From 7f16dc4d5da14061a5fb4a26c04bd5d23446354c Mon Sep 17 00:00:00 2001 From: Dominic Bennett Date: Wed, 27 Jun 2018 16:33:21 +0200 Subject: [PATCH] smaller outline image, paper date update --- README.Rmd | 2 +- README.md | 2 +- docs/index.html | 4 +--- docs/reference/db_delete.html | 4 ++-- docs/reference/demo_db_create.html | 4 ++-- docs/reference/entrez_fetch.html | 4 ++-- docs/reference/gb_definition_get.html | 4 ++-- docs/reference/gb_fasta_get.html | 4 ++-- docs/reference/gb_organism_get.html | 4 ++-- docs/reference/gb_record_get.html | 4 ++-- docs/reference/gb_sequence_get.html | 4 ++-- docs/reference/gb_version_get.html | 4 ++-- docs/reference/is_in_db.html | 4 ++-- docs/reference/list_db_ids.html | 4 ++-- docs/reference/restez_path_get.html | 6 +++--- docs/reference/restez_status.html | 2 +- paper/paper.md | 2 +- 17 files changed, 30 insertions(+), 32 deletions(-) diff --git a/README.Rmd b/README.Rmd index ac248fc..cd5d024 100644 --- a/README.Rmd +++ b/README.Rmd @@ -27,7 +27,7 @@ Downloading sequences and sequence information from GenBank and related NCBI tax This package aims to make sequence retrieval more efficient by allowing a user to download large sections of the GenBank database to their local machine and query this local database either through package specific functions or Entrez wrappers. This process is more efficient as GenBank downloads are made via NCBI's FTP using compressed sequence files. With a good internet connection and a middle-of-the-road computer, a database comprising 20 GB of sequence information can be generated in less than 10 minutes. -![restez outline](https://github.com/AntonelliLab/restez/tree/master/paper/outline.png) + **For more detailed information on the pacakge's functions and detailed guides on downloading, constructing and querying a database, visit the [restez website](https://antonellilab.github.io/restez/index.html).** diff --git a/README.md b/README.md index e0d1ee6..854b804 100644 --- a/README.md +++ b/README.md @@ -17,7 +17,7 @@ Downloading sequences and sequence information from GenBank and related NCBI tax This package aims to make sequence retrieval more efficient by allowing a user to download large sections of the GenBank database to their local machine and query this local database either through package specific functions or Entrez wrappers. This process is more efficient as GenBank downloads are made via NCBI's FTP using compressed sequence files. With a good internet connection and a middle-of-the-road computer, a database comprising 20 GB of sequence information can be generated in less than 10 minutes. -![restez outline](https://github.com/AntonelliLab/restez/tree/master/paper/outline.png) + **For more detailed information on the pacakge's functions and detailed guides on downloading, constructing and querying a database, visit the [restez website](https://antonellilab.github.io/restez/index.html).** diff --git a/docs/index.html b/docs/index.html index f600d1f..8fda2b2 100644 --- a/docs/index.html +++ b/docs/index.html @@ -105,9 +105,7 @@

Vous entrez, vous rentrez et, maintenant, vous …. restez!

Downloading sequences and sequence information from GenBank and related NCBI taxonomic databases is often performed via the NCBI API, Entrez. Entrez, however, has a limit on the number of requests and downloading large amounts of sequence data in this way can be inefficient. For programmatic situations where multiple Entrez calls are made, downloading may take days, weeks or even months.

This package aims to make sequence retrieval more efficient by allowing a user to download large sections of the GenBank database to their local machine and query this local database either through package specific functions or Entrez wrappers. This process is more efficient as GenBank downloads are made via NCBI’s FTP using compressed sequence files. With a good internet connection and a middle-of-the-road computer, a database comprising 20 GB of sequence information can be generated in less than 10 minutes.

