Entrez Direct--Appendices

附录

设置联系地址和脚本名称

EDirect自动从系统获取用户的电子邮件地址，以便有人在失控脚本导致Entrez服务器出现问题时通知，但是如果需要其他联系地址（例如，系统管理员或软件开发人员）可以在管道或脚本的开头显式设置：

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econtact -email author_email_address -tool name_of_script

这样，如果脚本中的无限循环意外滥用NCBI资源，NCBI就会有关于联系人的信息。 （为方便起见，还可以在所有电子实用程序调用操作中设置首选电子邮件地址和软件工具名称。）

命令行参数

下面列出了EDirect功能的参数：

使用esearch在索引条款上开始新的Entrez搜索：

查询规范

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-db          Database name
-query       Query string

文件订单

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-sort        Result presentation order

日期

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-days        Number of days in the past
-datetype    Date field abbreviation
-mindate     Start of date range
-maxdate     End of date range

按现场限制

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-field       Query words individually in field
-pairs       Query overlapping word pairs

拼写检查

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-spell       Correct misspellings in query

杂项参数

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-label       Alias for query step

elink函数查找相关文章或相关记录：

目标数据库

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related    Neighbors in same database
-target     Links in different database
-name       Link name (e.g., pubmed_protein_refseq)

直接记录选择

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-db         Database name
-id         Unique identifier(s)

高级控制

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-cmd        Command type (returns eLinkResult XML)
-mode       "ref" uses LinkOut provider's web site
-holding    Name of LinkOut provider

批量处理

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-batch      Bypass Entrez history mechanism

杂项参数

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-label      Alias for query step

使用efilter通过索引术语限制搜索或链接结果：

查询规范

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-query       Query string

文件订单

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-sort        Result presentation order

日期

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-days        Number of days in the past
-datetype    Date field abbreviation
-mindate     Start of date range
-maxdate     End of date range

按现场限制

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-field       Query words individually in field
-pairs       Query overlapping word pairs

拼写检查

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-spell       Correct misspellings in query

出版过滤器

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-pub         abstract, clinical, english, free, historical,
             journal, medline, preprint, published, review,
             structured
-journal     pnas, "j bacteriol", ...
-released    last_week, last_month, last_year, prev_years

序列过滤器

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-country     usa:minnesota, united_kingdom, "pacific ocean", ...
-feature     gene, mrna, cds, mat_peptide, ...
-location    mitochondrion, chloroplast, plasmid, plastid
-molecule    genomic, mrna, trna, rrna, ncrna
-organism    animals, archaea, bacteria, eukaryotes, fungi,
             human, insects, mammals, plants, prokaryotes,
             protists, rodents, viruses
-source      genbank, insd, pdb, pir, refseq, swissprot, tpa

基因过滤器

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-status      alive
-type        coding, pseudo

SNP过滤器

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-class       acceptor, donor, frameshift, indel, intron,
             missense, nonsense, synonymous

杂项参数

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-label       Alias for query step

记录检索功能是efetch：

格式选择

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-format        Format of record or report
-mode          text, xml, asn.1, json
-style         withparts, conwithfeat

直接记录选择

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-db            Database name
-id            Unique identifier or accession number

序列范围

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-seq_start     First sequence position to retrieve
-seq_stop      Last sequence position to retrieve
-strand        Strand of DNA to retrieve

基因范围

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-chr_start     Sequence range from 0-based coordinates
-chr_stop        in gene docsum GenomicInfoType object

序列标志

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-complexity    0 = default, 1 = bioseq, 3 = nuc-prot set
-extend        Extend sequence retrieval in both directions
-extrafeat     Bit flag specifying extra features

杂

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-raw           Skip database-specific XML modifications
-json          Convert adjusted XML output to JSON

xtract函数用于处理XML数据：

处理标志

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-strict          Remove HTML and MathML tags
-mixed           Allow mixed content XML
-accent          Excise Unicode accents and diacritical marks
-ascii           Unicode to numeric HTML character entities
-compress        Compress runs of spaces
-stops           Retain stop words in selected phrases

数据源

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-input           Read XML from file instead of stdin
-transform       File of substitutions for -translate

探索参数层次结构

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-pattern         Name of record within set
-group             Use of different argument
-block               names allows command-line
-subset                control of nested looping

勘探建筑

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Object           DateRevised
Parent/Child     Book/AuthorList
Heterogeneous    "PubmedArticleSet/*"
Exhaustive       "History/**"
Nested           "*/Taxon"
Recursive        "**/Gene-commentary"

条件执行

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-if              Element [@attribute] required
-unless          Skip if element matches
-and             All tests must pass
-or              Any passing test suffices
-else            Execute if conditional test failed
-position        [first|last|outer|inner|even|odd|all]
-select          Select record subset by conditions

字符串约束

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-equals          String must match exactly
-contains        Substring must be present
-is-within       String must be present
-starts-with     Substring must be at beginning
-ends-with       Substring must be at end
-is-not          String must not match

