# -*- tab-width:2;indent-tabs-mode:t;show-trailing-whitespace:t;rm-trailing-spaces:t -*-
# vi: set ts=2 noet:
library(plyr)
library(dplyr)
library(readr)
library(seqinr)
library(stringr)
library(Bethany)
library(BioChemPantry)
source("~/work/sets/uniprot_idmapping/scripts/uniprot_id_map.R")
pantry <- get_pantry("hgnc_151123")
staging_directory <- get_staging_directory("hgnc_151123")
genes <- pantry %>% tbl("genes") %>% collect
hgnc_human_fname <- paste0(staging_directory, "/data/uniprot_151123/hgnc_human.fasta")
scores <- blastp(hgnc_human_fname, hgnc_human_fname, "hgnc_human")
scores <- scores %>%
dplyr::rename(
uniprot_accn1 = ref_target,
uniprot_accn1 = query_target) %>%
dplyr::arrange(EValue) %>%
dplyr::distinct(target1, target2)
scores <- scores %>%
rename(
uniprot_accn1 = target1,
uniprot_accn2 = target2) %>%
left_join(
genes %>%
select(
symbol1 = symbol,
uniprot_accn1 = uniprot_accn,
uniprot_entry1 = uniprot_entry),
by="uniprot_accn1") %>%
left_join(
genes %>%
select(
symbol2 = symbol,
uniprot_accn2 = uniprot_accn,
uniprot_entry2 = uniprot_entry),
by="uniprot_accn2")
pantry %>% copy_to(
df=scores,
name="blastp_target_vs_target",
temporary=F,
indexes=list(
"symbol1",
"uniprot_accn1",
"uniprot_entry1",
"symbol2",
"uniprot_accn2",
"uniprot_entry2",
c("symbol1", "symbol2"),
c("uniprot_accn1", "uniprot_accn2"),
c("uniprot_entry1", "uniprot_entry2")),
fast=T)
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