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liyu95 / DeepSimulator

The first deep learning based Nanopore simulator which can simulate the process of Nanopore sequencing.
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DeepSimulator (branch discontinuous-fasta) dosen't handle multi-line fasta files correctly #31

Closed yjx1217 closed 5 years ago

yjx1217 commented 5 years ago

Dear Developers,

I've just noticed a new issue with the newly added support for multi-fasta input genome:

When the multi-fasta input genome is in single line fasta format (i.e. without line wraps for the sequence lines), it works as expected. However, When the input genome is in multi-line fasta format (the long sequence line are folded into multi lines with line wrap at the end), DeepSimulator will just take the first line and ignore the remaining sequences of the same chromosome/contig/scaffold.

Best, Jia-Xing

liyu95 commented 5 years ago

Hi, Jia-Xing, thank you for reporting the issue. This issue will be fixed very soon.

liyu95 commented 5 years ago

Hi, I have hopefully fixed the bug. But I am currently on a vacation and I do not have access to a machine that can run the code. Please feel free to test it before I go back to my school on 17th this month.

yjx1217 commented 5 years ago

Hi Yu,

Thanks for the fix! I am also on vacation right now but will have it tested soon after I get back before the weekend.

Best, Jia-Xing

On Tue, Oct 8, 2019, 4:41 PM Yu Li notifications@github.com wrote:

Hi, I have hopefully fixed the bug. But I am currently on a vacation and I do not have access to a machine that can run the code. Please feel free to test it before I go back to my school on 17th this month.

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub https://github.com/lykaust15/DeepSimulator/issues/31?email_source=notifications&email_token=AAFLL5SWPZVCOKP4JZ44JBTQNSLZZA5CNFSM4I5ONLA2YY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGOEAUNGKQ#issuecomment-539546410, or mute the thread https://github.com/notifications/unsubscribe-auth/AAFLL5X3LGEQQB6O35FCI63QNSLZZANCNFSM4I5ONLAQ .

liyu95 commented 5 years ago

Dear Jia-Xing:

The bug should be fixed now. Please have a try when you are free. Remember to install Biopython within the environment.

Sincerely, Yu

yjx1217 commented 5 years ago

Thanks Yu! I think it works as expected now.

Best, Jia-Xing