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refSeqOrder preservation from input fasta file #925

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dsenalik opened this Issue Sep 11, 2017 · 2 comments

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@dsenalik
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dsenalik commented Sep 11, 2017

In reference to previous closed issue #867 "Custom Sorting Reference Sequence" and open issue #919 "The refSeqOrder is not customisable", I propose a new parameter to prepare-refseqs.pl of "--unsorted" which will use the sequence order from the input FASTA file or gff file to control the order in the generated json output file. Currently the output is always alphabetically sorted. I have a pull request (#924) hopefully implementing this new feature (this is my first pull request so be gentle).

@liub1993

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liub1993 commented Sep 11, 2017

It' a good solution! But also, in some cases, the sequence order from FASTA file was sorted by ascii and not by common sense.

@rbuels

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rbuels commented Jan 25, 2018

@rbuels rbuels modified the milestones: 1.12.4, 1.12.5 Feb 2, 2018

@rbuels rbuels closed this in #1007 Feb 27, 2018

rbuels added a commit that referenced this issue Feb 27, 2018

Merge pull request #1007 from GMOD/refseqorder
ref sequence order enhancements, fixes #925, fixes #919

@wafflebot wafflebot bot removed the in progress label Feb 27, 2018

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