devonorourke/tidybug

🐞 methods and data describing filtering COI datasets and database construction 🐛

tidybug's Issues

Database construction Filter1 step

Hi Devon, firstly thanks for a really interesting paper and making the tidybug code so open and well documented!

I'm trying to run the steps outlined in database_construction.md and am getting a bit confused. I've successfully used bold_datapull_arths.R to query BOLD. However then the Filter1 step starts by using grep on a file 'boldCustom.allArth.seqNtaxa.csv' to remove any lines matching 'sequenceID,taxon,nucleotides'. However none of the bold_datapull scripts in the repo output a file with that name, and I don't think any of them output a csv with column names matching that pattern? The only two csvs output with similar names are boldCustom.allArth.seqs.csv and boldCustom.allArth.taxa_string.csv, but using the command from Filter1 on either of these generates an empty fasta.

Thanks very much
Dave