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私は FASTA 形式のファイルを持っています。これは本質的に特別なテキスト ファイルであり、多くのエントリを含みます。そのうちの 1 つは以下のようになり、R で「FASTA」という名前で割り当てました。 R の seqinr パッケージ。

FASTA<- structure(list(`tr|A1Z6G9|A1Z6G9_DROME` = structure("MSISASHPCGLNADGTATQYKESTATIQTSGLQSSPRSFLPEREDTLEYFIKFPKPSSKNEFVLAKDHDGEDSHVPIVMLLGWAGCQDRYLMKYSKIYEERGLITVRYTAPVDSLFWKRSEMIPIGEKILKLIQDMNFDAHPLIFHIFSNGGAYLYQHINLAVIKHKSPLQVRGVIFDSAPGERRIISLYRAITAIYGREKRCNCLAALVITITLSIMWFVEESISALKSLFVPSSPVRPSPFCDLKNEANRYPQLFLYSKGDIVIPYRDVEKFIRLRRDQGIQVSSVCFEDAEHVKIYTKYPKQYVQCVCNFIRNCMTIPPLKEAVNSEPSESVSRVNLKYD", name = "tr|A1Z6G9|A1Z6G9_DROME", Annot = ">tr|A1Z6G9|A1Z6G9_DROME CG8245 OS=Drosophila melanogaster GN=CG8245-RA PE=2 SV=1", class = "SeqFastaAA")))

この形式では、以下に示すように、grep を使用して検索すると、エントリの名前インデックスを取得できますが、

grep("A1Z6G9_DROME", names(FASTA))

または使用してその名前を分離します

as.vector(sapply(names(attributes(FASTA)), function(x) attr(FASTA, x)))

ただし、属性セクションのテキスト/情報を grep/regexpr することも、name= または Annot= セクションに続くテキストなどの属性を分離することもできません。誰でもこれで私を助けることができますか？

私が収集できる限り、Rでread.fastaをグーグルで検索すると、seqinrパッケージに関連するマニュアルには、注釈/属性が無視されていると記載されています(私は思う)が、これらの属性セクションには、エントリのアイデンティティに関する重要な情報が保持されています、私は必死に必要です！貼り付け機能を使用してリストから外すか折りたたむことを試みましたが、必要なすべての属性が削除されます!

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seqinrパッケージには多くのget*関数があります ( http://www.rdocumentation.org/packages/seqinrを参照)。これらの関数は、次のようなさまざまな属性にアクセスするように設計されています。

getAnnot(FASTA)
#[[1]]
#[1] ">tr|A1Z6G9|A1Z6G9_DROME CG8245 OS=Drosophila melanogaster GN=CG8245-RA PE=2 SV=1"

getSequence(FASTA)
#[[1]]
#  [1] "M" "S" "I" "S" "A" "S" "H" "P" "C" "G" "L" "N" "A" "D" "G" "T" "A" "T" "Q" "Y" "K" "E" "S" "T" "A" "T" "I" "Q" "T" "S" "G" "L" "Q" "S" "S" "P" "R" "S" "F" "L" "P" "E" "R" "E" "D" "T" "L" "E" "Y" "F" "I" "K" "F" "P" "K" "P" "S" "S" "K"
# [60] "N" "E" "F" "V" "L" "A" "K" "D" "H" "D" "G" "E" "D" "S" "H" "V" "P" "I" "V" "M" "L" "L" "G" "W" "A" "G" "C" "Q" "D" "R" "Y" "L" "M" "K" "Y" "S" "K" "I" "Y" "E" "E" "R" "G" "L" "I" "T" "V" "R" "Y" "T" "A" "P" "V" "D" "S" "L" "F" "W" "K"
#[119] "R" "S" "E" "M" "I" "P" "I" "G" "E" "K" "I" "L" "K" "L" "I" "Q" "D" "M" "N" "F" "D" "A" "H" "P" "L" "I" "F" "H" "I" "F" "S" "N" "G" "G" "A" "Y" "L" "Y" "Q" "H" "I" "N" "L" "A" "V" "I" "K" "H" "K" "S" "P" "L" "Q" "V" "R" "G" "V" "I" "F"
#[178] "D" "S" "A" "P" "G" "E" "R" "R" "I" "I" "S" "L" "Y" "R" "A" "I" "T" "A" "I" "Y" "G" "R" "E" "K" "R" "C" "N" "C" "L" "A" "A" "L" "V" "I" "T" "I" "T" "L" "S" "I" "M" "W" "F" "V" "E" "E" "S" "I" "S" "A" "L" "K" "S" "L" "F" "V" "P" "S" "S"
#[237] "P" "V" "R" "P" "S" "P" "F" "C" "D" "L" "K" "N" "E" "A" "N" "R" "Y" "P" "Q" "L" "F" "L" "Y" "S" "K" "G" "D" "I" "V" "I" "P" "Y" "R" "D" "V" "E" "K" "F" "I" "R" "L" "R" "R" "D" "Q" "G" "I" "Q" "V" "S" "S" "V" "C" "F" "E" "D" "A" "E" "H"
#[296] "V" "K" "I" "Y" "T" "K" "Y" "P" "K" "Q" "Y" "V" "Q" "C" "V" "C" "N" "F" "I" "R" "N" "C" "M" "T" "I" "P" "P" "L" "K" "E" "A" "V" "N" "S" "E" "P" "S" "E" "S" "V" "S" "R" "V" "N" "L" "K" "Y" "D"
于 2013-08-29T18:38:50.400 に答える