Description Usage Arguments Details Value Examples
Generates a temporary fasta file with the sequences provided and returns the matches in the provided fasta file.
1 2 | find_in_fasta(sequences, target_fasta, ssearch_exe, seq_names = NULL,
min_eval = 0.01)
|
sequences |
sequences to be searched |
target_fasta |
path to fasta file containing the target sequences |
ssearch_exe |
location of the ssearch executable (or alias in your path) |
seq_names |
optional names to be given to the sequences |
min_eval |
minimum E value to be reported, defaults to 0.01 |
It wraps sseach to do the search and then returns the console output
tabular console output of ssearch as a character vector (element per line)
1 | find_in_fasta(c('PEPTIDE'), 'arabidopsis.fasta', '~/usr/bin/ssearch36')
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