These changes implement prodigal filtering differently (now available through pdp.py filter --prodigal rather than pdp.py prodigal).
The GFF file is written as usual, but a new 'filtered' sequence is also written - the regions identified in the GFF file concatenated with Ns. The pdp.py eprimer3 command now takes a --filter argument that will use this concatenated file rather than the original sequence when designing primers.
This does not affect pdp.py extract as the primersearch output reflects the original genome sequence when searching, and these results are used to grab the amplified sequence in each case.
These changes implement prodigal filtering differently (now available through
pdp.py filter --prodigalrather thanpdp.py prodigal).The GFF file is written as usual, but a new 'filtered' sequence is also written - the regions identified in the GFF file concatenated with
Ns. Thepdp.py eprimer3command now takes a--filterargument that will use this concatenated file rather than the original sequence when designing primers.This does not affect
pdp.py extractas the primersearch output reflects the original genome sequence when searching, and these results are used to grab the amplified sequence in each case.