Multi FASTAのGC含量や長さを表示する EMBOSSのinfoseqコマンド

EMBOSSパッケージのinfoseq は、1 つ以上の入力配列に関する基本情報を画面上に表示する。これには、Uniform Sequence Address (USA)、名前、アクセッション番号、タイプ（核酸またはタンパク質）、長さ、C+Gの割合、および説明が含まれる。オプションでHTMLテーブル出力することもできる。

EMBOSS explorer （a graphical user interface to the EMBOSS suite）

https://www.bioinformatics.nl/cgi-bin/emboss/infoseq

インストール

condaやbrewで導入できる。

#bioconda
conda install -c bioconda -y emboss 

#homebrew 
brew install emboss

> infoseq -help

$ infoseq -help

Display basic information about sequences

Version: EMBOSS:6.6.0.0

Standard (Mandatory) qualifiers:

[-sequence] seqall (Gapped) sequence(s) filename and optional

format, or reference (input USA)

Additional (Optional) qualifiers:

-outfile outfile [stdout] If you enter the name of a file

here then this program will write the

sequence details into that file.

-html boolean [N] Format output as an HTML table

Advanced (Unprompted) qualifiers:

-[no]columns boolean [Y] Set this option on (Y) to print the

sequence information into neat, aligned

columns in the output file. Alternatively,

leave it unset (N), in which case the

information records will be delimited by a

character, which you may specify by using

the -delimiter option. In other words, if

-columns is set on, the -delimiter option is

overriden.

-delimiter string [|] This string, which is usually a single

character only, is used to delimit

individual records in the text output file.

It could be a space character, a tab

character, a pipe character or any other

character or string. (Any string)

-only boolean [N] This is a way of shortening the command

line if you only want a few things to be

displayed. Instead of specifying:

'-nohead -noname -noacc -notype -nopgc

-nodesc'

to get only the length output, you can

specify

'-only -length'

-[no]heading boolean [Y] Display column headings

-usa boolean [@(!$(only))] Display the USA of the

sequence

-database boolean [@(!$(only))] Display 'database' column

-name boolean [@(!$(only))] Display 'name' column

-accession boolean [@(!$(only))] Display 'accession' column

-gi boolean [N] Display 'GI' column

-seqversion boolean [N] Display 'version' column

-type boolean [@(!$(only))] Display 'type' column

-length boolean [@(!$(only))] Display 'length' column

-pgc boolean [@(!$(only))] Display 'percent GC content'

column

-organism boolean [@(!$(only))] Display 'organism' column

-description boolean [@(!$(only))] Display 'description' column

General qualifiers:

-help boolean Report command line options and exit. More

information on associated and general

qualifiers can be found with -help -verbose

実行方法

EMBOSSの各コマンドは、コマンドだけ打てば対話モードで実行できる。

infoseq

または入力のFASTAファイルを引数指定する。

infoseq input.fasta

出力

fasta::rename.fa:contig1 - contig1 - N 2328312 47.92

fasta::rename.fa:contig2 - contig2 - N 1875280 46.73

fasta::rename.fa:contig3 - contig3 - N 1753326 48.22

fasta::rename.fa:contig4 - contig4 - N 1691583 46.81

fasta::rename.fa:contig5 - contig5 - N 1658655 47.94

右端に長さとlengthがつく。

出力される情報は指定できる。Contig名、length、GCを出力。

infoseq -only -name -length -pgc input.fasta |head

-only This is a way of shortening the command line if you only want a few things to be displayed
-database Display 'database' column
-name Display 'name' column
-accession Display 'accession' column
-gi Display 'GI' column
-seqversion Display 'version' column
-type Display 'type' column
-length Display 'length' column
-pgc Display 'percent GC content' column
-organism Display 'organism' column
-description Display 'description' column