available on CRAN

ropensci · Nov 26, 2018 · 5fdb176 · 5fdb176
1 parent 87501dd
commit 5fdb176
Show file tree

Hide file tree

Showing 2 changed files with 44 additions and 53 deletions.
diff --git a/README.Rmd b/README.Rmd
@@ -21,7 +21,7 @@ assignInNamespace(x = 'gb_build2', value = restez:::gb_build,
 
 # Locally query GenBank <img src="https://raw.githubusercontent.com/ropensci/restez/master/logo.png" height="200" align="right"/>
 
-[![Build Status](https://travis-ci.org/ropensci/restez.svg?branch=master)](https://travis-ci.org/ropensci/restez) [![Coverage Status](https://coveralls.io/repos/github/ropensci/restez/badge.svg?branch=master)](https://coveralls.io/github/ropensci/restez?branch=master) [![ROpenSci status](https://badges.ropensci.org/232_status.svg)](https://github.com/ropensci/onboarding/issues/232) <!--[![CRAN downloads](http://cranlogs.r-pkg.org/badges/grand-total/restez)](https://CRAN.R-project.org/package=restez)--> [![DOI](https://zenodo.org/badge/129107980.svg)](https://zenodo.org/badge/latestdoi/129107980)
+[![Build Status](https://travis-ci.org/ropensci/restez.svg?branch=master)](https://travis-ci.org/ropensci/restez) [![Coverage Status](https://coveralls.io/repos/github/ropensci/restez/badge.svg?branch=master)](https://coveralls.io/github/ropensci/restez?branch=master) [![ROpenSci status](https://badges.ropensci.org/232_status.svg)](https://github.com/ropensci/onboarding/issues/232) [![CRAN downloads](http://cranlogs.r-pkg.org/badges/grand-total/restez)](https://CRAN.R-project.org/package=restez) [![DOI](https://zenodo.org/badge/129107980.svg)](https://zenodo.org/badge/latestdoi/129107980)
 
 Download parts of [NCBI's GenBank](https://www.ncbi.nlm.nih.gov/nuccore) to a local folder and create a simple SQL-like database. Use 'get' tools to query the database by accession IDs. [rentrez](https://github.com/ropensci/rentrez) wrappers are available, so that if sequences are not available locally they can be searched for online through [Entrez](https://www.ncbi.nlm.nih.gov/books/NBK25500/).
 
@@ -39,7 +39,13 @@ This package aims to make sequence retrieval more efficient by allowing a user t
 
 ## Installation
 
-You can install `restez` from GitHub with:
+`restez` is available via CRAN and can be installed:
+
+```{r cran-installation, include=TRUE, echo=TRUE, eval=FALSE}
+install.packages("restez")
+```
+
+Or you can install the development version via GitHub with:
 
 ```{r gh-installation, include=TRUE, echo=TRUE, eval=FALSE}
 # install.packages("devtools")

diff --git a/README.md b/README.md
@@ -5,7 +5,7 @@
 Locally query GenBank <img src="https://raw.githubusercontent.com/ropensci/restez/master/logo.png" height="200" align="right"/>
 ===============================================================================================================================
 
-[![Build Status](https://travis-ci.org/ropensci/restez.svg?branch=master)](https://travis-ci.org/ropensci/restez) [![Coverage Status](https://coveralls.io/repos/github/ropensci/restez/badge.svg?branch=master)](https://coveralls.io/github/ropensci/restez?branch=master) [![ROpenSci status](https://badges.ropensci.org/232_status.svg)](https://github.com/ropensci/onboarding/issues/232) <!--[![CRAN downloads](http://cranlogs.r-pkg.org/badges/grand-total/restez)](https://CRAN.R-project.org/package=restez)--> [![DOI](https://zenodo.org/badge/129107980.svg)](https://zenodo.org/badge/latestdoi/129107980)
+[![Build Status](https://travis-ci.org/ropensci/restez.svg?branch=master)](https://travis-ci.org/ropensci/restez) [![Coverage Status](https://coveralls.io/repos/github/ropensci/restez/badge.svg?branch=master)](https://coveralls.io/github/ropensci/restez?branch=master) [![ROpenSci status](https://badges.ropensci.org/232_status.svg)](https://github.com/ropensci/onboarding/issues/232) [![CRAN downloads](http://cranlogs.r-pkg.org/badges/grand-total/restez)](https://CRAN.R-project.org/package=restez) [![DOI](https://zenodo.org/badge/129107980.svg)](https://zenodo.org/badge/latestdoi/129107980)
 
 Download parts of [NCBI's GenBank](https://www.ncbi.nlm.nih.gov/nuccore) to a local folder and create a simple SQL-like database. Use 'get' tools to query the database by accession IDs. [rentrez](https://github.com/ropensci/rentrez) wrappers are available, so that if sequences are not available locally they can be searched for online through [Entrez](https://www.ncbi.nlm.nih.gov/books/NBK25500/).
 
@@ -25,7 +25,13 @@ This package aims to make sequence retrieval more efficient by allowing a user t
 Installation
 ------------
 
-You can install `restez` from GitHub with:
+`restez` is available via CRAN and can be installed:
+
+``` r
+install.packages("restez")
+```
+
+Or you can install the development version via GitHub with:
 
