gbseqextractorはタイトルの通りgbseqextractorはGenbankファイルから遺伝子やrNRA、tRNAの配列を返すツール。Biopython (http://www.biopython.org/) が使われている。
インストール
#ここではcondaの仮想環境に導入。
mamba create -n gbseqextractor python=3 -y
conda activate gbseqextractor
pip install gbseqextractor
> gbseqextractor
$ gbseqextractor
usage: gbseqextractor [-h] -f <STR> -prefix <STR> [-seqPrefix <STR>] [-types {CDS,rRNA,tRNA,wholeseq,gene} [{CDS,rRNA,tRNA,wholeseq,gene} ...]] [-cds_translation] [-gi] [-p] [-t] [-s] [-l] [-rv] [-F]
Extract any CDS or rNRA or tRNA DNA sequences of genes from Genbank file.
Seqid will be the value of '/gene=' or '/product=', if they both were not
present, the gene will not be output!
version 20201128:
Now we can handle compounlocation (feature location with "join")!
We can also output the translation for each CDS (retrived from '/translation=')
Please cite:
Guanliang Meng, Yiyuan Li, Chentao Yang, Shanlin Liu,
MitoZ: a toolkit for animal mitochondrial genome assembly, annotation
and visualization, Nucleic Acids Research, https://doi.org/10.1093/nar/gkz173
options:
-h, --help show this help message and exit
-f <STR> Genbank file
-prefix <STR> prefix of output file. required.
-seqPrefix <STR> prefix of each seq id. default: None
-types {CDS,rRNA,tRNA,wholeseq,gene} [{CDS,rRNA,tRNA,wholeseq,gene} ...]
what kind of genes you want to extract? wholeseq for whole fasta seq. WARNING: Each sequence in the result files corresponds to ONE feature in the GenBank file, I will NOT combine
multiple CDS of the same gene into ONE! [CDS]
-cds_translation Also output translated CDS (required -types CDS). The translations are retrived directly from the '/translation=' key word. [False]
-gi use gi number as sequence ID instead of accession number when " gi number is present. (default: accession number)
-p output the position information on the ID line. Warning: the position on ID line is 0 left-most! [False]
-t output the taxonomy lineage on ID line [False]
-s output the species name on the ID line [False]
-l output the seq length on the ID line [False]
-rv reverse and complement the sequences if the gene is on minus strand. Always True!
-F only output full length genes,i.e., exclude the genes with '>' or '<' in their location [False]
(gbseqextractor) kamisakakazumanoMac-Studio:Downloads kamisakakazuma$ gbseqextractor -f
usage: gbseqextractor [-h] -f <STR> -prefix <STR> [-seqPrefix <STR>] [-types {CDS,rRNA,tRNA,wholeseq,gene} [{CDS,rRNA,tRNA,wholeseq,gene} ...]] [-cds_translation] [-gi] [-p] [-t] [-s] [-l] [-rv] [-F]
gbseqextractor: error: argument -f: expected one argument
実行方法
GenBankファイルを指定する。遺伝子フィーチャのCDS（coding sequence）を取り出す。
gbseqextractor -f input.gbk -prefix outpredix -types CDS
- -f. Genbank file
- -prefix prefix of output file. required.
- -seqPrefix prefix of each seq id. default: None
- -types {CDS,rRNA,tRNA,wholeseq,gene} [{CDS,rRNA,tRNA,wholeseq,gene} ...] what kind of genes you want to extract? wholeseq for whole fasta seq. WARNING: Each sequence in the result files corresponds to ONE feature in the GenBank file, I will NOT combine multiple CDS of the same gene into ONE! [CDS]
- -cds_translation Also output translated CDS (required -types CDS). The translations are retrived directly from the '/translation=' key word. [False]
output.cds_translation.fastaが出力される。
rRNAの配列を取り出す。
gbseqextractor -f input.gbk -prefix outpredix -types rRNA
- "-cds_translation"をつけると翻訳後の配列も取り出される。
引用
Guanliang Meng, Yiyuan Li, Chentao Yang, Shanlin Liu,
MitoZ: a toolkit for animal mitochondrial genome assembly, annotation and visualization, Nucleic Acids Research, https://doi.org/10.1093/nar/gkz173
関連
