCAACAACTCAACCGACACTGTTGACACAGTACTTGAAAAGAATGTGACAGTGACCCACTCTGTCAATCTACTTGAGGACAGTCACAATGGAAAACTGTGCCTGTTAAAGGGAATAGCCCCCCTACAATTGGGTAATTGCAGCGTTGCCGGATGGATATTAGGAAACCCAGAATGCGAATCACTGATTTCCAAGAAATCATGGTCCTACATTGTAGAAGCACCCAATTCTGATAATGGTGCATGTTACCCAGGGCAGTTTGCCGACTATGAGGAGCTAAGGGAGCAATTGAGTTCAGTGTCTTCATTTGAGAGATTCGAAATATTCCCCAGAGAAAGCTCATGGCCCAACCACACTGTAACCGGAGGGTCAGTATCATGCTCCCATAATGGGGAAGGAAGTTTTTACAGAAATCTGATCTGGCTGACAGTGAAAAATGGTTTGTACCCAAACCTGAGCAAGTCCTATAAGAACGAAAAAGGGAAAGAAGTCCTTATATTATGGGGTGTTCATCATCCGTCTAACATAGGGGACCAAAAGACCCTCTATCACACGGAAAATGCTTATGTATCTGTAATGTCTTCACATTATAGCAGAAGATTCACCCCAGAAATAACCAAAAGGCCCAAAGTAAGAGATCAGGAAGGAAGAATCAACTACTACTGGACTCTGCTGGAGCCCGGAGACACAATAATATTTGAAACAAATGGAAATCTAATAGCTCCATGGTATGCTTTCGCACTGAGTAGAGGCCTTGGATCAGGAATCATCACCTCTAAAGCACCAATGGACGAGTGTGATGCAAAGTGTCAAACACCAAAGGGAGCTATAAACAGCAATCTTCCTTTCCAGAATGTACATCCAGTCACAATAGGAGAATGTCCAAAATATGTCAGGAGTACAAAATTAAGGATGGTAACAGGACTAAGGAATATCCCATCTATTCAATCCAGAGGTTTGTTTGGGGCCATTGCCGGTTTCATTGAAGGGGGGTGGACTGGAATGGTAGATGGGTGGTATGGTTATCATCATCAGAATGAGCAAGGAACTGGCTATGCTGCAGATCAAGAAAGCACACAAAATGCCATTAACGGAATTACAAACAAGGTGAATTCCGTAATTGAGAAAATGAACACTCAATTCACAGCTGTGGGCAAAGAATTCAACAAATTGGAAAGAAGACTGGAAAACTTAAATAAAAAGGTTGATGATGGGTTTCTAGACATTTGGACATACAACGCAGAGTTGTTGGTTCTACTGGAAAATGAAAGAACTTTGGACTTCCACGATTCCAATGTGAAGAGTCTGTACGAGAAAGTAAAAAGCCAATTAAAGAATAATGCTAAAGAAATAGGAAATGGGTGCTTTGAATTCTATCACAAGTGTAACAACGAATGCATGGAGAGTGTTAGAAATGGGACCTATGACTATCCAAAATATTCCGAAGAATCAAAATTAAACAGGGAAAAAATTGATGGAGTGAAATTGGACTCAATGGGGGTCTATCGGATTCTGTCGATCTACTCAACTGTTGCCAGTTCCCTGGTTCTTTTGGTCTCCCTGGGGGCAATCAGCTTCTGGATGTGTTCCAATGGGTCTTTGCAATGTAGAATATGCATCTAA"tmpphy2 <- tempfile(fileext = '.phy')
phy_read(tmpphy) %>% phy_write(tmpphy2, type="interleaved")
readLines(tmpphy2)[1:4]## [1] "8 \t 1720"
## [2] "KU242635 A/swine/Iowa/A01795851/2015 2015/11/09 4 (HA) ATGAAAGTAA AACTACTGAT CCTGTTATGT ACATTTACAG CTGCATATGC"
## [3] "KU877368 A/swine/Indiana/A01731716/2016 2016/02/15 4 (HA) ATGAAAGTAA AACTACTGAT CCTGTTATGT ACATTTACAG CTGCATATGC"
## [4] "EU566990 A/Wisconsin/35/2007 2007/12/05 4 (HA) ATGAAAGTAA AACTACTGGT CCTGTTATGC ACATTTACAG CTACATATGC"Sequence manipulation
