NcbimakeblastdbCommandline クラス

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


class NcbimakeblastdbCommandline(AbstractCommandline)


__init__(cmd=’makeblastdb’, **kwargs)

@ [APIドキュメント]


**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)

h-hboolPrint USAGE and DESCRIPTION; ignore other arguments.
help-helpboolPrint USAGE, DESCRIPTION and ARGUMENTS description; ignore other arguments.
versionversionboolPrint version number; ignore other arguments.
out-outstrOutput file for alignment.
dbtype-dbtypestrMolecule type of target db (‘nucl’ or ‘prot’)
input_file-instrInput file/database name
input_type-input_typestr‘fasta’Type of the data specified in input_file.
title-titlestrTitle for BLAST database
parse_seqids-parse_seqidsboolOption to parse seqid for FASTA input if set, for all other input types seqids are parsed automatically.
hash_index-hash_indexboolCreate index of sequence hash values.
mask_data-mask_datastrComma-separated list of input files containing masking data as produced by NCBI masking applications (e.g. dustmasker, segmasker, windowmasker)
mask_id-mask_idstrComma-separated list of strings to uniquely identify the masking algorithm
mask_desc-mask_descstrComma-separated list of free form strings to describe the masking algorithm details
gi_mask-gi_maskboolCreate GI indexed masking data.
gi_mask_name-gi_mask_namestrComma-separated list of masking data output files.
max_file_sz-max_file_szstr‘1GB’Maximum file size for BLAST database files.
logfile-logfilestrFile to which the program log should be redirected
taxid-taxidstrTaxonomy ID to assign to all sequences
taxid_map-taxid_mapstrText file mapping sequence IDs to taxonomy IDs. “Format:<SequenceId> <TaxonomyId><newline>


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