NCBI Blast API 的调用

介绍

在NCIBI的Develop版块中，含有官方的APIs调用方法，包括了Entrez Programming Utilities (E-utilities)、BLAST URL API、PubChem Power User Gateway (PUG)、PubMed Central (PMC) APIs。

因此，NCBI的BLAST比对不仅有网页端的在线程序，也含有本地脚本的使用方法。本篇文章着重介绍Blast比对的方法。

使用方法

NCBI Blast API调用的官网文档

相关参数：

Parameter	Definition	Type	CMD	Allowed values
QUERY	Search query	String	Put *	Accession, GI, or FASTA.
DATABASE	BLAST database	String	Put *	Database from appendix 2 or one uploaded to blastdb_custom (see appendix 4)
PROGRAM	BLAST program	String	Put *	One of blastn, blastp, blastx, tblastn, tblastx. To enable megablast, use PROGRAM=blastn&MEGABLAST=on.
FILTER	Low complexity filtering	String	Put	F to disable. T or L to enable. Prepend “m” for mask at lookup (e.g., mL)
FORMAT_TYPE	Report type	String	Put, Get	HTML, Text, XML, XML2, JSON2, or Tabular. HTML is the default.
EXPECT	Expect value	Double	Put	Number greater than zero.
NUCL_REWARD	Reward for matching bases (BLASTN and megaBLAST)	Integer	Put	Integer greater than zero.
NUCL_PENALTY	Cost for mismatched bases (BLASTN and megaBLAST)	Integer	Put	Integer less than zero.
GAPCOSTS	Gap existence and extension costs	String	Put	Pair of positive integers separated by a space such as “11 1”.
MATRIX	Scoring matrix name	String	Put	One of BLOSUM45, BLOSUM50, BLOSUM62, BLOSUM80, BLOSUM90, PAM250, PAM30 or PAM70. Default: BLOSUM62 for all applicable programs
HITLIST_SIZE	Number of databases sequences to keep	Integer	Put,Get	Integer greater than zero.
DESCRIPTIONS	Number of descriptions to print (applies to HTML and Text)	Integer	Put,Get	Integer greater than zero.
ALIGNMENTS	Number of alignments to print (applies to HTML and Text)	Integer	Put,Get	Integer greater than zero.
NCBI_GI	Show NCBI GIs in report	String	Put, Get	T or F
RID	BLAST search request identifier	String	Get , Delete	The Request ID (RID) returned when the search was submitted
THRESHOLD	Neighboring score for initial words	Integer	Put	Positive integer (BLASTP default is 11). Does not apply to BLASTN or MegaBLAST).
WORD_SIZE	Size of word for initial matches	Integer	Put	Positive integer.
COMPOSITION_BASED_STATISTICS	Composition based statistics algorithm to use	Integer	Put	One of 0, 1, 2, or 3. See comp_based_stats command line option in the BLAST+ user manual for details.
FORMAT_OBJECT	Object type	String	Get	SearchInfo (status check) or Alignment (report formatting).
NUM_THREADS	Number of virtual CPUs to use	Integer	Put	Integer greater than zero and less than the maximum number of cores on the instance (default is the maximum number of cores on the instance). Supported only on the cloud

示例

官方文档中，含有Perl语言的脚本（官方示例），本文提供Python版本的代码

import requests
headers={
    'Content-type':'application/x-www-form-urlencoded'
}

#以下参数根据自己的需求写
data={
    'CMD':'Put',
    'PROGRAM':program,  #比如 blastp，blastn等
    'DATABASE':database,
    'QUERY':encoded_query
}

r=requests.post(url,headers=headers)
#若响应值为json格式，可使用print(r.json())
print(r.text)

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