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wrf / genomeGTFtools

convert various features into a GFF-like file for use in genome browsers
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blast2genomegff.py missing in repository #1

Closed Eduardo-Alves closed 7 years ago

Eduardo-Alves commented 7 years ago

Missing blast2genomegff.py but found it in youre bitbucket https://bitbucket.org/wrf/sequences/src Also, are you ok with wrapping the repository into a usegalaxy.org tool?

wrf commented 7 years ago

Thanks for letting me know. Regarding galaxy, if you were on track to write a wrapper, please go ahead, as I may not get to this any time soon.

Eduardo-Alves commented 7 years ago

Thank you, will do. I have a quick question. How would you approach converting a blastp result on a protein prediction for a contig such as the transdecoder? I'm thinking of passing the predicted mrna gff and multiply all protein query coordinates by three but not sure if this would work.

Eduardo

On Nov 25, 2016 15:07, "Warren Francis" notifications@github.com wrote:

Thanks for letting me know. Regarding galaxy, if you were on track to write a wrapper, please go ahead, as I may not get to this any time soon.

— You are receiving this because you modified the open/close state. Reply to this email directly, view it on GitHub https://github.com/wrf/genomeGTFtools/issues/1#issuecomment-262974665, or mute the thread https://github.com/notifications/unsubscribe-auth/AJUvUXY5HosK3rTq7u9DotKY42YIvX7Zks5rBvlLgaJpZM4K8Wt6 .

wrf commented 7 years ago

If the first base of the transcript is the start of the CDS, then that would work, otherwise you have to offset the start of the protein within the transcript. I think I have implemented something similar in the pfam2gff.py script that makes use of the TransDecoder genome gff output, which includes both exon and CDS features.

Eduardo-Alves commented 7 years ago

Thank you, I will look into that as it should be similar to what I am trying to do.

Eduardo

On Fri, Nov 25, 2016 at 4:04 PM, Warren Francis notifications@github.com wrote:

If the first base of the transcript is the start of the CDS, then that would work, otherwise you have to offset the start of the protein within the transcript. I think I have implemented something similar in the pfam2gff.py script that makes use of the TransDecoder genome gff output, which includes both exon and CDS features.

— You are receiving this because you modified the open/close state. Reply to this email directly, view it on GitHub https://github.com/wrf/genomeGTFtools/issues/1#issuecomment-262987310, or mute the thread https://github.com/notifications/unsubscribe-auth/AJUvUbti0tj78yLBdsZdWZoEj6cpDUJSks5rBwb2gaJpZM4K8Wt6 .