[Seqinr-commits] r2116 - pkg/man

Tue May 18 16:02:37 CEST 2021

Author: simonpenel
Date: 2021-05-18 16:02:37 +0200 (Tue, 18 May 2021)
New Revision: 2116

Modified:
   pkg/man/oriloc.Rd
Log:
replace ftp by https in oriloc.Rd

Modified: pkg/man/oriloc.Rd
===================================================================

--- pkg/man/oriloc.Rd	2021-05-18 14:01:25 UTC (rev 2115)
+++ pkg/man/oriloc.Rd	2021-05-18 14:02:37 UTC (rev 2116)
@@ -2,7 +2,7 @@
 \alias{oriloc}
 \title{ Prediction of origin and terminus of replication in bacteria.}
 \description{
-This program finds the putative origin and terminus of 
+This program finds the putative origin and terminus of
 replication in procaryotic genomes. The program discriminates
 between codon positions.
 }
@@ -27,7 +27,7 @@
     glimmer program (\code{*.predict} in glimmer version 3)}
   \item{glimmer.version}{Numeric: glimmer version used, could be 2 or 3}
   \item{oldoriloc}{Logical: to be set at TRUE to reproduce the
-(deprecated) outputs of previous (publication date: 2000) version 
+(deprecated) outputs of previous (publication date: 2000) version
 of the oriloc program.}
   \item{gbk}{Character: the URL of a file in GenBank format. When provided
     \code{oriloc} use as input a single GenBank file instead of the \code{seq.fasta}
@@ -63,18 +63,18 @@
 T - A skew in third codon position, \code{y} for the cummulated C - G
 skew in third codon positions.
 }
-\references{ 
+\references{
 
 More illustrated explanations to help understand oriloc outputs
 are available there:
 \url{https://pbil.univ-lyon1.fr/software/Oriloc/howto.html}.\cr
 
-Examples of oriloc outputs on real sequence data are there: 
+Examples of oriloc outputs on real sequence data are there:
 \url{https://pbil.univ-lyon1.fr/software/Oriloc/index.html}.\cr
 
 The original paper for oriloc:\cr
 Frank, A.C., Lobry, J.R. (2000) Oriloc: prediction of replication
-boundaries in unannotated bacterial chromosomes. \emph{Bioinformatics}, 
+boundaries in unannotated bacterial chromosomes. \emph{Bioinformatics},
 \bold{16}:566-567.\cr
 \url{https://doi.org/10.1093/bioinformatics/16.6.560}\cr\cr
 
@@ -84,7 +84,7 @@
 \url{https://seqinr.r-forge.r-project.org/MicrTod_1999_26_164.pdf}\cr\cr
 
 An early and somewhat historical application of DNA-walks:\cr
-Lobry, J.R. (1996) A simple vectorial representation of DNA sequences 
+Lobry, J.R. (1996) A simple vectorial representation of DNA sequences
 for the detection of replication origins in bacteria. \emph{Biochimie},
 \bold{78}:323-326.\cr
 
@@ -93,11 +93,11 @@
 For a description of Glimmer 1.0 and 2.0 see:\cr
 
 Delcher, A.L., Harmon, D., Kasif, S., White, O., Salzberg, S.L. (1999)
-Improved microbial gene identification with GLIMMER, 
+Improved microbial gene identification with GLIMMER,
 \emph{Nucleic Acids Research}, \bold{27}:4636-4641.\cr
 
 Salzberg, S., Delcher, A., Kasif, S., White, O. (1998)
-Microbial gene identification using interpolated Markov models, 
+Microbial gene identification using interpolated Markov models,
 \emph{Nucleic Acids Research}, \bold{26}:544-548.\cr
 
 \code{citation("seqinr")}
@@ -105,23 +105,23 @@
 \author{J.R. Lobry, A.C. Frank}
 \seealso{ \code{\link{draw.oriloc}}, \code{\link{rearranged.oriloc}} }
 
-\note{ The method works only for genomes having a single origin of replication 
+\note{ The method works only for genomes having a single origin of replication
 from which the replication is bidirectional. To detect the composition changes,
-a DNA-walk is performed. In a 2-dimensional DNA walk, a C in the sequence 
-corresponds to the movement in the positive y-direction and G to a movement 
-in the negative y-direction. T and A are mapped by analogous steps along the 
-x-axis. When there is a strand asymmetry, this will form a trajectory that 
-turns at the origin and terminus of replication. Each step is the sum of 
-nucleotides in a gene in third codon positions. Then orthogonal regression is 
-used to find a line through this trajectory. Each point in the trajectory will 
-have a corresponding point on the line, and the coordinates of each are 
+a DNA-walk is performed. In a 2-dimensional DNA walk, a C in the sequence
+corresponds to the movement in the positive y-direction and G to a movement
+in the negative y-direction. T and A are mapped by analogous steps along the
+x-axis. When there is a strand asymmetry, this will form a trajectory that
+turns at the origin and terminus of replication. Each step is the sum of
+nucleotides in a gene in third codon positions. Then orthogonal regression is
+used to find a line through this trajectory. Each point in the trajectory will
+have a corresponding point on the line, and the coordinates of each are
 calculated. Thereafter, the distances from each of these points to the origin
-(of the plane), are calculated. These distances will represent a form of 
-cumulative skew. This permets us to make a plot with the gene position (gene 
+(of the plane), are calculated. These distances will represent a form of
+cumulative skew. This permets us to make a plot with the gene position (gene
 number, start or end position) on the x-axis and the cumulative skew (distance)
-at the y-axis. Depending on where the sequence starts, such a plot will display 
-one or two peaks. Positive peak means origin, and negative means terminus. 
-In the case of only one peak, the sequence starts at the origin or terminus 
+at the y-axis. Depending on where the sequence starts, such a plot will display
+one or two peaks. Positive peak means origin, and negative means terminus.
+In the case of only one peak, the sequence starts at the origin or terminus
 site. }
 \examples{
 \dontrun{
@@ -132,12 +132,12 @@
 #
 out <- oriloc()
 plot(out$st, out$sk, type = "l", xlab = "Map position in Kb",
-    ylab = "Cumulated composite skew", 
+    ylab = "Cumulated composite skew",
     main = expression(italic(Chlamydia~~trachomatis)~~complete~~genome))
 #
 # Example with a single GenBank file:
 #
-out2 <- oriloc(gbk="ftp://pbil.univ-lyon1.fr/pub/seqinr/data/ct.gbk")
+out2 <- oriloc(gbk="https://pbil.univ-lyon1.fr/datasets/seqinr/data/ct.gbk")
 draw.oriloc(out2)
 #
 # (some warnings are generated because of join in features and a gene that

