In grunwaldlab/oomycetedbtools: Tools for managing the OomyceteDB website and database

knitr::opts_chunk$set(echo = TRUE)
# Date: 
clipr::write_clip(paste0('## ', format(Sys.time(), "%F (%A %B %e)\n\n")))
# Date and time:
clipr::write_clip(paste0('## ', format(Sys.time(), "%F %X %Z (%A %B %e)\n\n")))

Next Meeting

• I had to redo the unique ID for sequences becuase the ones in the FASTA file I was reformatting are not unique.

> seq_data[duplicated(seq_data$oodb_id), ]
# A tibble: 11 × 6
   name                         strain     ncbi_acc ncbi_taxid oodb_id
   <chr>                        <chr>      <chr>    <chr>        <dbl>
 1 Aphanomyces euteiches        MER4       NA       100861          11
 2 Phytophthora alni subsp.alni P16203     NA       299391         102
 3 Phytophthora andina          P13365     NA       283009         110
 4 Phytophthora boehmeriae      CBS 291.29 NA       109152         134
 5 Phytophthora cryptogea       P1088      NA       4786           284
 6 Phytophthora gemini          P15880     NA       565057         317
 7 Phytophthora ipomoeae        P10225     NA       283007         388
 8 Phytophthora hibernalis      P3822      NA       175300         597
 9 Phytophthora infestans       P10650     NA       4787           598
10 Pythium rhizoterrae          CBS 146585 MW661036 NA             744
11 Pythium aquasilvae           CBS 146586 MW661032 NA             745

grunwaldlab/oomycetedbtools documentation built on March 23, 2022, 6:54 a.m.