数字约束

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-gt              Greater than
-ge              Greater than or equal to
-lt              Less than
-le              Less than or equal to
-eq              Equal to
-ne              Not equal to

格式定制

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-ret             Override line break between patterns
-tab             Replace tab character between fields
-sep             Separator between group members
-pfx             Prefix to print before group
-sfx             Suffix to print after group
-plg             Prologue to print once before elements
-elg             Epilogue to print once after elements
-rst             Reset -sep through -elg
-clr             Clear queued tab separator
-pfc             Preface combines -clr and -pfx
-deq             Delete and replace queued tab separator
-wrp             Wrap elements in XML object
-def             Default placeholder for missing fields
-lbl             Insert arbitrary text

元素选择

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-element         Print all items that match tag name
-first           Only print value of first item
-last            Only print value of last item
-NAME            Record value in named variable

-element Constructs

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Tag              Caption
Group            Initials,LastName
Parent/Child     MedlineCitation/PMID
Recursive        "**/Gene-commentary_accession"
Unrestricted     "PubDate/*"
Attribute        DescriptorName@MajorTopicYN
Range            MedlineDate[1:4]
Substring        "Title[phospholipase | rattlesnake]"
Object Count     "#Author"
Item Length      "%Title"
Element Depth    "^PMID"
Variable         "&NAME"

特殊元素操作

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Parent Index     "+"
Object Name      "?"
XML Subtree      "*"
Children         "$"
Attributes       "@"

数字处理

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-num             Count
-len             Length
-sum             Sum
-min             Minimum
-max             Maximum
-inc             Increment
-dec             Decrement
-sub             Difference
-avg             Average
-dev             Deviation
-med             Median
-bin             Binary
-bit             Bit Count

字符串处理

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-encode          URL-encode <, >, &, ", and ' characters
-upper           Convert text to upper-case
-lower           Convert text to lower-case
-title           Capitalize initial letters of words
-year            Extract first 4-digit year from string
-translate       Substitute values with -transform table

文字处理

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-terms           Partition text at spaces
-words           Split at punctuation marks
-pairs           Adjacent informative words
-reverse         Reverse words in string
-letters         Separate individual letters
-clauses         Break at phrase separators
-indices         Index normalized words

序列处理

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-revcomp         Reverse-complement nucleotide sequence
-nucleic         Subrange determines forward or revcomp

序列坐标

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-0-based         Zero-Based
-1-based         One-Based
-ucsc-based      Half-Open

命令生成器

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-insd            Generate INSDSeq extraction commands

-insd参数顺序

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Descriptors      INSDSeq_sequence INSDSeq_definition INSDSeq_division
Flags            [complete|partial]
Feature(s)       CDS,mRNA
Qualifiers       INSDFeature_key "#INSDInterval" gene product

杂

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-head            Print before everything else
-tail            Print after everything else
-hd              Print before each record
-tl              Print after each record

重新格式化

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-format          [copy|compact|flush|indent|expand]

修改

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-filter          Object
                       [retain|remove|encode|decode|shrink|expand|accent]
                         [content|cdata|comment|object|attributes|container]

验证

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-verify          Report XML data integrity problems

摘要

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-outline         Display outline of XML structure
-synopsis        Display count of unique XML paths

文档

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-examples        Examples of EDirect and xtract usage

einfo函数返回有关Entrez索引字段的信息：

数据库选择

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-db        Database name
-dbs       Get all database names

数据摘要

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-fields    Print field names
-links     Print link names

EDirect提供了几个附加功能：

epost

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-db        Database name
-id        Unique identifier(s) or accession number(s)
-format    uid or acc
-input     Read from file instead of stdin
-label     Alias for query step

eproxy

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-alias     File of aliases
-pipe      Read aliases from stdin

econtact

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-email     Contact person's address
-tool      Name of script or program

nquire

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-get       Uses HTTP GET instead of POST
-url       Base URL for external search

此外，-email和-tool在所有E-utilities调用函数中都可用于覆盖默认值，-http get将强制使用GET而不是POST，-alias将指定快捷键关键字和查询字符串或URL的文件sections和-help将打印每个函数的参数列表。

对于调试，-silent将禁止链接失败重试消息，-verbose将在每一步显示字段值，-debug将打印内部URL查询和每个步骤的XML结果，-base将指定特定的服务器质量保证测试。

EFetch格式

每个数据库的EFetch -format和-mode值如下所示：

This is an image This is an image
ESearch排序

下面列出了几个数据库的ESearch -sort值：

This is an image
ELink命令

ELink -cmd选项生成结果为LinkSet XML：

-cmd Result
neighbor Neighbors or links
neighbor_score Neighbors with computed similarity scores
acheck All links available
ncheck Existence of neighbors
lcheck Existence of external links (LinkOuts)
llinks Non-library LinkOut providers
llinkslib All LinkOut providers
prlinks Primary LinkOut provider,or URL for single UID with -mode ref

