pSeqBuilder_DB(PAnnBuilder)
pSeqBuilder_DB()所属R语言包：PAnnBuilder
Build Data Packages for Query Sequences
建立查询序列的数据包
译者：生物统计家园网 机器人LoveR
描述----------Description----------
This function use previous data annotation packages and employ blast program to creates a new data package for query sequences.
此功能使用以前的数据注解包，并聘请爆破方案，以创建一个新的数据包查询序列。
用法----------Usage----------
pSeqBuilder_DB(query, annPkgs, seqName, blast, match,
prefix, pkgPath, version, author)
参数----------Arguments----------
参数：query
a named string vector to be used as query sequences. Blast will be called to map between query sequences and sequences from the given protein sequence package, and then get corresponding annotation data from the given annotation package.
一个名为字符串矢量被用来作为查询序列。高炉将被称为查询序列和序列从给定的蛋白质序列包之间的映射，然后得到相应的注释数据，从给定的注解包。
参数：annPkgs
a string vector containing the name of annotation packages. In annotation package, data is saved as R environment or SQLite object. The Key is protein, and the value is its annotation.
注释包的名称字符串向量。数据被保存在注释包，R环境或SQLite对象。最关键的是蛋白质，和价值是它的注解。
参数：seqName
a string vector which has the same length with parameter "annPkgs", and indicating the name of protein-sequence mapping in the package.
一个字符串向量具有相同的长度与参数“annPkgs”，并表示包中的蛋白质序列映射名称。
参数：blast
a named character vector defining the parameters of blastall.
一个名为特征向量定义blastall的参数。
参数：match
a named character vector defining the parameters of two sequence matching.
一个命名的特征向量确定两个序列匹配的参数。
参数：prefix
the prefix of the name of the data package to be built. (e.g. "hsaSP"). The name of builded package is prefix+".db".
兴建的数据包名称的前缀。 （例如“hsaSP”）。建造包的名称为前缀+“DB”。
参数：pkgPath
a character string for the full path of an existing directory where the built backage will be stored.
为建backage将存储现有目录的完整路径的字符串。
参数：version
a character string for the version number.
一个版本号的字符串。
参数：author
a list with named elements "authors" containing a character vector of author names and "maintainer" containing the complete character string for the maintainer field, for example, "Jane Doe <jdoe@doe.com>".
与元素命名为“作者”包含作者姓名的特征向量和“维护者”，含有完整的字符串维护者领域，例如，“Jane Doe的<jdoe@doe.com>”的名单。
Details
详情----------Details----------
Build annotation data packages for query protein sequences. formatdb and blastall are need to be installed.
建立查询的蛋白质序列数据包注释。 formatdb和blastall都需要安装。
Parameter "blast" is a named character vector defining the parameters of blastall. Possible names and their meaning are listed as follows: p: Program Name [String]. e: Expectation value (E) [Real]. M: Matrix [String]. W: World Size, default if zero (blastn 11, megablast 28, all others 3) [Integer] default = 0. G: Cost to open a gap (-1 invokes default behavior) [Integer]. E: Cost to open a gap (-1 invokes default behavior) [Integer]. U: Use lower case filtering of FASTA sequence [T/F] Optional. F: Filter query sequence (DUST with blastn, SEG with others) [String].
