[Seqinr-commits] r2151 - in pkg: . man
noreply at r-forge.r-project.org
noreply at r-forge.r-project.org
Mon Nov 28 15:23:36 CET 2022
Author: simonpenel
Date: 2022-11-28 15:23:35 +0100 (Mon, 28 Nov 2022)
New Revision: 2151
Modified:
pkg/DESCRIPTION
pkg/man/aaindex.Rd
pkg/man/acnucopen.Rd
pkg/man/read.alignment.Rd
Log:
Removing Escaped LaTeX specials
Modified: pkg/DESCRIPTION
===================================================================
--- pkg/DESCRIPTION 2022-11-28 13:23:33 UTC (rev 2150)
+++ pkg/DESCRIPTION 2022-11-28 14:23:35 UTC (rev 2151)
@@ -1,6 +1,6 @@
Encoding: UTF-8
Package: seqinr
-Version: 4.2-21
+Version: 4.2-22
Date: 2022-11-28
Title: Biological Sequences Retrieval and Analysis
Authors at R: c(person("Delphine", "Charif", role = "aut"),
Modified: pkg/man/aaindex.Rd
===================================================================
--- pkg/man/aaindex.Rd 2022-11-28 13:23:33 UTC (rev 2150)
+++ pkg/man/aaindex.Rd 2022-11-28 14:23:35 UTC (rev 2151)
@@ -15,8 +15,8 @@
\item{A}{String: Author(s).}
\item{T}{String: Title of the article.}
\item{J}{String: Journal reference and comments.}
- \item{C}{String: Accession numbers of similar entries with the correlation
- coefficients of 0.8 (-0.8) or more (less). Notice: The correlation
+ \item{C}{String: Accession numbers of similar entries with the correlation
+ coefficients of 0.8 (-0.8) or more (less). Notice: The correlation
coefficient is calculated with zeros filled for missing values.}
\item{I}{Numeric named vector: amino acid index data.}
}
@@ -522,8 +522,8 @@
Interactivity scale obtained by maximizing the mean of correlation coefficient over single-domain globular proteins (Bastolla et al., 2005)\cr
Interactivity scale obtained by maximizing the mean of correlation coefficient over pairs of sequences sharing the TIM barrel fold (Bastolla et al., 2005)\cr
Linker propensity index (Suyama-Ohara, 2003)\cr
-Knowledge-based membrane-propensity scale from 1D\_Helix in MPtopo databases (Punta-Maritan, 2003)\cr
-Knowledge-based membrane-propensity scale from 3D\_Helix in MPtopo databases (Punta-Maritan, 2003)\cr
+Knowledge-based membrane-propensity scale from 1D Helix in MPtopo databases (Punta-Maritan, 2003)\cr
+Knowledge-based membrane-propensity scale from 3D Helix in MPtopo databases (Punta-Maritan, 2003)\cr
Linker propensity from all dataset (George-Heringa, 2003)\cr
Linker propensity from 1-linker dataset (George-Heringa, 2003)\cr
Linker propensity from 2-linker dataset (George-Heringa, 2003)\cr
@@ -578,7 +578,7 @@
Please cite the following references when making use of the database:
-Kawashima, S. and Kanehisa, M. (2000) AAindex: amino acid index
+Kawashima, S. and Kanehisa, M. (2000) AAindex: amino acid index
database. \emph{Nucleic Acids Res.}, \bold{28}:374.\cr
Tomii, K. and Kanehisa, M. (1996) Analysis of amino acid indices and
Modified: pkg/man/acnucopen.Rd
===================================================================
--- pkg/man/acnucopen.Rd 2022-11-28 13:23:33 UTC (rev 2150)
+++ pkg/man/acnucopen.Rd 2022-11-28 14:23:35 UTC (rev 2151)
@@ -26,7 +26,7 @@
}
\details{
-these low level functions are usually not used directly by the user.
+these low level functions are usually not used directly by the user.
Use \code{\link{choosebank}} to open a remote ACNUC database
and \code{\link{closebank}} to close it.
}
@@ -35,11 +35,11 @@
For \code{openacnuc} a list with the following
components: type : the type of database that was opened.
totseqs, totspec, totkey : total number of seqs, species, keywords in opened database.
-ACC\_LENGTH, L\_MNEMO, WIDTH\_KW, WIDTH\_SP, WIDTH\_SMJ, WIDTH\_AUT,
-WIDTH\_BIB, lrtxt, SUBINLNG: max lengths of record keys in database.
+ACC_LENGTH, L_MNEMO, WIDTH_KW, WIDTH_SP, WIDTH_SMJ, WIDTH_AUT,
+WIDTH_BIB, lrtxt, SUBINLNG: max lengths of record keys in database.
