Aligning fasta files containing multiple sequences

[ChriKub]

Hi, I am trying to build a graph from two full genomes, consisting of several chromosomes, but the paths in the resulting gfa do not allow me to rebuild my input data. The resulting gfa only has a single path for each of the input files, instead of paths for each fasta sequence (I can split the path using a fasta index) but the path in the gfa is no concatenated path of all fasta sequences in the input file, but something completely different. The sequence of nodes that are adjacent in the path are not adjacent in my input sequence. They even originate from different fasta sequences in the input file Is there a way to align two or more fasta files containing multiple sequences? Thanks, Chris

[jasperlinthorst]

Hi Chris, Can you let me know which commit id (and branch) you are using? I just ran into a similar problem myself, not sure its the same problem though..

Thanks, Jasper

On Thu, Sep 28, 2017 at 2:30 PM, ChriKub notifications@github.com wrote:

Hi, I am trying to build a graph from two full genomes, consisting of several chromosomes, but the paths in the resulting gfa do not allow me to rebuild my input data. The resulting gfa only has a single path for each of the input files, instead of paths for each fasta sequence (I can split the path using a fasta index) but the path in the gfa is no concatenated path of all fasta sequences in the input file, but something completely different. The sequence of nodes that are adjacent in the path are not adjacent in my input sequence. They even originate from different fasta sequences in the input file Is there a way to align two or more fasta files containing multiple sequences? Thanks, Chris

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[ChriKub]

Hi Jasper, it seems I am using a pretty old commit: commit 64c01b9cdb29d733d2075dad74cb15f5906bb78c (branch master)

Thanks, Chris

[jasperlinthorst]

Ok, thanks, I'll have a look at it.

On Thu, Sep 28, 2017 at 2:54 PM, ChriKub notifications@github.com wrote:

Hi Jasper, it seems I am using a pretty old commit: commit 64c01b9 https://github.com/jasperlinthorst/reveal/commit/64c01b9cdb29d733d2075dad74cb15f5906bb78c (branch master)

Thanks, Chris

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[jasperlinthorst]

Ok, I managed to reproduce the problem. I'm currently in the middle of quite a big transition with respect to how I encode paths and samples in graphs, I see that in my local branch it's already fixed, so I'll try to push a sort of stable version to the dev branch by the end of the day. Would that work for you?

On Thu, Sep 28, 2017 at 3:01 PM, Jasper Linthorst < jasper.linthorst@gmail.com> wrote:

Ok, thanks, I'll have a look at it.

On Thu, Sep 28, 2017 at 2:54 PM, ChriKub notifications@github.com wrote:

Hi Jasper, it seems I am using a pretty old commit: commit 64c01b9 https://github.com/jasperlinthorst/reveal/commit/64c01b9cdb29d733d2075dad74cb15f5906bb78c (branch master)

Thanks, Chris

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[ChriKub]

That would be perfect. Thank you.

[jasperlinthorst]

This should be fixed in the dev branch now. Will close this issue once its in the master.