biojulia / biocore.jl

Core types and interfaces for BioJulia packages

Bio

This package has been depreceated. Full details are available here. You might still download and use this package, as we don't want old scripts to break. However going forward, know that this repository is archived and read only, no further updates or fixes will be committed. You should use the packages that replace Bio.jl - a list is available here.

biocore.jl's Issues

Bump the compatibility to newer Automa

BioCore seems to be still using old Automa which is problematic.

Expected Behavior

Installable BioCore that does not attempt to downgrade Automa

Current Behavior

Attempts to downgrade Automa to pre 1.x.x version.

Possible Solution / Implementation

Bump the compatibility in Project.toml file?

Release metadata

@bicycle1885 did the version you just release go to METADATA.jl? If not attobot might need another restart for us.

Feature request: More helpful IO error messages

Expected Behavior

It would be nice to get some more information back from readers when they fail to parse. If I know why the reader is failing, I might be able to correct the problem.

Current Behavior

Here are some current error messages:

ERROR: GFF3.Reader file format error on line 1 ~>"191\tgene"
ERROR: BED.Reader file format error on line 1 ~>".\t-\tFLAI"

Possible Solution / Implementation

I think these messages could be a bit more helpful, using the information available to the parser. Some useful things to know would be:

• What field caused the error?
• What values would be expected?
• What spec is being followed for this file format? This could maybe just be handled in the docs, but it would be nice to have a link to the spec somewhere.

Context

I was trying to read a gtf file, then a bed file when I got the errors above. The bed file had been converted from the gtf using convert2bed. Both of these files work fine with bedtools, igv, and bedops. So what's going on? If the error message described what value didn't match what expression, I'd could try and fix the file and move on. Instead it becomes a search though source code.

Your Environment

  [8e4a8c10] BED v0.1.0
  [37cfa864] BioCore v2.0.5
  [af1dc308] GFF3 v0.1.0
  [4f8a0a0a] GenomicAnnotations v0.1.4
  [899a7d2d] GenomicFeatures v2.0.0

Renaming of BioCore.Ragel

BioCore.Ragel module should either be moved, renamed, or both.