Erroneous sequence reported in insert fasta file

[Nifaste]

Ask away!

I have observed an error with the sequences of the inserts in the FASTA format: {{ alias }}.insert.fasta. I investigated the issue and it appears to originate from the following code in find_insert.py:

rev_comp = reverse_complement(whole_seq) strand_seq = {'-': rev_comp, '+': whole_seq} parse_seq = strand_seq[str(df['strand'][0])] final_seq = parse_seq[df['start'][0]::] + parse_seq[:df['end'][0]:] df['sequence'][0] = final_seq

The start and stop coordinates are not being adjusted when taking the reverse complement of the sequence.

I fixed the issue with an update of the code

insert_seq=whole_seq[df['start'][0]::] + whole_seq[:df['end'][0]:] rev_comp = reverse_complement(insert_seq) strand_seq = {'-': rev_comp, '+': insert_seq} final_seq = strand_seq[str(df['strand'][0])]

Has anyone else experienced this? Is my bug fix correct?

[sarahjeeeze]

Hi, thanks for reporting this. We will investigate and amend if required and let you know once implemented.

[sarahjeeeze]

Hi, After some investigation I see seqkit amplicon which we use for getting this sequence changed (fixed) the way it reported start and end sequences in the bed file from 2.4.0 which has resulted in this bug in the workflow. It previously did output the reverse complement start and end points. see - shenwei356/seqkit#367. We will amend with your fix. Thanks again for drawing our attention to this!

[sarahjeeeze]

Hi, we have now released the fix for this in the latest release.

[sarahjeeeze]

Closing as this is now fixed, let us know if you have further troubles