Improve gitignore, add stats script

.gitignore

@@ -6,3 +6,4 @@
 Rplot001.pdf
 playground/
 .~lock*
+AncientMetagenomeDir-*.zip

CHANGELOG.md

@@ -51,7 +51,6 @@ and this project follows to [Calendar Versioning](https://calver.org/).
 - Fixed Schuenemann2011 Put the accession ID of the full plasmid sequence not partial
 - Fixed Martin2013 corrected archive name (incorrectly reported in publication)
 - Fixed Seersholm2016 archive ENA (from incorrectly specified as SRA)
-- Fixed Vagene2018 polymerase typo
 - Fixed Eisenhofer2020 date rounding error (originally added 230 rather than 200)
 - Fixed BravoLopez2020 typo in site name (Inmaculate -> Immaculate)
 - Fixed Willmann2018 project_name (originally missing the second 'n')

assets/analysis/release-stats-script.R

@@ -0,0 +1,90 @@
+#!/usr/bin/env R
+
+library(tidyverse)
+library(zen4R)
+
+##############################
+## Release Stats Generation ##
+##############################
+
+
+## Download previous release from Zenodo: https://doi.org/10.5281/zenodo.3980833
+
+## Load previous release files
+old_path <- "/home/jfellows/Downloads/AncientMetagenomeDir-v21.09/SPAAM-community-AncientMetagenomeDir-d9610d3/"
+
+old_senv <- read_tsv(paste0(old_path, "ancientmetagenome-environmental/ancientmetagenome-environmental.tsv"))
+old_shos <- read_tsv(paste0(old_path, "ancientmetagenome-hostassociated/ancientmetagenome-hostassociated.tsv"))
+old_ssin <- read_tsv(paste0(old_path, "ancientsinglegenome-hostassociated/ancientsinglegenome-hostassociated.tsv"))
+
+## after v22.09 onwards
+#old_senv <- read_tsv(paste0(old_path, "ancientmetagenome-environmental/samples/ancientmetagenome-environmental_samples.tsv"))
+#old_shos <- read_tsv(paste0(old_path, "ancientmetagenome-hostassociated/samples/ancientmetagenome-hostassociated_samples.tsv"))
+#old_ssin <- read_tsv(paste0(old_path, "ancientsinglegenome-hostassociated/samples/ancientsinglegenome-hostassociated_samples.tsv"))
+#old_lenv <- read_tsv(paste0(old_path, "ancientmetagenome-environmental/libraries/ancientmetagenome-environmental_libraries.tsv"))
+#old_lhos <- read_tsv(paste0(old_path, "ancientmetagenome-hostassociated/libraries/ancientmetagenome-hostassociated_libraries.tsv"))
+#old_lsin <- read_tsv(paste0(old_path, "ancientsinglegenome-hostassociated/libraries/ancientsinglegenome-hostassociated_libraries.tsv"))
+
+## Load new release files
+
+new_senv <- read_tsv("ancientmetagenome-environmental/samples/ancientmetagenome-environmental_samples.tsv")
+new_shos <- read_tsv("ancientmetagenome-hostassociated/samples/ancientmetagenome-hostassociated_samples.tsv")
+new_ssin <- read_tsv("ancientsinglegenome-hostassociated/samples/ancientsinglegenome-hostassociated_samples.tsv")
+new_lenv <- read_tsv("ancientmetagenome-environmental/libraries/ancientmetagenome-environmental_libraries.tsv")
+new_lhos <- read_tsv("ancientmetagenome-hostassociated/libraries/ancientmetagenome-hostassociated_libraries.tsv")
+new_lsin <- read_tsv("ancientsinglegenome-hostassociated/libraries/ancientsinglegenome-hostassociated_libraries.tsv")
+
+## Find differences
+
+## New
+print("PUBLICATIONS")
+
+old_pubs <- c(old_senv$project_name, old_shos$project_name, old_ssin$project_name) %>% unique
+new_pubs <- c(new_senv$project_name, new_shos$project_name, new_ssin$project_name) %>% unique
+
+## DOESN'T REPORT REMOVED!
+print(paste("New:", length(new_pubs), "Old:", length(old_pubs), "Gain:", length(new_pubs) - length(old_pubs)))
+
+print("SAMPLES")
+for ( i in c("senv", "shos", "ssin")) {
+  old_res <- paste0("old_", i)
+  new_res <- paste0("new_", i)
+
+  old_n <- nrow(eval(as.name(old_res)))
+  new_n <-  nrow(eval(as.name(new_res)))
+
+  new_diff <- new_n - old_n
+
+  print(paste(old_res,":", old_n))
+  print(paste(new_res,":", new_n))
+  print(paste(i, "change:", new_diff))
+}
+
+print("LIBRARIES")
+for ( i in c("lenv", "lhos", "lsin")) {
+  #old_res <- paste0("old_", i)
+  new_res <- paste0("new_", i)
+
+  #old_n <- nrow(eval(as.name(old_res)))
+  new_n <-  nrow(eval(as.name(new_res)))
+
+  #new_diff <- new_n - old_n
+
+  #print(paste(old_res,":", old_n))
+  print(paste(new_res,":", new_n))
+  #print(paste("change:", new_diff))
+}
+
+### MESSAGE
+
+##Release v22.09 includes 7 new publications, representing XXX new ancient host-associated metagenome samples, XX new ancient microbial genomes, and XX new ancient environmental samples.
+
+##It adds XXX new new ancient host-associated metagenome libraries, XX new ancient microbial genome libraries, and XX new ancient environmental libraries.
+
+
+##This brings the repository to a total of 132 publications, 1038 new ancient host-associated metagenome samples, 368 ancient microbial genomes, and 375 new ancient environmental samples.
+
+
+## Load latest release
+
+## Compare and print stats test