EInfo数据

EInfo字段数据包含多个术语列表索引属性的状态标志：

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<Field>
  <Name>ALL</Name>
  <FullName>All Fields</FullName>
  <Description>All terms from all searchable fields</Description>
  <TermCount>138982028</TermCount>
  <IsDate>N</IsDate>
  <IsNumerical>N</IsNumerical>
  <SingleToken>N</SingleToken>
  <Hierarchy>N</Hierarchy>
  <IsHidden>N</IsHidden>
  <IsTruncatable>Y</IsTruncatable>
  <IsRangable>N</IsRangable>
</Field>
UNIX实用程序

下面介绍了几个有用的UNIX文本处理过滤器类，带有选定的参数：

按内容处理：

sort Sorts lines of text
-f Ignore case
-n Numeric comparison
-r Reverse result order 
-k  |  Field key (start,stop or first)
-u  |  Unique lines with identical keys

-b  |  Ignore leading blanks
-s  |  Stable sort
-t  |  Specify field separator

uniq | Removes repeated lines

-c  |  Count occurrences
-i  |  Ignore case

-f  |  Ignore first n fields
-s  |  Ignore first n characters

-d  |  Only output repeated lines
-u  |  Only output non-repeated lines

grep | Matches patterns using regular expressions

-i  |  Ignore case
-v  |  Invert search
-w  |  Search expression as a word
-x  |  Search expression as whole line

-e  |  Specify individual pattern

-c  |  Only count number of matches
-n  |  Print line numbers

常用表达：

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Characters
  .     Any single character (except newline)
  \w    Alphabetic [A-Za-z], numeric [0-9], or underscore (_)
  \s    Whitespace (space or tab)
  \     Escapes special characters
  []    Matches any enclosed characters
Positions
  ^     Beginning of line
  $     End of line
  \b    Word boundary
Repeat Matches
  ?     0 or 1
  *     0 or more
  +     1 or more
  {n}   Exactly n

修改内容：

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sed     Replaces text strings
  -e    Specify individual expression
tr      Translates characters
  -d    Delete character
rev     Reverses characters on line

格式内容：

列按内容宽度对齐列

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-s    Specify field separator
-t    Create table

expand将列对齐到指定位置

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-t    Tab positions

fold以特定宽度包裹线条

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-w    Line width

按位置筛选：

cut删除部分线条

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-c    Characters to keep
-f    Fields to keep
-d    Specify field separator
-s    Suppress lines with no delimiters

head打印第一行

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-n    Number of lines

tail打印最后一行

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-n    Number of lines

杂：

wc计算单词，行或字符

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-c    Characters
-l    Lines
-w    Words

xargs构造参数

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-n    Number of words per batch

文件压缩：

tar存档文件

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-c    Create archive
-f    Name of output file
-z    Compress archive with gzip

gzip压缩文件

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-k    Keep original file
-9    Best compression

解压缩.zip存档

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-p    Pipe to stdout

gzcat解压缩.gz归档和管道到stdout
目录和文件导航：

cd更改目录

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/     Root
~     Home
.     Current
..    Parent
-     Previous

ls列出文件名

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-1    One entry per line
-a    Show files beginning with dot (.)
-l    List in long format
-R    Recursively explore subdirectories
-S    Sort files by size
-t    Sort by most recently modified

pwd打印工作目录路径
通过键入“man”后跟命令名称，可以获得包含详细说明和示例的其他文档。

终端键盘快捷键

可以在终端会话中使用控制和转义序列来浏览命令历史记录并移动光标以编辑当前输入的命令：

命令历史：

Ctrl-n 下一个命令
Ctrl-p 上一个命令
向前移动光标：

Ctrl-e 到行尾
Ctrl-f 由一个字符组成
Esc-f 一个论点
向后移动光标：

Ctrl-a 到行首
Ctrl-b 一个字符
Esc-b 一个论点
删除：

Esc-Del以前的论点上一个角色
Ctrl-d 下一个字符
Ctrl-k 到行尾
Ctrl-u 整行
Ctrl-w 上一个单词
Esc-Del 以前的论点
Esc-d 下一个参数
自动完成：

Tab 选项卡完成目录或文件名
程序控制：

Ctrl-c 退出正在运行的程序
^x^y 运行最后一个命令将x替换为y
（注意，通过按住Control，按下另一个键并释放Control来键入控制序列，同时通过按Escape然后按另一个键来键入Escape序列。）

技术

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tag:

    缺失模块。
    1、在博客根目录（注意不是yilia根目录）执行以下命令：
    npm i hexo-generator-json-content --save

    2、在根目录_config.yml里添加配置： 

      jsonContent:
    meta: false
    pages: false
    posts:
      title: true
      date: true
      path: true
      text: true
      raw: false
      content: false
      slug: false
      updated: false
      comments: false
      link: false
      permalink: false
      excerpt: false
      categories: false
      tags: true

“众少成多，积小致钜。”<br><br>千里之行始于足下<br>