updating gene pages

[raynamharris]

as per #28 (comment)

the GETex, Transcripts, and UCSC browsers on only a few gene pages, as indicated by these files

• data/input/gene_IDs_for_expression_widget.txt
• data/input/gene_IDs_for_transcript_widget.txt
• data/input/gene_IDs_for_UCSC_genome_browser_widget.txt

the alias table and the Appyter widgets are displayed on nearly all gene pages. they are different for dev and for staging

• data/input/DEV_PORTAL__available_genes__2022-07-01.txt
• data/input/STAGING_PORTAL__available_genes__2022-07-13.txt

Here's what I've done to create these

1. Visit the Gene page on the CFDE Search Portal
2. Export the search results to a csv
3. Read the CSV file into R. Extract only the ENSG IDs. Save the list as a .txt doc
4. Update the Snakefule with the new data. Attempt to submit. Get error messages about failed genes.
5. Make list of failed genes. Remove failed genes for list of ENSG IDs in the .txt doc. Update Snakemake file. Resubmit. Repeat until successful.

library(tidyverse)

failedgenes <- c("ENSG00000093134",  "ENSG00000164393", "ENSG00000184293",
            "ENSG00000184293", "ENSG00000203812", "ENSG00000188707",
            "ENSG00000221995",  "ENSG00000214534", "ENSG00000225932",
            "ENSG00000244693", "ENSG00000256374", "ENSG00000263464",
            "ENSG00000105501", "ENSG00000161133")

missinggenes <-  read.table("./data/inputs/missing.txt")

df <- read.csv("/data/inputs/Gene.csv") %>%
  arrange(id) %>%
  filter(!id %in% failedgenes) %>%
  filter(!id %in% missinggenes$V1) %>%
  select(id)
names(df) <- NULL
head(df)

write.table(df, 
            "./data/inputs/STAGING_PORTAL__available_genes__2022-07-13.txt",
            row.names = F, quote = F)