“爆炸”的参数是一个命名的特征向量定义blastall的参数。可能名称和它们的含义如下：号码：项目名称字符串]。 E：期望值（五）[房地产]。男：矩阵[字符串]。女：世界的大小，默认情况下，如果为零（BLASTN，megablast 11月28日，所有其他3）[整数]默认值= 0。 G：打开一个缺口成本（-1调用默认行为）[整数]。电子邮件：成本打开了一个缺口（-1调用默认行为）[整数]。 üFASTA格式序列的筛选[T / F]可选：使用小写。传真：过滤查询序列（BLASTN灰尘，与他人赛格）[字符串]。
Parameter "match" a named character vector defining the parameters of two sequence matching. Possible names and their meaning are listed as follows: e: Expectation value of two sequence matching [Real]. c: Coverage of the longest High-scoring Segment Pair (HSP) to the whole protein sequence. (range: 0~1) i: Identity of the longest High-scoring Segment Pair (HSP). (range: 0~1)
参数“匹配”命名的特征向量确定两个序列匹配的参数。列出可能的名字和它们的含义如下：E：两个序列匹配的期待值[实时]。 C：最长段对高得分（HSP）的整个蛋白质序列的覆盖率。 （范围：0~1）我：最长的高得分段对（HSP）的身份。 （范围：0~1）
Data files in the database will be automatically downloaded to the tmp directory, so enough space is needed for the data files. After downloading, files are parsed by perl, so perl must be installed. It may take a long time to parse database and build R package. Alternatively, we have produced diverse R packages by PAnnBuilder, and you can download appropriate package via http://www.biosino.org/PAnnBuilder/example.jsp.
数据库中的数据文件将被自动下载到tmp目录，以便有足够的空间所需的数据文件。下载后，文件是由Perl解析，所以必须安装perl的。这可能需要很长的时间解析数据库和建立R包。另外，我们由PAnnBuilder生产多样化的R包，你可以通过http://www.biosino.org/PAnnBuilder/example.jsp下载相应的包。
作者（S）----------Author(s)----------
Hong Li
举例----------Examples----------
## Set path, version and author for the package.[＃设置包的路径，版本和作者。]
pkgPath <- tempdir()
version <- "1.0.0"
author <- list()
author[["authors"]] <- "Hong Li"
author[["maintainer"]] <- "Hong Li <sysptm@gmail.com>"
## Set query sequences.[＃设置的查询序列。]
tmp = system.file("extdata", "query.example", package=" AnnBuilder")
tmp = readLines(tmp)
tag = grep("^>",tmp)
query <- sapply(1 length(tag)-1), function(x){
paste(tmp[(tag[x]+1)tag[x+1]-1)], collapse="") })
query <- c(query, paste(tmp[(tag[length(tag)]+1):length(tmp)], collapse="") )
names(query) = sub(">","",tmp[tag])
## Set parameters for sequence similarity.[＃设置参数，序列相似性。]
blast <- c("blastp", "10.0", "BLOSUM62", "0", "-1", "-1", "T", "F")
names(blast) <- c("p","e","M","W","G","E","U","F")
match <- c(0.00001, 0.95, 0.95)
names(match) <- c("e","c","i")
if(FALSE){
## NOTE: THESE PACKAGES ARE NO LONGER AVAILABLE, YOU NEED TO GENERATE[＃注意：这些包不再可用，您需要生成]
## THEM FOLLOWING THE INSTRUCTIONS IN THE VIGNETTE[＃他们的小品文说明]
## Use packages "org.Hs.sp.db", "org.Hs.ipi.db" to produce annotation R[＃使用“org.Hs.sp.db”包“org.Hs.ipi.db”产生注解ŕ]
## package for query sequence. Packages "org.Hs.sp.db", "org.Hs.ipi.db"[＃查询序列包。软件包“org.Hs.sp.db的”，“org.Hs.ipi.db”]
## can be downloaded from http://www.biosino.org/PAnnBuilder/example.jsp. [＃可以从http://www.biosino.org/PAnnBuilder/example.jsp下载。]
annPkgs = c("org.Hs.sp.db","org.Hs.ipi.db")
seqName = c("org.Hs.spSEQ","org.Hs.ipiSEQ")
pSeqBuilder_DB(query, annPkgs, seqName, blast, match,
prefix="test1", pkgPath, version, author)
}
转载请注明:出自 生物统计家园网(http://www.biostatistic.net)。
注：
注1：为了方便大家学习，本文档为生物统计家园网机器人LoveR翻译而成，仅供个人R语言学习参考使用，生物统计家园保留版权。
注2：由于是机器人自动翻译，难免有不准确之处，使用时仔细对照中、英文内容进行反复理解，可以帮助R语言的学习。
注3：如遇到不准确之处，请在本贴的后面进行回帖，我们会逐渐进行修订。
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发表于 2012-2-26 10:19:33
