Strange encoding characters in output file

Question

Strange encoding characters in output file

Closed this issue 5 years ago · 5 comments

theo-allnutt-bioinformatics commented 5 years ago

Hi,
my blast style output is including some very unusual text codes, e.g.

��

i.e.

(ENQ)(ENQ)(ENQ)(LF)
(LF)
(ENQ)(BS)(ENQ)(SOH)

This prevents any downstream processing of the files and they are difficult to remove automatically.
Is ths a bug that can be fixed easily?

Thanks,

Theo

Answer 1 · 2019-11-19T04:05:51.000Z

I added this to my pipeline for burst.. removed all special text codes and lines starting with tabs or newlines.

sed -i 's/[^[:print:]\t]//g' out.burst
sed -i '/^$/d' out.burst
sed -i '/^\t/ d' out.burst

Answer 2 · 2019-11-19T22:47:39.000Z

Hi Theo, BURST does not add these codes. It could either be a bug or some issue with the formatting of your queries and references. If you suspect it is a bug, could you provide a minimal reproducible example so I can debug the problem? Including the reference sequence file and commands to make DB, and query file and commands to align, as well as the output file you're getting and what version of burst was used. Thanks! Gabe

…

On Mon, Nov 18, 2019, 11:05 PM Theo Allnutt Bioinformatics < ***@***.***> wrote: I added this to my pipeline for burst.. removed all special text codes and lines starting with tabs or newlines. sed -i 's/[^[:print:]\t]//g' out.burst sed -i '/^$/d' out.burst sed -i '/^\t/ d' out.burst — You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub <#20?email_source=notifications&email_token=AB5NOBSFFLC7IACZMWMW4Q3QUNQZ7A5CNFSM4JO5MHF2YY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGOEEMZAPQ#issuecomment-555323454>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AB5NOBS6ISKIMAZB52ZNXDDQUNQZ7ANCNFSM4JO5MHFQ> .

Answer 3 · 2019-11-20T03:54:28.000Z

Thanks, on further checking I think this is a problem with how I am saving reads with no alignment.. more difficult than I had thought.

Answer 4 · 2019-11-26T01:17:36.000Z

I've had to reopen this issue. The problem definitely is with the BURST output file but it is very difficult to replicate. Random output files contain the bad text codes. I may have to upload the full db and input files causing the problem. I will update when I can nail it down.

Thanks,

Theo

Answer 5 · 2020-02-25T22:00:27.000Z

This is not resolved, but it is not possible to replicate.