Can't load MPA output for Metaproteomics Data Processing

[Eoc-93]

Hello,

I am repeatedly getting an error message when I load my output from MPA. I check all fields in MPA for the csv output but when I load it into this tool I get an error saying more columns than column names. When I delete the extra columns I get the following error:
"try again network error"
<simpleError in if (stringr::str_detect(res$Cross.reference..EGGNOG., "COG\d{4}") & !is.na(res$Cross.reference..EGGNOG.)) { df_cog[i, "AllCOGs"] <- ifelse(df_cog[i, "AllCOGs"] == "", paste(unlist(stringr::str_extract_all(res$Cross.reference..EGGNOG., "COG\d{4}")), collapse = " "), paste(df_cog[i, "AllCOGs"], paste(unlist(stringr::str_extract_all(res$Cross.reference..EGGNOG., "COG\d{4}")), collapse = " ")))}: argument is of length zero>

Where the shiny app stops at:
Progress:
Read in Data
Getting data from UniProt
0.63%

I followed the instructions for exporting MPA tables from the walkthrough.

Thanks.

[nickp60]

Hi @Eoc-93 , thanks for trying chordomics, and welcome to GitHub! I'd be happy to look into this. Would it be possible to share the your MPA output with us?

[Eoc-93]

Thanks! Here's an example of one of my inputs.

MPA_Chordomics_SampleL.csv

[nickp60]

Hi @Eoc-93, thanks so much for your patience, so sorry for the delay! There are two issues: one ours, and one minor one yours. On your end, your file is called a csv but it is tab delimited. You need to re-save it as a true csv with commas as the separator. Additionally, there are a number of proteins without uniprot accessions in the Proteins column, instead having names like contig103643000045_5. Where do those come from?

The biggest issue centers around changes to Uniprot's API from a few years ago -- I have attempted to fix those calls in the code, but let @KevinMcDonnell6 and I know if you run into additional issues.

Thanks again for your patience, keep me posted!