-
-restez outline

restez outline

-
+

For more detailed information on the pacakge’s functions and detailed guides on downloading, constructing and querying a database, visit the restez website.

diff --git a/docs/reference/db_delete.html b/docs/reference/db_delete.html index 9f90200..4d29b8f 100644 --- a/docs/reference/db_delete.html +++ b/docs/reference/db_delete.html @@ -157,8 +157,8 @@

See a

Examples

library(restez)
 fp <- tempdir()
-restez_path_set(filepath = fp)
#> ... Creating '/var/folders/ps/g89999v12490dmp0jnsfmykm0043m3/T//Rtmp1lZ1sb/restez'
-#> ... Creating '/var/folders/ps/g89999v12490dmp0jnsfmykm0043m3/T//Rtmp1lZ1sb/restez/downloads'
demo_db_create(n = 10)
+restez_path_set(filepath = fp)
#> ... Creating '/var/folders/ps/g89999v12490dmp0jnsfmykm0043m3/T//RtmpqJBaKI/restez'
+#> ... Creating '/var/folders/ps/g89999v12490dmp0jnsfmykm0043m3/T//RtmpqJBaKI/restez/downloads'
demo_db_create(n = 10)
 db_delete(everything = FALSE)
#> NULL
# Will not run: gb_sequence_get(id = 'demo_1')
 # only the SQL database is deleted
 db_delete(everything = TRUE)
#> NULL
# Now returns NULL
diff --git a/docs/reference/demo_db_create.html b/docs/reference/demo_db_create.html
index 7653187..285a054 100644
--- a/docs/reference/demo_db_create.html
+++ b/docs/reference/demo_db_create.html
@@ -163,8 +163,8 @@ 
See a
     
Examples

     
library(restez)
 # set the restez path to a temporary dir
-restez_path_set(filepath = tempdir())
#> ... Creating '/var/folders/ps/g89999v12490dmp0jnsfmykm0043m3/T//Rtmp1lZ1sb/restez'
-#> ... Creating '/var/folders/ps/g89999v12490dmp0jnsfmykm0043m3/T//Rtmp1lZ1sb/restez/downloads'
# create demo database
+restez_path_set(filepath = tempdir())
#> ... Creating '/var/folders/ps/g89999v12490dmp0jnsfmykm0043m3/T//RtmpqJBaKI/restez'
+#> ... Creating '/var/folders/ps/g89999v12490dmp0jnsfmykm0043m3/T//RtmpqJBaKI/restez/downloads'
# create demo database
 demo_db_create(n = 100)
 # in the demo, IDs are 'demo_1', 'demo_2' ...
 (gb_sequence_get(id = 'demo_1'))
#>       demo_1 
diff --git a/docs/reference/entrez_fetch.html b/docs/reference/entrez_fetch.html
index d7e996b..07feb8a 100644
--- a/docs/reference/entrez_fetch.html
+++ b/docs/reference/entrez_fetch.html
@@ -187,8 +187,8 @@ 
See a
 
     
Examples

     
library(restez)
-restez_path_set(tempdir())
#> ... Creating '/var/folders/ps/g89999v12490dmp0jnsfmykm0043m3/T//Rtmp1lZ1sb/restez'
-#> ... Creating '/var/folders/ps/g89999v12490dmp0jnsfmykm0043m3/T//Rtmp1lZ1sb/restez/downloads'
demo_db_create()
+restez_path_set(tempdir())
#> ... Creating '/var/folders/ps/g89999v12490dmp0jnsfmykm0043m3/T//RtmpqJBaKI/restez'
+#> ... Creating '/var/folders/ps/g89999v12490dmp0jnsfmykm0043m3/T//RtmpqJBaKI/restez/downloads'
demo_db_create()
 # return fasta record
 fasta_res <- entrez_fetch(db = 'nucleotide',
                           id = c('demo_1', 'demo_2'),
diff --git a/docs/reference/gb_definition_get.html b/docs/reference/gb_definition_get.html
index dcfbac0..b5bee15 100644
--- a/docs/reference/gb_definition_get.html
+++ b/docs/reference/gb_definition_get.html
@@ -160,8 +160,8 @@ 
See a
 
     
Examples

     
library(restez)
-restez_path_set(filepath = tempdir())
#> ... Creating '/var/folders/ps/g89999v12490dmp0jnsfmykm0043m3/T//Rtmp1lZ1sb/restez'
-#> ... Creating '/var/folders/ps/g89999v12490dmp0jnsfmykm0043m3/T//Rtmp1lZ1sb/restez/downloads'
demo_db_create()
+restez_path_set(filepath = tempdir())
#> ... Creating '/var/folders/ps/g89999v12490dmp0jnsfmykm0043m3/T//RtmpqJBaKI/restez'
+#> ... Creating '/var/folders/ps/g89999v12490dmp0jnsfmykm0043m3/T//RtmpqJBaKI/restez/downloads'
demo_db_create()
 (def <- gb_definition_get(id = 'demo_1'))
#>                                 demo_1 
 #> "A demonstration sequence | id demo_1" 
(defs <- gb_definition_get(id = c('demo_1', 'demo_2')))
#>                                 demo_1                                 demo_2 
 #> "A demonstration sequence | id demo_1" "A demonstration sequence | id demo_2" 

diff --git a/docs/reference/gb_fasta_get.html b/docs/reference/gb_fasta_get.html
index aee1b70..2e3959d 100644
--- a/docs/reference/gb_fasta_get.html
+++ b/docs/reference/gb_fasta_get.html
@@ -164,8 +164,8 @@ 
See a
 