 ``` r
 # install.packages("devtools")
@@ -71,55 +77,48 @@ id <- sample(list_db_ids(), 1)
 # sequences
 seq <- gb_sequence_get(id)[[1]]
 str(seq)
-#>  chr "GATCCGGCCGCAGCCGCAGTGTCGGCATTGTTCCCGCTGGGCGAGACGGAGATCACCCTCACGGTCTTCTCGGGCGATCAGTCCGACGCCGAGACGACGACGGTGACGATC"| __truncated__
+#>  chr "CCCTCGAAGCCCTCATCGCTGAGGCTGCCCCGGATACCGAGGTTCTTTACAAAGACCGGATGGACTCCAGCAACGACACCTCGCTGGTAACAGCCCTCATGACGACCTATGACGGCACTCTTGAGG"
 # definitions
 def <- gb_definition_get(id)[[1]]
 print(def)
-#> [1] "Unidentified clone B15 DNA sequence from ocean beach sand"
+#> [1] "Unidentified RNA clone P10.11"
 # organisms
 org <- gb_organism_get(id)[[1]]
 print(org)
 #> [1] "unidentified"
 # or whole records
 rec <- gb_record_get(id)[[1]]
 cat(rec)
-#> LOCUS       AF298094                 581 bp    DNA     linear   UNA 23-NOV-2000
-#> DEFINITION  Unidentified clone B15 DNA sequence from ocean beach sand.
-#> ACCESSION   AF298094
-#> VERSION     AF298094.1
+#> LOCUS       AF040893                 126 bp    RNA     linear   UNA 06-MAR-1998
+#> DEFINITION  Unidentified RNA clone P10.11.
+#> ACCESSION   AF040893
+#> VERSION     AF040893.1
 #> KEYWORDS    .
 #> SOURCE      unidentified
 #>   ORGANISM  unidentified
 #>             unclassified sequences.
-#> REFERENCE   1  (bases 1 to 581)
-#>   AUTHORS   Naviaux,R.K.
-#>   TITLE     Sand DNA: a multigenomic library on the beach
+#> REFERENCE   1  (bases 1 to 126)
+#>   AUTHORS   Pan,W.S., Ji,X.Y., Wang,H.T. and Zhong,Y.S.
+#>   TITLE     RNA from plasma of patient NO.10
 #>   JOURNAL   Unpublished
-#> REFERENCE   2  (bases 1 to 581)
-#>   AUTHORS   Naviaux,R.K.
+#> REFERENCE   2  (bases 1 to 126)
+#>   AUTHORS   Pan,W.S., Ji,X.Y., Wang,H.T. and Zhong,Y.S.
 #>   TITLE     Direct Submission
-#>   JOURNAL   Submitted (21-AUG-2000) Medicine, University of California, San
-#>             Diego School of Medicine, 200 West Arbor Drive, San Diego, CA
-#>             92103-8467, USA
+#>   JOURNAL   Submitted (31-DEC-1997) Department of Applied Molecular Biology,
+#>             Microbiology & Epidemiology Institution, 20 Dongdajie Street,
+#>             Fengtai, Beijing 100071, China
 #> FEATURES             Location/Qualifiers
-#>      source          1..581
+#>      source          1..126
 #>                      /organism="unidentified"
-#>                      /mol_type="genomic DNA"
+#>                      /mol_type="genomic RNA"
 #>                      /db_xref="taxon:32644"
-#>                      /clone="B15"
-#>                      /note="anonymous environmental sample sequence from ocean
-#>                      beach sand"
+#>                      /clone="P10.11"
+#>                      /note="from the plasma of patient no.10, a person infected
+#>                      by an unknown hepatitis virus"
 #> ORIGIN      
-#>         1 gatccggccg cagccgcagt gtcggcattg ttcccgctgg gcgagacgga gatcaccctc
-#>        61 acggtcttct cgggcgatca gtccgacgcc gagacgacga cggtgacgat cgaggacacg
-#>       121 accgcgccga cgttcaccca cgcactgggt gatgtccttc cgatggtgac gaaggaggca
-#>       181 acggagcccg gagggcatga cttcagcccg gccacgccgg acgcctggga ccatggagac