## A AAStringSet instance of length 8
## width seq names
## [1] 1698 ATGAAAGTAAAACTACTGATCCT...TGCAATGTAGAATATGCATCTAA KU242635 A/swine/...
## [2] 1698 ATGAAAGTAAAACTACTGATCCT...TGCAATGTAGAATATGCATCTAA KU877368 A/swine/...
## [3] 1698 ATGAAAGTAAAACTACTGGTCCT...TGCTGTGTAGAATATGCATCTAA EU566990 A/Wiscon...
## [4] 1698 ATGAAAGTAAAACTACTGATCCT...TGCAATGTAGAATATGCATCTGA KF234475 A/swine/...
## [5] 1698 ATGAAAGTAAAACTAATTGTTCT...TACAGTGTAGAATATGCATCTAA KU565170 A/swine/...
## [6] 1698 ATGAAAGTAAAACTACTGATCCT...TGCAATGTAGAATATGCATCTAA KP412349 A/swine/...
## [7] 1720 ATGAAAGTAAAACTACTGGTCCT...AGACCAGAATTTCAGAAATATAA CY073927 A/Mexico...
## [8] 1698 ATGAAAGTAAAACTACTGACCCT...TGCAATGTAGAATATGCATCTGA KC013577 A/swine/...## A AAStringSet instance of length 8
## width seq names
## [1] 1720 ATGAAAGTAAAACTACTGATCCT...A---------------------- KU242635 A/swine/...
## [2] 1720 ATGAAAGTAAAACTACTGATCCT...A---------------------- KU877368 A/swine/...
## [3] 1720 ATGAAAGTAAAACTACTGGTCCT...A---------------------- EU566990 A/Wiscon...
## [4] 1720 ATGAAAGTAAAACTACTGATCCT...A---------------------- KF234475 A/swine/...
## [5] 1720 ATGAAAGTAAAACTAATTGTTCT...A---------------------- KU565170 A/swine/...
## [6] 1720 ATGAAAGTAAAACTACTGATCCT...A---------------------- KP412349 A/swine/...
## [7] 1720 ATGAAAGTAAAACTACTGGTCCT...AGACCAGAATTTCAGAAATATAA CY073927 A/Mexico...
## [8] 1720 ATGAAAGTAAAACTACTGACCCT...A---------------------- KC013577 A/swine/...## [1] "ATGAAAGTAAAACTASTTYGGCTGGTYTGGACATTTYCAGCTYCSTATGCYGACACAATATGTYTAGGSTACCATGCGAACAAGTCYACGGACACTGTTGACACAGTACTTGAYAYYAATGTTACAGTGACSCACTCTGTGAAGCTYCTTGAGYACAGGCACAATGGYAAYCTYTGGCTYGTAAAYGGAATYGCGCCSCTACAATTGGGTAYTTGCAGCGTTGCSGGYTGGATSTTAGGAAACCCAGAYTGCGAAGGYCTGATTTCCAAGYAYTCATGGTCCTAGATTGTAGAAYSACCSAATGCTGYYAATGGCYCATGTTACCCAGGGKATTTGYCSGACTATGAYGAYCTYAGGGAYCAYTTGAGTTCAGTYTCTTCATTTYAYAGYTTCGAYATATTCCCCAYAGAYAYSTCYTGGCCCAASCACACGGGAACCGGAGYGTCATGSTCATGCTCCCAGAAGGGGYASYYBAGGTTGTACAGAAATGTGBTSTGGCTGACYGTGAAYYAGYYTGTGTACCCYAACCTGAGCAAGTCCTATYSYAACYASAAYGYYAAAGAYGTCCTTYTAGTATGGGGTGTGCATCAGCCYGCCAACATAGYTYACCAAAYGYCCCTGTATCYSACYGAAAATGCTTATGTSTCTGTAYTGTCTTCACATTATAGCYGAAYATTCACCCCAGAAATAYGCAYYAGYCCCAAYGTYAGAYATCAYGAAGGAAGYATGAACTACTACTGGACTGTGCTYGAYCCCGGYGAGACCATAAGATTTYAYYCAASTGGAAATCTAATAGCYCCACGYTATGCGTTCYSACTGAGTAYYGGGGTTYGYTCAGGAATSATGASGTCCAACGCACCSATGGYGYYYTGTYATTCYAAYTGGCAAACACCCSAYGGYGCTATAAACAGCAYTCTTCCTTTCCAGAAGGTACAGCCYGTSSCAATAGGAGAYTGTCCSAAYTATGTGAYGAGTYCAAAATTAAGGATGGGCACAGGACTAAGGAAGAGCCCYTCGATGCAATCCAGAGGTTTGTTTGGYGCSATTGCCGGTTTCATTGAAGGYGGYTGGACTGGAATGGTAGATGGTTGGTATGGTTATCAGCATCAYAATGAYCAYGGYCCTGGSTATGCTGCAGAGCAABAAAGCACACAAASTGCCATTAAGGGYATGACAAACAAGGTYAATTCGGTAATTGAYAAAATYAACACTCAYTTCACAGCCGTGGGCAAYGAATTCAACAAATTGGAAAGAAGYSTGGAAAACTTYAAGAAAAAYGTTGATGATGGGTTTSTAGACATTTGGACATAGAAGGCCGAYGTGTTYGTTCTACTGGAAAATGAAAGYACTTTGGAGTTCCAGGAGTCCAAGGTGAAGAYTCTGTAGGAGAAAGTAAYAAGCCAYTTAAAYAAGAATGCGAAYGAAATAGGYAAGGGGTGGTTTGAATTCTATCAGAAGTGTAACYAGGAATGCATGGAGAGTGTYAYYAATGGYACGTATGACTATCCAAAATATTSGGAAGAATCAAAYTTAAACAGGGAYAAAATTGATGGYGTTAYATTGGASTCAYTGGGYGTSTATSYTATGCTYTCGATCTACTCAACCGTGGCCAGTTCGCTYGTTCTTTTYGTCTCCCTGGGGGCAATCAGCTTCTGGATGTGTTCCAATGGGTCTTTYCCYTGTAGAATATGCATCTYAGACCAGAATTTCAGAAATATAA"Bugs/Feature requests
If you have any, let me know. Thx!
Session info
Here is the output of sessionInfo() on the system on which this document was compiled:
## R version 3.6.1 (2019-07-05)
## Platform: x86_64-pc-linux-gnu (64-bit)
## Running under: Arch Linux
##
## Matrix products: default
## BLAS: /usr/lib/libblas.so.3.8.0
## LAPACK: /usr/lib/liblapack.so.3.8.0
##
## locale:
## [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C
## [3] LC_TIME=en_US.UTF-8 LC_COLLATE=C
## [5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8
## [7] LC_PAPER=en_US.UTF-8 LC_NAME=C
## [9] LC_ADDRESS=C LC_TELEPHONE=C
## [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
##
## attached base packages:
## [1] stats4 parallel stats graphics grDevices utils datasets
## [8] methods base
##
## other attached packages:
## [1] seqmagick_0.1.1 muscle_3.28.0 Biostrings_2.54.0
## [4] XVector_0.26.0 IRanges_2.20.1 S4Vectors_0.24.1
## [7] BiocGenerics_0.32.0 magrittr_1.5
##
## loaded via a namespace (and not attached):
## [1] Rcpp_1.0.3 knitr_1.26
## [3] GenomicRanges_1.38.0 zlibbioc_1.32.0
## [5] GenomicAlignments_1.22.1 BiocParallel_1.20.0
## [7] lattice_0.20-38 rlang_0.4.2
## [9] stringr_1.4.0 GenomeInfoDb_1.22.0
## [11] tools_3.6.1 grid_3.6.1
## [13] SummarizedExperiment_1.16.0 Biobase_2.46.0
## [15] xfun_0.11 matrixStats_0.55.0
## [17] htmltools_0.4.0 yaml_2.2.0
## [19] digest_0.6.23 Matrix_1.2-17
## [21] GenomeInfoDbData_1.2.2 prettydoc_0.3.1
## [23] bitops_1.0-6 RCurl_1.95-4.12
## [25] evaluate_0.14 rmarkdown_1.18
## [27] DelayedArray_0.12.0 stringi_1.4.3
## [29] downloader_0.4 compiler_3.6.1
## [31] Rsamtools_2.2.1