RdRp minscore does not change output

[LanderDC]

Hi,

Thanks for this great tool, it really helps accelerating my research. However, I noticed that setting the minscore option doesn't change anything in the output (I expected it to filter out hits with a score lower than the given threshold). Is this the expected behavior?

For example, if I run

palm_annot.py --input input.fasta --seqtype nt --fullnt output_nt.fasta --fev output.fev --minscore 90

it gives me following results:

        1840   Sequences
         607   RdRp score == 100 (33.0%)
           3   RdRp score >=  90 (0.2%)
         203   RdRp score >=  50 (11.0%)
           0   RdRp score >    0 (0.0%)
        1027   RdRp score =    0 (55.8%)

1840 of 271848 (0.6768%) palm sequences reported

But these 1230 with a score < 90 are still reported in the fev file.

[rcedgar]

This is a bug in palmscan2. I posted a (hopefully) fixed binary here:

https://drive5.com/tmp/palmscan2_binary-2024-06-12.tar.gz

Please try replacing bin/palmscan2 with this binary and let me know it it works now.

[LanderDC]

Thanks, yes this fixes the fev output and the trimmed RdRp fasta. Although, the fullnt fasta output still contains all sequences that have an identified palmprint (regardless of their rdrp score), because this is not generated with palmscan2 but with following code in palm_annot.py:

palm_annot/py/palm_annot.py

Lines 261 to 270 in 52ccaad

	if not Args.fullnt is None:
	if Args.seqtype != "nt":
	sys.stderr
	fFull = open(Args.fullnt, "w")
	NtLabels = set()
	for Label in OutputLabels:
	NtLabel = Label.split(Args.framestr)[0]
	NtLabels.add(NtLabel)
	fasta.ReadSeqsOnSeq(CleanFN, OnSeqFull)
	fFull.close()

---

FYI, there is also one sequence that with the new palmscan2 binary gets an rdrp score of 64.3 where it was previously 0.

        1840   Sequences
         607   RdRp score == 100 (33.0%)
           3   RdRp score >=  90 (0.2%)
         204   RdRp score >=  50 (11.1%)
           0   RdRp score >    0 (0.0%)
        1026   RdRp score =    0 (55.8%)

1840 of 271848 (0.6768%) palm sequences reported