-#>       241 agcgacctcg acatcgcttg cggtacggaa ctcccgcatc tcttcccgat cggggataca
-#>       301 gagatcacct ggacggcgac ggacgatcag gacctttcga cgacggcaac gcagatcatc
-#>       361 cggatcgagg acaacacgcc gccgaccttc atccagcgcg atgatcaggt cgtggcgacc
-#>       421 acgtacgatc cggtcggtct caggaaggag cacgttccgc tcgcgggcac cgtcatcgcg
-#>       481 gtggacttcg gacagcccgt accgctcacg aacaccgccc cggacgtntt tcggttgggg
-#>       541 agcacggaga tncctggacc gcgacggtgc gtncgggaac t
+#>         1 ccctcgaagc cctcatcgct gaggctgccc cggataccga ggttctttac aaagaccgga
+#>        61 tggactccag caacgacacc tcgctggtaa cagccctcat gacgacctat gacggcactc
+#>       121 ttgagg
 #> //
 ```
 
@@ -129,32 +128,18 @@ cat(rec)
 # use the entrez_* wrappers to access GB data
 res <- entrez_fetch(db = 'nucleotide', id = id, rettype = 'fasta')
 cat(res)
-#> >AF298094.1 Unidentified clone B15 DNA sequence from ocean beach sand
-#> GATCCGGCCGCAGCCGCAGTGTCGGCATTGTTCCCGCTGGGCGAGACGGAGATCACCCTCACGGTCTTCT
-#> CGGGCGATCAGTCCGACGCCGAGACGACGACGGTGACGATCGAGGACACGACCGCGCCGACGTTCACCCA
-#> CGCACTGGGTGATGTCCTTCCGATGGTGACGAAGGAGGCAACGGAGCCCGGAGGGCATGACTTCAGCCCG
-#> GCCACGCCGGACGCCTGGGACCATGGAGACAGCGACCTCGACATCGCTTGCGGTACGGAACTCCCGCATC
-#> TCTTCCCGATCGGGGATACAGAGATCACCTGGACGGCGACGGACGATCAGGACCTTTCGACGACGGCAAC
-#> GCAGATCATCCGGATCGAGGACAACACGCCGCCGACCTTCATCCAGCGCGATGATCAGGTCGTGGCGACC
-#> ACGTACGATCCGGTCGGTCTCAGGAAGGAGCACGTTCCGCTCGCGGGCACCGTCATCGCGGTGGACTTCG
-#> GACAGCCCGTACCGCTCACGAACACCGCCCCGGACGTNTTTCGGTTGGGGAGCACGGAGATNCCTGGACC
-#> GCGACGGTGCGTNCGGGAACT
+#> >AF040893.1 Unidentified RNA clone P10.11
+#> CCCTCGAAGCCCTCATCGCTGAGGCTGCCCCGGATACCGAGGTTCTTTACAAAGACCGGATGGACTCCAG
+#> CAACGACACCTCGCTGGTAACAGCCCTCATGACGACCTATGACGGCACTCTTGAGG
 # if the id is not in the local database
 # these wrappers will search online via the rentrez package
 res <- entrez_fetch(db = 'nucleotide', id = c('S71333.1', id),
                     rettype = 'fasta')
 #> [1] id(s) are unavailable locally, searching online.
 cat(res)
-#> >AF298094.1 Unidentified clone B15 DNA sequence from ocean beach sand
-#> GATCCGGCCGCAGCCGCAGTGTCGGCATTGTTCCCGCTGGGCGAGACGGAGATCACCCTCACGGTCTTCT
-#> CGGGCGATCAGTCCGACGCCGAGACGACGACGGTGACGATCGAGGACACGACCGCGCCGACGTTCACCCA
-#> CGCACTGGGTGATGTCCTTCCGATGGTGACGAAGGAGGCAACGGAGCCCGGAGGGCATGACTTCAGCCCG
-#> GCCACGCCGGACGCCTGGGACCATGGAGACAGCGACCTCGACATCGCTTGCGGTACGGAACTCCCGCATC
-#> TCTTCCCGATCGGGGATACAGAGATCACCTGGACGGCGACGGACGATCAGGACCTTTCGACGACGGCAAC
-#> GCAGATCATCCGGATCGAGGACAACACGCCGCCGACCTTCATCCAGCGCGATGATCAGGTCGTGGCGACC
-#> ACGTACGATCCGGTCGGTCTCAGGAAGGAGCACGTTCCGCTCGCGGGCACCGTCATCGCGGTGGACTTCG
-#> GACAGCCCGTACCGCTCACGAACACCGCCCCGGACGTNTTTCGGTTGGGGAGCACGGAGATNCCTGGACC
-#> GCGACGGTGCGTNCGGGAACT
+#> >AF040893.1 Unidentified RNA clone P10.11
+#> CCCTCGAAGCCCTCATCGCTGAGGCTGCCCCGGATACCGAGGTTCTTTACAAAGACCGGATGGACTCCAG
+#> CAACGACACCTCGCTGGTAACAGCCCTCATGACGACCTATGACGGCACTCTTGAGG
 #> 
 #> >S71333.1 alpha 1,3 galactosyltransferase [New World monkeys, mermoset lymphoid cell line B95.8, mRNA Partial, 1131 nt]
 #> ATGAATGTCAAAGGAAAAGTAATTCTGTCGATGCTGGTTGTCTCAACTGTGATTGTTGTGTTTTGGGAAT