[CHNOSZ-commits] r220 - in pkg/CHNOSZ: . inst inst/extdata/refseq man

[noreply at r-forge.r-project.org]

Author: jedick
Date: 2017-09-26 15:42:26 +0200 (Tue, 26 Sep 2017)
New Revision: 220

Modified:
   pkg/CHNOSZ/DESCRIPTION
   pkg/CHNOSZ/inst/NEWS
   pkg/CHNOSZ/inst/extdata/refseq/README.txt
   pkg/CHNOSZ/inst/extdata/refseq/taxid_names.csv.xz
   pkg/CHNOSZ/man/extdata.Rd
Log:
reduce size of extdata/refseq/taxid_names.csv.xz


Modified: pkg/CHNOSZ/DESCRIPTION
===================================================================
--- pkg/CHNOSZ/DESCRIPTION	2017-09-26 13:11:14 UTC (rev 219)
+++ pkg/CHNOSZ/DESCRIPTION	2017-09-26 13:42:26 UTC (rev 220)
@@ -1,6 +1,6 @@
 Date: 2017-09-26
 Package: CHNOSZ
-Version: 1.1.0-18
+Version: 1.1.0-19
 Title: Thermodynamic Calculations for Geobiochemistry
 Author: Jeffrey Dick
 Maintainer: Jeffrey Dick <j3ffdick at gmail.com>

Modified: pkg/CHNOSZ/inst/NEWS
===================================================================
--- pkg/CHNOSZ/inst/NEWS	2017-09-26 13:11:14 UTC (rev 219)
+++ pkg/CHNOSZ/inst/NEWS	2017-09-26 13:42:26 UTC (rev 220)
@@ -1,4 +1,4 @@
-CHANGES IN CHNOSZ 1.1.0-18 (2017-09-26)
+CHANGES IN CHNOSZ 1.1.0-19 (2017-09-26)
 ---------------------------------------
 
 MAJOR CHANGES:
@@ -57,6 +57,9 @@
 - calculations of the g function (but not its derivatives) are now
   enabled for DEW and IAPWS-95.
 
+- To save space, taxid_names.csv has been trimmed to hold only those
+  taxids listed in extdata/bison/gi.taxid.txt.
+
 CHANGES IN CHNOSZ 1.1.0 (2017-05-04)
 ------------------------------------
 

Modified: pkg/CHNOSZ/inst/extdata/refseq/README.txt
===================================================================
--- pkg/CHNOSZ/inst/extdata/refseq/README.txt	2017-09-26 13:11:14 UTC (rev 219)
+++ pkg/CHNOSZ/inst/extdata/refseq/README.txt	2017-09-26 13:42:26 UTC (rev 220)
@@ -2,7 +2,7 @@
 # RefSeq database (release 61, 2013-09-09)
 protein_refseq.csv: overall (average) amino acid composition of all proteins for each
   microbial genome in the RefSeq collection (n=6758)
-taxid_names.csv: taxid, phylum name and species name for 6758 microbial taxa
+taxid_names.csv: taxid, phylum name and species name for 788 microbial taxa
 
 # these functions/scripts have the following purpose (output files listed in parentheses):
 gencat.sh - extract gi number, taxid, sequence length from RefSeq release catalog (gi.taxid.txt)
@@ -39,6 +39,8 @@
     'names.dmp' and 'nodes.dmp' are present. these files can be downloaded from
     ftp://ftp.ncbi.nih.gov/pub/taxonomy/taxdump.tar.gz (accessed on 2013-09-18)
 10. source 'taxid.names.R' to generate the file 'taxid_names.csv' [~5.5 hours]
+10a. 20170926: To save space for the package, the file has been trimmed to
+     hold only those taxids listed in extdata/bison/gi.taxid.txt.
 
 # BLAST stuff (optional)
 11. run ls protein/*.gz > filelist

Modified: pkg/CHNOSZ/inst/extdata/refseq/taxid_names.csv.xz
===================================================================
(Binary files differ)

Modified: pkg/CHNOSZ/man/extdata.Rd
===================================================================
--- pkg/CHNOSZ/man/extdata.Rd	2017-09-26 13:11:14 UTC (rev 219)
+++ pkg/CHNOSZ/man/extdata.Rd	2017-09-26 13:42:26 UTC (rev 220)
@@ -76,6 +76,7 @@
     \item \code{taxid.names.R} Generate a table of scientific names for the provided taxids. Requires the complete \code{names.dmp} and \code{nodes.dmp} from NCBI taxonomy files.
     \item \code{taxid_names.csv.xz} Output from above.
       NOTE: For backward compatibility with the example BLAST files for the Bison Pool metagenome, the packaged file merges records for taxids found in either RefSeq 57 or 61.
+      NOTE 2: To save space for the package, the file has been trimmed to hold only those taxids listed in extdata/bison/gi.taxid.txt.
       Certain taxids in release 57 were not located in the current RefSeq catalog, probably related to the transition to the \dQuote{WP} multispecies accessions (\url{ftp://ftp.ncbi.nlm.nih.gov/refseq/release/announcements/WP-proteins-06.10.2013.pdf}).
       See example for \code{\link{id.blast}}.
   }