Direct:命令行访问NCBI

命令行访问和获取NCBI数据当选Entrez Direct: E-utilities on the UNIX Command Line.

工具集

esearch 搜索功能;
elink looks up neighbors (within a database) or links (between databases).
efilter 搜索结果过滤,搜索结果以特定格式输出.
efetch 以指定格式下载搜索结果.
xtract 转化XML格式为table.
einfo obtains information on indexed fields in an Entrez database.
epost uploads unique identifiers (UIDs) or sequence accession numbers.
nquire sends a URL request to a web page or CGI service.

数据库查询

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esearch -db pubmed -query "lycopene cyclase" | efetch -format abstract
esearch -db protein -query "lycopene cyclase" | efetch -format fasta

当查询数据是蛋白或核酸时-format参数可以是fasta(fasta_cds_na, fasta_cds_aa, and gene_fasta),gb(GenBank), gp(GenPept),

搜索和过滤

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esearch -db pubmed -query "opsin gene conversion" | elink -related | 
efilter -query "tetrachromacy"
efilter -days 60 -datetype PDAT #过去2个月
efilter -mindate 1990 -maxdate 1999 -datetype PDAT #1990s

XML格式转换为制表符

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$ esearch -db protein -query "lycopene cyclase" 
<ENTREZ_DIRECT>
<Db>protein</Db>
<WebEnv>NCID_1_322844954_130.14.22.215_9001_1484487403_837234396_0MetA0_S_MegaStore_F_1</WebEnv>
<QueryKey>1</QueryKey>
<Count>12380</Count>
<Step>1</Step>
</ENTREZ_DIRECT>
$ esearch -db protein -query "lycopene cyclase" | xtract -pattern ENTREZ_DIRECT -element Count
12380

某一领域最多产的作者

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$ SortUniqCountRank() {
sort -f |
uniq -i -c |
perl -pe 's/\s*(\d+)\s(.+)/$1\t$2/' |
sort -t $'\t' -k 1,1nr -k 2f
$ alias sort-uniq-count-rank='SortUniqCountRank'
$ esearch -db pubmed -query \
"crotalid venoms [MAJR] AND phospholipase [TIAB]" |
efetch -format xml |
xtract -pattern PubmedArticle \
-block Author -sep " " -tab "\n" -element LastName,Initials |
sort-uniq-count-rank

某一领域每年文章发表情况

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esearch -db pubmed -query "legionnaires disease [TITL]" |
efetch -format docsum |
xtract -pattern DocumentSummary -element PubDate |
cut -c 1-4 |
sort-uniq-count-rank

人每条染色体上有多少基因

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for chr in {1..22} X Y MT
do
esearch -db gene -query "Homo sapiens [ORGN] AND $chr [CHR]" |
efilter -query "alive [PROP] AND genetype protein coding [PROP]" |
efetch -format docsum |
xtract -pattern DocumentSummary -NAME Name \
-block GenomicInfoType -if ChrLoc -equals "$chr" \
-tab "\n" -element ChrLoc,"&NAME" |
sort | uniq | cut -f 1 | sort-uniq-count-rank
done
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