}
-\references{
+\references{
\code{citation("seqinr")}
}
\author{J.R. Lobry}
@@ -49,27 +49,27 @@
\examples{
\dontrun{# Need internet connection
- mysocket <- socketConnection( host = "pbil.univ-lyon1.fr",
+ mysocket <- socketConnection( host = "pbil.univ-lyon1.fr",
port = 5558, server = FALSE, blocking = TRUE)
readLines(mysocket, n = 1) # OK acnuc socket started
acnucopen("emblTP", socket = mysocket) -> res
- expected <- c("EMBL", "14138095", "236401", "1186228", "8",
+ expected <- c("EMBL", "14138095", "236401", "1186228", "8",
"16", "40", "40", "20", "20", "40", "60", "504")
stopifnot(all(unlist(res) == expected))
tryalreadyopen <- try(acnucopen("emblTP", socket = mysocket))
stopifnot(inherits(tryalreadyopen, "try-error"))
# Need a fresh socket because acnucopen() close it if error:
- mysocket <- socketConnection( host = "pbil.univ-lyon1.fr",
+ mysocket <- socketConnection( host = "pbil.univ-lyon1.fr",
port = 5558, server = FALSE, blocking = TRUE)
tryoff <- try(acnucopen("off", socket = mysocket))
stopifnot(inherits(tryoff, "try-error"))
- mysocket <- socketConnection( host = "pbil.univ-lyon1.fr",
+ mysocket <- socketConnection( host = "pbil.univ-lyon1.fr",
port = 5558, server = FALSE, blocking = TRUE)
tryinexistent <- try(acnucopen("tagadatagadatsointsoin", socket = mysocket))
stopifnot(inherits(tryinexistent, "try-error"))
- mysocket <- socketConnection( host = "pbil.univ-lyon1.fr",
+ mysocket <- socketConnection( host = "pbil.univ-lyon1.fr",
port = 5558, server = FALSE, blocking = TRUE)
trycloseunopened <- try(acnucclose(mysocket))
stopifnot(inherits(trycloseunopened, "try-error"))
Modified: pkg/man/read.alignment.Rd
===================================================================
--- pkg/man/read.alignment.Rd 2022-11-28 13:23:33 UTC (rev 2150)
+++ pkg/man/read.alignment.Rd 2022-11-28 14:23:35 UTC (rev 2151)
@@ -2,17 +2,17 @@
\alias{read.alignment}
\title{Read aligned sequence files in mase, clustal, phylip, fasta or msf format}
\description{
- Read a file in \code{mase}, \code{clustal}, \code{phylip}, \code{fasta} or \code{msf} format.
- These formats are used to store nucleotide or protein multiple alignments.
+ Read a file in \code{mase}, \code{clustal}, \code{phylip}, \code{fasta} or \code{msf} format.
+ These formats are used to store nucleotide or protein multiple alignments.
}
\usage{
read.alignment(file, format, forceToLower = TRUE, ...)
}
\arguments{
- \item{file}{the name of the file which the aligned sequences are to be read from.
- If it does not contain an absolute or relative path, the file name is relative
+ \item{file}{the name of the file which the aligned sequences are to be read from.
+ If it does not contain an absolute or relative path, the file name is relative
to the current working directory, \code{\link{getwd}}. }
- \item{format}{a character string specifying the format of the file : \code{mase},
+ \item{format}{a character string specifying the format of the file : \code{mase},
\code{clustal}, \code{phylip}, \code{fasta} or \code{msf} }
\item{forceToLower}{a logical defaulting to TRUE stating whether the returned
characters in the sequence should be in lower case (introduced in seqinR
@@ -22,50 +22,50 @@
}
\details{
\describe{
- \item{"mase"}{The mase format is used to store nucleotide or protein
- multiple alignments. The beginning of the file must contain a header
- containing at least one line (but the content of this header may be
- empty). The header lines must begin by \code{;;}. The body of the
- file has the following structure: First, each entry must begin by
- one (or more) commentary line. Commentary lines begin by the character
- \code{;}. Again, this commentary line may be empty. After the
- commentaries, the name of the sequence is written on a separate
+ \item{"mase"}{The mase format is used to store nucleotide or protein
+ multiple alignments. The beginning of the file must contain a header
+ containing at least one line (but the content of this header may be
+ empty). The header lines must begin by \code{;;}. The body of the
+ file has the following structure: First, each entry must begin by
+ one (or more) commentary line. Commentary lines begin by the character
+ \code{;}. Again, this commentary line may be empty. After the
+ commentaries, the name of the sequence is written on a separate
line. At last, the sequence itself is written on the following lines.
}
- \item{"clustal"}{The CLUSTAL format (*.aln) is the format of the
- ClustalW multialignment tool output. It can be described as follows.
- The word CLUSTAL is on the first line of the file. The alignment
- is displayed in blocks of a fixed length, each line in the block
- corresponding to one sequence. Each line of each block starts with
- the sequence name (maximum of 10 characters), followed by at least
- one space character. The sequence is then displayed in upper or
- lower cases, '-' denotes gaps. The residue number may be displayed
+ \item{"clustal"}{The CLUSTAL format (*.aln) is the format of the
+ ClustalW multialignment tool output. It can be described as follows.
