feature request: read gzipped genomes

[ctb]

I've been working on running mummer from within a script (for #144) and it would be super nice if future versions of mummer could read gzipped files without me having to uncompress them first -- e.g. mashmap reads gzipped files natively!
(not sure if it requires that the extension be .gz or not)

[alekseyzimin]

Thank you for your suggestion. Reading gzipped genomes is easy to incorporate, but it would break the downstream functionality, as the programs like delta-filter, dnadiff or mummerplot rely in unzipped fasta to be present at the location specified in delta file. It is possible to change all of the programs in the suite, I will look into that.

[ctb]

thanks! I really appreciate the response & thanks again for mummer!

[Caiyulu-818]

so when i run dnadiff -p 10 ~/data1/LUCY/magdrep21077/SRR10159350bin.26.fa /home/ec2-user/data1/LUCY/refseq/undownr1/GCF_003988655.1_ASM398865v1_genomic.fna.gz
Building alignments
terminate called after throwing an instance of 'std::runtime_error'
what(): Unsupported format
ERROR: Failed to run nucmer, aborting.

it cannot read "gz files,how can i solve this problem ,thanks a lot.

[alekseyzimin]

Hello, At this time mummer does not support gzipped genomes. Due to complications in integration with other software, this feature is not easy to incorporate and at this time it is not a priority. Please gunzip the fasta file and run mummer.

…

--Aleksey

On Wed, Apr 6, 2022 at 5:06 AM Caiyu ***@***.***> wrote: so when i run dnadiff -p 10 ~/data1/LUCY/magdrep21077/SRR10159350bin.26.fa /home/ec2-user/data1/LUCY/refseq/undownr1/GCF_003988655.1_ASM398865v1_genomic.fna.gz Building alignments terminate called after throwing an instance of 'std::runtime_error' what(): Unsupported format ERROR: Failed to run nucmer, aborting. it cannot read "gz files,how can i solve this problem ,thanks a lot. — Reply to this email directly, view it on GitHub <#145 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AGPXGHMEODUY37GOV7KKHV3VDVH3DANCNFSM4T6VKTOA> . You are receiving this because you commented.Message ID: ***@***.***>

-- Dr. Alexey V. Zimin Associate Research Scientist Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD, USA (301)-437-6260 website http://ccb.jhu.edu/people/alekseyz/ blog http://masurca.blogspot.com