Improve autocomplete

[simone-pignotti]

Hi @gbouras13, I have encountered a case where there are multiple blast hits with very low evalue (1e-180) that just happened to miss the start of the target by few residues, so they were discarded and a random gene ("nearest" option) was used instead.
I think that in those cases it would be best to use the ORF that overlaps the best blast hit, and even make this the default when --autocomplete is not specified. What do you think?

[simone-pignotti]

At least that's my interpretation based on:

dnaapler/src/dnaapler/utils/processing.py

Lines 78 to 82 in 6a672fd

	for i in range(0, len(blast_df.qseq)):
	if blast_df["qseq"][i][0] in ["M", "V", "L"] and (
	blast_df["sstart"][i] == 1
	):
	reorient_sequence(blast_df, input, out_file, gene, i)

But correct me if I am wrong, I can take a closer look at the logs

[gbouras13]

I chose to have a strict match of the start codon in dnaapler to ensure the rotation does not interrupt a CDS, but I agree this would be a good feature.

I will aim to add this in the next week or two. It will require some refactoring and so isn't trivial but shouldn't be too hard.

George

[gbouras13]

Hi @simone-pignotti ,

I've made your suggestion the default within all BLAST based commands in dnaapler (aka it will take the top row of the blastx table, and if it the matching alignment doesn't start with a start codon, it will run pyrodigal to find the CDS with the most overlap).

Available in v0.4.0

George

[simone-pignotti]

Wonderful, thank you so much @gbouras13!