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[BUG] ClustalO wrapper example from the docs is not working correctly

See original GitHub issue

Describe the bug The example throws an error when it wants to read some temporary files

System.IO.IOException: The process cannot access the file 'C:\Users\schne\AppData\Local\Temp\ac7bce1d-efe2-45ba-8ffa-90d0a60e0f49.fasta' because it is being used by another process.   at System.IO.FileSystem.DeleteFile(String fullPath)
   at System.IO.File.Delete(String path)
   at BioFSharp.IO.ClustalOWrapper.ClustalOWrapper.AlignSequences(IEnumerable`1 input, IEnumerable`1 parameters, FSharpOption`1 name) in C:\Users\schne\source\repos\CSBiology\BioFSharp\src\BioFSharp.IO\ClustalOWrapper.fs:line 347
   at <StartupCode$FSI_0010>.$FSI_0010.main@()
Stopped due to error

To Reproduce

#r "nuget: BioFSharp, 2.0.0-beta5"
#r "nuget: BioFSharp.IO, 2.0.0-beta5"

open BioFSharp
open BioFSharp.IO

open ClustalOWrapper
let cw = ClustalOWrapper()

let sequences = 
    [
    TaggedSequence.createTaggedSequence "pep1" ("AAGECGEK")
    TaggedSequence.createTaggedSequence "pep2" ("AAGEGEK")
    TaggedSequence.createTaggedSequence "pep3" ("AAAGECGEK")
    TaggedSequence.createTaggedSequence "pep4" ("AAGECGEL")
    ]

let alignedSequences = 
    cw.AlignSequences(sequences,Seq.empty)

Additional context

Also, conversion functions or overloads for AlignSequences that work on all BioSequences (BioArray, BioList, BioSeq), so something like TaggedSequence<string,seq<IBioItem>> would be awesome. Tagging @HLWeil as you’re the creator 😉

Issue Analytics

State:
Created 2 years ago
Comments:8 (8 by maintainers)

Top GitHub Comments

1reaction

HLWeilcommented, May 8, 2021

well yes, but actually no

This is the path it tries for me: C:\Users\schne\source\repos\CSBiology\BioFSharp\lib\clustal-omega\clustalo.exe 💯

I think either we change it to look for a global clustal installation or we make the parameter mandatory?

(Edit: Yes that was the intention. Not sure if building the repo yourself should be regarded as a a case in the code though)

1reaction

kMutagenecommented, May 8, 2021

Should be fixed with https://github.com/CSBiology/BioFSharp/commit/beb4158e8e8d71e7c956347db1df2f2e99f8a5e4

Adaptions to work on biosequences would still be highly appreciated

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