     
Examples

     
library(restez)
-restez_path_set(filepath = tempdir())
#> ... Creating '/var/folders/ps/g89999v12490dmp0jnsfmykm0043m3/T//Rtmp1lZ1sb/restez'
-#> ... Creating '/var/folders/ps/g89999v12490dmp0jnsfmykm0043m3/T//Rtmp1lZ1sb/restez/downloads'
demo_db_create()
+restez_path_set(filepath = tempdir())
#> ... Creating '/var/folders/ps/g89999v12490dmp0jnsfmykm0043m3/T//RtmpqJBaKI/restez'
+#> ... Creating '/var/folders/ps/g89999v12490dmp0jnsfmykm0043m3/T//RtmpqJBaKI/restez/downloads'
demo_db_create()
 (fasta <- gb_fasta_get(id = 'demo_1'))
#>                                              demo_1 
 #> ">A demonstration sequence | id demo_1\nttgcgaaatt" 
(fastas <- gb_fasta_get(id = c('demo_1', 'demo_2')))
#>                                              demo_1 
 #> ">A demonstration sequence | id demo_1\nttgcgaaatt" 
diff --git a/docs/reference/gb_organism_get.html b/docs/reference/gb_organism_get.html
index 50af5d2..69ba22f 100644
--- a/docs/reference/gb_organism_get.html
+++ b/docs/reference/gb_organism_get.html
@@ -159,8 +159,8 @@ 
See a
 
     
Examples

     
library(restez)
-restez_path_set(filepath = tempdir())
#> ... Creating '/var/folders/ps/g89999v12490dmp0jnsfmykm0043m3/T//Rtmp1lZ1sb/restez'
-#> ... Creating '/var/folders/ps/g89999v12490dmp0jnsfmykm0043m3/T//Rtmp1lZ1sb/restez/downloads'
demo_db_create()
+restez_path_set(filepath = tempdir())
#> ... Creating '/var/folders/ps/g89999v12490dmp0jnsfmykm0043m3/T//RtmpqJBaKI/restez'
+#> ... Creating '/var/folders/ps/g89999v12490dmp0jnsfmykm0043m3/T//RtmpqJBaKI/restez/downloads'
demo_db_create()
 (org <- gb_organism_get(id = 'demo_1'))
#>              demo_1 
 #> "Unreal organism 1" 
(orgs <- gb_organism_get(id = c('demo_1', 'demo_2')))
#>              demo_1              demo_2 
 #> "Unreal organism 1" "Unreal organism 2" 

diff --git a/docs/reference/gb_record_get.html b/docs/reference/gb_record_get.html
index 299ca99..25fe993 100644
--- a/docs/reference/gb_record_get.html
+++ b/docs/reference/gb_record_get.html
@@ -160,8 +160,8 @@ 
See a
 
