version 1.1.3

G3viz · Aug 25, 2020 · ae52b8e · ae52b8e
1 parent 2ce3a5e
commit ae52b8e
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Showing 2 changed files with 13 additions and 13 deletions.
diff --git a/R/zzz.R b/R/zzz.R
@@ -1,7 +1,7 @@
 .onAttach <- function(libname, pkgname){
   packageStartupMessage(
-    "g3viz: visualizing gene/genome/gentics data for fun.\n
-    - Pfam (v33.1)\n
+    "g3viz: visualizing gene/genome/gentics data for fun.
+    - Pfam (v33.1)
     - UniProt (date: 2020/08/24)\n
     Any questions, please send emails to <[email protected]> or post on GitHub <https://github.com/G3viz/g3viz/issues>."
     )

diff --git a/prepare_data/generate_hgnc2pfam.R b/prepare_data/generate_hgnc2pfam.R
@@ -28,7 +28,7 @@ message("Parsing filtered human data from UniProt ...")
 # - Length
 # --------------------------
 
-uniprot_fn = "uniprot-filtered-organism__Homo+sapiens+(Human)+[9606]_+AND+review--.tab.gz"
+uniprot_fn <- "uniprot-filtered-organism__Homo+sapiens+(Human)+[9606]_+AND+review--.tab.gz"
 
 uniprot.file <- gzcon(file(uniprot_fn, "r"))
 uniprot.txt <- readLines(uniprot.file)
@@ -57,8 +57,8 @@ for(idx in 1:nrow(uniprot.to.parse.df)){
 # Date: 2020-08-24
 # Version: 33.1
 message("Download Pfam data from Pfam website ...")
-pfam_url = "ftp://ftp.ebi.ac.uk/pub/databases/Pfam/current_release/proteomes/9606.tsv.gz"
-pfam_fn = "data-raw/hgnc_to_pfam/9606.tsv.gz"
+pfam_url <- "ftp://ftp.ebi.ac.uk/pub/databases/Pfam/current_release/proteomes/9606.tsv.gz"
+pfam_fn <- "9606.tsv.gz"
 download.file(pfam_url, pfam_fn)
 
 # --------------------------
@@ -75,17 +75,17 @@ pfam.df <- read.table(
   header = FALSE
 )
 
-colnames(pfam.df) = c("id", "align.start", "align.end", "start", "end",
-                      "hmm.acc", "hmm.name", "type", "hmm.start", "hmm.end", "hmm.length",
-                      "bit.score", "e.value", "clan")
-pfam.sub.df = pfam.df[, c("id", "start", "end", "hmm.acc", "hmm.name", "type")]
+colnames(pfam.df) <- c("id", "align.start", "align.end", "start", "end",
+                       "hmm.acc", "hmm.name", "type", "hmm.start", "hmm.end", "hmm.length",
+                       "bit.score", "e.value", "clan")
+pfam.sub.df <- pfam.df[, c("id", "start", "end", "hmm.acc", "hmm.name", "type")]
 
 # merge by UniProt
 message("Generating mapping table ...")
-hgnc2pfam.df = merge(uniprot.single.df, pfam.sub.df, by.x="uniprot", by.y = "id", all.x=TRUE, sort = FALSE)
-hgnc2pfam.df = hgnc2pfam.df[with(hgnc2pfam.df, order(symbol, uniprot, start, end)), ]
-hgnc2pfam.df = hgnc2pfam.df[, c("symbol", "uniprot", "length",
-                                "start", "end", "hmm.acc", "hmm.name", "type")]
+hgnc2pfam.df <- merge(uniprot.single.df, pfam.sub.df, by.x="uniprot", by.y = "id", all.x=TRUE, sort = FALSE)
+hgnc2pfam.df <- hgnc2pfam.df[with(hgnc2pfam.df, order(symbol, uniprot, start, end)), ]
+hgnc2pfam.df <- hgnc2pfam.df[, c("symbol", "uniprot", "length",
+                                 "start", "end", "hmm.acc", "hmm.name", "type")]
 
 # create Rdata, move this to "data" directory
 save(hgnc2pfam.df, file="hgnc2pfam.df.rda")