NcbimakeblastdbCommandline クラス (Bio.Blast.Applications モジュール)

[APIドキュメント]

class NcbimakeblastdbCommandline(AbstractCommandline)

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特殊メソッド

__init__(cmd=’makeblastdb’, **kwargs)

@ [APIドキュメント] ↑

BLASTのmakeblastdbコマンドを表すインスタンスを生成します。

**kwargsに指定する引数とmakeblastdb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をもとに作成)

引数	makeblastdb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.
dbtype	-dbtype	str		Molecule type of target db (‘nucl’ or ‘prot’)
input_file	-in	str		Input file/database name
input_type	-input_type	str	‘fasta’	Type of the data specified in input_file.
title	-title	str		Title for BLAST database
parse_seqids	-parse_seqids	bool		Option to parse seqid for FASTA input if set, for all other input types seqids are parsed automatically.
hash_index	-hash_index	bool		Create index of sequence hash values.
mask_data	-mask_data	str		Comma-separated list of input files containing masking data as produced by NCBI masking applications (e.g. dustmasker, segmasker, windowmasker)
mask_id	-mask_id	str		Comma-separated list of strings to uniquely identify the masking algorithm
mask_desc	-mask_desc	str		Comma-separated list of free form strings to describe the masking algorithm details
gi_mask	-gi_mask	bool		Create GI indexed masking data.
gi_mask_name	-gi_mask_name	str		Comma-separated list of masking data output files.
max_file_sz	-max_file_sz	str	‘1GB’	Maximum file size for BLAST database files.
logfile	-logfile	str		File to which the program log should be redirected
taxid	-taxid	str		Taxonomy ID to assign to all sequences
taxid_map	-taxid_map	str		Text file mapping sequence IDs to taxonomy IDs. “Format:<SequenceId> <TaxonomyId><newline>