     
Examples

     
library(restez)
-restez_path_set(filepath = tempdir())
#> ... Creating '/var/folders/ps/g89999v12490dmp0jnsfmykm0043m3/T//Rtmp1lZ1sb/restez'
-#> ... Creating '/var/folders/ps/g89999v12490dmp0jnsfmykm0043m3/T//Rtmp1lZ1sb/restez/downloads'
demo_db_create()
+restez_path_set(filepath = tempdir())
#> ... Creating '/var/folders/ps/g89999v12490dmp0jnsfmykm0043m3/T//RtmpqJBaKI/restez'
+#> ... Creating '/var/folders/ps/g89999v12490dmp0jnsfmykm0043m3/T//RtmpqJBaKI/restez/downloads'
demo_db_create()
 (rec <- gb_record_get(id = 'demo_1'))
#>                                                                                                                                                                                                                                                                                                                                                                                                  demo_1 
 #> "LOCUS       [This is a mock GenBank data record]\nDEFINITION  A demonstration sequence | id demo_1\nACCESSION   demo_1\nVERSION     demo_1.3\nKEYWORDS    [keyword]\nSOURCE      [tissue, organism]\nORGANISM    Unreal organism 1\nREFERENCE   [reference data]\nAUTHORS     [all the authors]\nTITLE       [title]\nJOURNAL     [journal]\nFEATURES    [features]\nORIGIN\n        1 ttcagcccac\n//" 
(recs <- gb_record_get(id = c('demo_1', 'demo_2')))
#>                                                                                                                                                                                                                                                                                                                                                                                                  demo_1 
 #> "LOCUS       [This is a mock GenBank data record]\nDEFINITION  A demonstration sequence | id demo_1\nACCESSION   demo_1\nVERSION     demo_1.3\nKEYWORDS    [keyword]\nSOURCE      [tissue, organism]\nORGANISM    Unreal organism 1\nREFERENCE   [reference data]\nAUTHORS     [all the authors]\nTITLE       [title]\nJOURNAL     [journal]\nFEATURES    [features]\nORIGIN\n        1 ttcagcccac\n//" 
diff --git a/docs/reference/gb_sequence_get.html b/docs/reference/gb_sequence_get.html
index fc6149b..d2f078d 100644
--- a/docs/reference/gb_sequence_get.html
+++ b/docs/reference/gb_sequence_get.html
@@ -160,8 +160,8 @@ 
See a
 
     
Examples

     
library(restez)
-restez_path_set(filepath = tempdir())
#> ... Creating '/var/folders/ps/g89999v12490dmp0jnsfmykm0043m3/T//Rtmp1lZ1sb/restez'
-#> ... Creating '/var/folders/ps/g89999v12490dmp0jnsfmykm0043m3/T//Rtmp1lZ1sb/restez/downloads'
demo_db_create()
+restez_path_set(filepath = tempdir())
#> ... Creating '/var/folders/ps/g89999v12490dmp0jnsfmykm0043m3/T//RtmpqJBaKI/restez'
+#> ... Creating '/var/folders/ps/g89999v12490dmp0jnsfmykm0043m3/T//RtmpqJBaKI/restez/downloads'
demo_db_create()
 (seq <- gb_sequence_get(id = 'demo_1'))
#>       demo_1 
 #> "ctaggtatcc" 
(seqs <- gb_sequence_get(id = c('demo_1', 'demo_2')))
#>       demo_1       demo_2 
 #> "ctaggtatcc" "tgaacaccct" 

diff --git a/docs/reference/gb_version_get.html b/docs/reference/gb_version_get.html
index ce74364..c607623 100644
--- a/docs/reference/gb_version_get.html
+++ b/docs/reference/gb_version_get.html
@@ -160,8 +160,8 @@ 
See a
 
     
Examples

     
library(restez)
-restez_path_set(filepath = tempdir())
#> ... Creating '/var/folders/ps/g89999v12490dmp0jnsfmykm0043m3/T//Rtmp1lZ1sb/restez'
-#> ... Creating '/var/folders/ps/g89999v12490dmp0jnsfmykm0043m3/T//Rtmp1lZ1sb/restez/downloads'
demo_db_create()
+restez_path_set(filepath = tempdir())
#> ... Creating '/var/folders/ps/g89999v12490dmp0jnsfmykm0043m3/T//RtmpqJBaKI/restez'
+#> ... Creating '/var/folders/ps/g89999v12490dmp0jnsfmykm0043m3/T//RtmpqJBaKI/restez/downloads'
demo_db_create()
 (ver <- gb_version_get(id = 'demo_1'))
#>     demo_1 
 #> "demo_1.1" 
(vers <- gb_version_get(id = c('demo_1', 'demo_2')))
#>     demo_1     demo_2 
 #> "demo_1.1" "demo_2.2" 

diff --git a/docs/reference/is_in_db.html b/docs/reference/is_in_db.html
index a244506..1b1baf6 100644
--- a/docs/reference/is_in_db.html
+++ b/docs/reference/is_in_db.html
@@ -165,8 +165,8 @@ 
See a
     
