get.blast()

[Former user]

I believe there should be a minor correction in the get.blast() code. My objection is in the line: colnames(raw) <- c("queryid", "subjectids", "identity", "positives", "alignmentlength", "mismatches", "gapopens", "q.start", "q.end", "s.start", "s.end", "evalue", "bitscore")

It looks like (from the results I obtain) the "positives" shoud be the last column name:

colnames(raw) <- c("queryid", "subjectids", "identity", "alignmentlength", "mismatches", "gapopens", "q.start", "q.end", "s.start", "s.end", "evalue", "bitscore", "positives")

[Xinqiu Yao]

Hi,

Thanks for catching the error. It seems NCBI has recently updated Blast output format. It should be fixed by this commit now.

Please update your local bio3d to the latest patched or development version. See here for instructions on installation.

[Lars Skjærven]

fixed with commit 08afbd1