Hi, in my script I am looping through a bunch of files using primersearch_raw. Some files contain one fasta file others contain multiple fasta files. For some files primersearch_raw return 0 results without errors, for other files amplicons are returned, but for some files I get the error produced below and the script stops. My Embossversion is 6.5.0.0. Appreciate any help to resolve this issue.
fastafilepath
[1] "path to file\71168_Geotria_australis.fasta"
forward_primer
[1] "GGATTAGATACCCYACTATGC"
reverse_primer
[1] "GATTGCGCTGTTATCCCTAG"
mismatch_pr
[1] 10
primersearch_raw(file = fastafilepath, forward = forward_primer, reverse = reverse_primer, mismatch = mismatch_pr)
Results in:
Error in names(x) <- value :
'names' attribute [10] must be the same length as the vector [2
traceback()
4: colnames<-(*tmp*, value = c("pair_name", "amplimer", "input",
"name", "f_primer", "f_start", "f_mismatch", "r_primer",
"r_start", "r_mismatch"))
3: parse_primersearch(output_path)
2: dplyr::as_tibble(parse_primersearch(output_path))
1: primersearch_raw(file = fastafilepath, forward = forward_primer,
reverse = reverse_primer, mismatch = mismatch_pr)
Note that the fileextension had to be changed from fasta to txt to allow upload. Fastafile downloaded from genbank using entrez_fetch from the rentrez package.
71168_Geotria_australis.txt
]
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