+ The word CLUSTAL is on the first line of the file. The alignment
+ is displayed in blocks of a fixed length, each line in the block
+ corresponding to one sequence. Each line of each block starts with
+ the sequence name (maximum of 10 characters), followed by at least
+ one space character. The sequence is then displayed in upper or
+ lower cases, '-' denotes gaps. The residue number may be displayed
at the end of the first line of each block.
}
- \item{"msf"}{ MSF is the multiple sequence alignment format of the
- GCG sequence analysis package. It begins with the line (all
- uppercase) !!NA\_MULTIPLE\_ALIGNMENT 1.0 for nucleic acid sequences
- or !!AA\_MULTIPLE\_ALIGNMENT 1.0 for amino acid sequences. Do
- not edit or delete the file type if its present.(optional).
- A description line which contains informative text describing what
- is in the file. You can add this information to the top of the MSF
- file using a text editor.(optional) A dividing line which contains
- the number of bases or residues in the sequence, when the file was
- created, and importantly, two dots (..) which act as a divider
- between the descriptive information and the following sequence
- information.(required) msf files contain some other information:
- the Name/Weight, a Separating Line which must include two slashes
- (//) to divide the name/weight information from the sequence
+ \item{"msf"}{ MSF is the multiple sequence alignment format of the
+ GCG sequence analysis package. It begins with the line (all
+ uppercase) !!NA_MULTIPLE_ALIGNMENT 1.0 for nucleic acid sequences
+ or !!AA_MULTIPLE_ALIGNMENT 1.0 for amino acid sequences. Do
+ not edit or delete the file type if its present.(optional).
+ A description line which contains informative text describing what
+ is in the file. You can add this information to the top of the MSF
+ file using a text editor.(optional) A dividing line which contains
+ the number of bases or residues in the sequence, when the file was
+ created, and importantly, two dots (..) which act as a divider
+ between the descriptive information and the following sequence
+ information.(required) msf files contain some other information:
+ the Name/Weight, a Separating Line which must include two slashes
+ (//) to divide the name/weight information from the sequence
alignment.(required) and the multiple sequence alignment.
}
- \item{"phylip"}{ PHYLIP is a tree construction program. The format
- is as follows: the number of sequences and their length (in characters)
- is on the first line of the file. The alignment is displayed in an
- interleaved or sequential format. The sequence names are limited
- to 10 characters and may contain blanks.
+ \item{"phylip"}{ PHYLIP is a tree construction program. The format
+ is as follows: the number of sequences and their length (in characters)
+ is on the first line of the file. The alignment is displayed in an
+ interleaved or sequential format. The sequence names are limited
+ to 10 characters and may contain blanks.
}
- \item{"fasta"}{ Sequence in fasta format begins with a single-line
- description (distinguished by a greater-than (>) symbol), followed
+ \item{"fasta"}{ Sequence in fasta format begins with a single-line
+ description (distinguished by a greater-than (>) symbol), followed
by sequence data on the next line.
}
}
@@ -73,22 +73,22 @@
\value{
An object of class \code{alignment} which is a list with the following components:
\item{nb}{ the number of aligned sequences }
- \item{nam}{ a vector of strings containing the names of the aligned sequences }
- \item{seq}{ a vector of strings containing the aligned sequences}
+ \item{nam}{ a vector of strings containing the names of the aligned sequences }
+ \item{seq}{ a vector of strings containing the aligned sequences}
\item{com}{ a vector of strings containing the commentaries for each sequence or \code{NA} if there are no comments }
}
-\references{
+\references{
\code{citation("seqinr")}
}
\author{D. Charif, J.R. Lobry}
\seealso{
-To read aligned sequences in NEXUS format, see the function
+To read aligned sequences in NEXUS format, see the function
\code{read.nexus} that was available in the \code{CompPairWise} package
(not sure it is still maintained as of 09/09/09).
The NEXUS format was mainly used by the non-GPL commercial PAUP
software.
-Related functions: \code{\link{as.matrix.alignment}}, \code{\link{read.fasta}},
+Related functions: \code{\link{as.matrix.alignment}}, \code{\link{read.fasta}},
\code{\link{write.fasta}}, \code{\link{reverse.align}}, \code{\link{dist.alignment}}.
}
@@ -119,15 +119,14 @@
# whole headers for sequences names.
#
-whole.header.test <-
- read.alignment(file = system.file("sequences/LTPs128_SSU_aligned_First_Two.fasta",
+whole.header.test <-
+ read.alignment(file = system.file("sequences/LTPs128_SSU_aligned_First_Two.fasta",
package = "seqinr"), format = "fasta", whole.header = TRUE)
whole.header.test$nam
# Sould be:
#
-# [1] "D50541\t1\t1411\t1411bp\trna\tAbiotrophia defectiva\tAerococcaceae"
+# [1] "D50541\t1\t1411\t1411bp\trna\tAbiotrophia defectiva\tAerococcaceae"
# [2] "KP233895\t1\t1520\t1520bp\trna\tAbyssivirga alkaniphila\tLachnospiraceae"
#
}
-
More information about the Seqinr-commits
mailing list