chimera.seqs(method=bellerophon) progress, breakpoint, bug

  1. Like the hclust() request previously submitted, I would like to see some kind of visual indication of progress on screen.

  2. I would like to see the putative chimera breakpoint output in the *.chimera file. This makes manual confirmation much easier.

  3. The chimera count output to stderr under-reports by one.


a workaround for #2 is to run mothur in batchmode to capture stdout:

mothur "#chimera.seqs(fasta=myfasta,method=bellerophon)" > chimeras.txt

The subsequent output can be handled with a perl 1-liner:

perl -nle "print $1 if /breakpoint (\d+)/" chimeras.txt > breakpoints.txt