Examples

     
library(restez)
 # set the restez path to a temporary dir
-restez_path_set(filepath = tempdir())
#> ... Creating '/var/folders/ps/g89999v12490dmp0jnsfmykm0043m3/T//Rtmp1lZ1sb/restez'
-#> ... Creating '/var/folders/ps/g89999v12490dmp0jnsfmykm0043m3/T//Rtmp1lZ1sb/restez/downloads'
# create demo database
+restez_path_set(filepath = tempdir())
#> ... Creating '/var/folders/ps/g89999v12490dmp0jnsfmykm0043m3/T//RtmpqJBaKI/restez'
+#> ... Creating '/var/folders/ps/g89999v12490dmp0jnsfmykm0043m3/T//RtmpqJBaKI/restez/downloads'
# create demo database
 demo_db_create(n = 100)
 # in the demo, IDs are 'demo_1', 'demo_2' ...
 ids <- c('thisisnotanid', 'demo_1', 'demo_2')
diff --git a/docs/reference/list_db_ids.html b/docs/reference/list_db_ids.html
index 640b1de..9d63d82 100644
--- a/docs/reference/list_db_ids.html
+++ b/docs/reference/list_db_ids.html
@@ -169,8 +169,8 @@ 
See a
 
     
Examples

     
library(restez)
-restez_path_set(filepath = tempdir())
#> ... Creating '/var/folders/ps/g89999v12490dmp0jnsfmykm0043m3/T//Rtmp1lZ1sb/restez'
-#> ... Creating '/var/folders/ps/g89999v12490dmp0jnsfmykm0043m3/T//Rtmp1lZ1sb/restez/downloads'
demo_db_create(n = 10)
+restez_path_set(filepath = tempdir())
#> ... Creating '/var/folders/ps/g89999v12490dmp0jnsfmykm0043m3/T//RtmpqJBaKI/restez'
+#> ... Creating '/var/folders/ps/g89999v12490dmp0jnsfmykm0043m3/T//RtmpqJBaKI/restez/downloads'
demo_db_create(n = 10)
 # Warning: not recommended for real databases
 #  with potentially millions of IDs
 all_ids <- list_db_ids()
diff --git a/docs/reference/restez_path_get.html b/docs/reference/restez_path_get.html
index 28ad784..2b53e51 100644
--- a/docs/reference/restez_path_get.html
+++ b/docs/reference/restez_path_get.html
@@ -152,9 +152,9 @@ 
See a
     
Examples

     
library(restez)
 # set a restez path with a tempdir
-restez_path_set(filepath = tempdir())
#> ... Creating '/var/folders/ps/g89999v12490dmp0jnsfmykm0043m3/T//Rtmp1lZ1sb/restez'
-#> ... Creating '/var/folders/ps/g89999v12490dmp0jnsfmykm0043m3/T//Rtmp1lZ1sb/restez/downloads'
# check what the set path is
-(restez_path_get())
#> [1] "/var/folders/ps/g89999v12490dmp0jnsfmykm0043m3/T//Rtmp1lZ1sb/restez"

+restez_path_set(filepath = tempdir())
#> ... Creating '/var/folders/ps/g89999v12490dmp0jnsfmykm0043m3/T//RtmpqJBaKI/restez'
+#> ... Creating '/var/folders/ps/g89999v12490dmp0jnsfmykm0043m3/T//RtmpqJBaKI/restez/downloads'
# check what the set path is
+(restez_path_get())
#> [1] "/var/folders/ps/g89999v12490dmp0jnsfmykm0043m3/T//RtmpqJBaKI/restez"

   

   
#> Checking setup status at '/var/folders/ps/g89999v12490dmp0jnsfmykm0043m3/T//Rtmp1lZ1sb/restez' ...
+restez_status()
#> Checking setup status at '/var/folders/ps/g89999v12490dmp0jnsfmykm0043m3/T//RtmpqJBaKI/restez' ...
 #> ... no files in 'downloads/'
 #> ... found 'sql_db' of 0 GB
#> [1] TRUE
db_delete()
#> NULL
restez_status()
#> Checking setup status at  ...
 #> ... restez path not set
#> You need to use restez_path_set()
#> [1] FALSE

diff --git a/paper/paper.md b/paper/paper.md
index 5941b98..a732642 100644
--- a/paper/paper.md
+++ b/paper/paper.md
@@ -33,7 +33,7 @@ affiliations:
    index: 4
  - name: Harvard University, Department of Organismic and Evolutionary Biology, Cambridge, MA 02138 U.S.A.
    index: 5
-date: 19 June 2018
+date: 27 June 2018
 bibliography: paper.bib
 ---