_NcbibaseblastCommandline クラス (Bio.Blast.Applications モジュール)
[GitHub]
class _NcbibaseblastCommandline(AbstractCommandline)
継承関係：Application.AbstractCommandline → _NcbibaseblastCommandline
NCBI BLAST+のラッパーのコマンドラインオブジェクトのための基底クラスです。
[toc]目次
特殊メソッド
__init__(cmd=None, **kwargs)
**kwargsに指定する引数とBLASTコマンドのオプションとの対応は次のようになります。(source code(GitHub)をもとに作成)
| 引数 | コマンドオプション | データ型 | デフォルト値 | 説明 |
|---|---|---|---|---|
| h | -h | bool | Print USAGE and DESCRIPTION; ignore other arguments. | |
| help | -help | bool | Print USAGE, DESCRIPTION and ARGUMENTS description; ignore other arguments. | |
| version | -version | bool | Print version number; ignore other arguments. | |
| out | -out | str | Output file for alignment. | |
| outfmt | -outfmt | int | Alignment view. Typically an integer 0-14 but for some formats can be named columns like ‘6 qseqid sseqid’. Use 5 for XML output (differs from classic BLAST which used 7 for XML). | |
| show_gis | -show_gis | bool | Show NCBI GIs in deflines? | |
| num_descriptions | -num_descriptions | int | 500 | Number of database sequences to show one-line descriptions for. Integer argument (at least zero). |
| num_alignments | -num_alignments | int | 200 | Number of database sequences to show num_alignments for. Integer argument (at least zero). |
| line_length | -line_length | int | 60 | Line length for formatting alignments. |
| html | -html | bool | Produce HTML output? | |
| parse_deflines | -parse_deflines | bool | Should the query and subject defline(s) be parsed? |
コメント