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nathanweeks / exonerate

A fork of exonerate: a generic tool for sequence alignment
GNU General Public License v3.0
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Merging with gff3-capable fork of 2.2.0 version? #24

Open mmokrejs opened 2 years ago

mmokrejs commented 2 years ago

Hi Nathan,

1. are you aware of this forked repo?

https://github.com/hotdogee/exonerate-gff3 which is an improved version of exonerate-2.2.0 with GFF3 format output support

Maybe you could unite the efforts.

2. Some patches and compile/install tricks can be inferred from the ebuild https://data.gpo.zugaina.org/science/sci-biology/exonerate-gff3 https://cgit.gentoo.org/proj/sci.git/tree/sci-biology/exonerate-gff3/files/exonerate-gff3-9999-asneeded.patch?id=d209b24ac3b9de78f7048fb76467c42bad604263 # well this patch chnages the part you commented out but

3. There is also an on-top utility https://github.com/lufuhao/ExonerateTransferAnnotation .

4. There is a similar utility https://cgit.gentoo.org/proj/sci.git/commit/sci-biology/ESTate/ESTate-0.5.ebuild?id=4c181b3959260dbe65d3801005b99f1a6e4db33c

nathanweeks commented 2 years ago

are you aware of this forked repo?

https://github.com/hotdogee/exonerate-gff3 which is an improved version of exonerate-2.2.0 with GFF3 format output support

Maybe you could unite the efforts.

Thanks @mmokrejs, I was not aware of that repo. It can be possible to post-process exonerate output to get GFF3 (e.g., https://github.com/nathanweeks/exonerate/issues/14#issuecomment-373154847 ), but having the capability built-in would be more convenient. I'm happy to accept PRs (or provide PRs for features/fixes made in this exonerate repo to another exonerate fork).

Some patches and compile/install tricks can be inferred from the ebuild https://data.gpo.zugaina.org/science/sci-biology/exonerate-gff3 https://cgit.gentoo.org/proj/sci.git/tree/sci-biology/exonerate-gff3/files/exonerate-gff3-9999-asneeded.patch?id=d209b24ac3b9de78f7048fb76467c42bad604263 # well this patch chnages the part you commented out but

Thanks for the tips. The pthreads code was commented out due to data races in exonerate when multiple threads are used.

There is also an on-top utility https://github.com/lufuhao/ExonerateTransferAnnotation .

There is a similar utility https://cgit.gentoo.org/proj/sci.git/commit/sci-biology/ESTate/ESTate-0.5.ebuild?id=4c181b3959260dbe65d3801005b99f1a6e4db33c

I wasn't aware of either tool. I appreciate the links!