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G3viz · Jul 29, 2024 · 3f42971 · 3f42971
1 parent f303f99
commit 3f42971
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Showing 2 changed files with 5 additions and 5 deletions.
diff --git a/data/hgnc2pfam.df.rda b/data/hgnc2pfam.df.rda
diff --git a/prepare_data/generate_hgnc2pfam.R b/prepare_data/generate_hgnc2pfam.R
@@ -63,7 +63,7 @@ for(idx in 1:nrow(uniprot_to_parse_df)){
 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 <- "prepare_data/9606.tsv.gz"
-download.file(pfam_url, pfam_fn)
+# download.file(pfam_url, pfam_fn)
 
 # --------------------------
 message("Read Pfam information ...")
@@ -87,11 +87,11 @@ 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",
+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", compress = "xz")
+save(hgnc2pfam.df, file="data/hgnc2pfam.df.rda", compress = "xz")