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Bioconductor / Biostrings

Efficient manipulation of biological strings
https://bioconductor.org/packages/Biostrings
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Unnecessary warning when using `readQualityScaledDNAStringSet` #106

Closed LTLA closed 3 days ago

LTLA commented 10 months ago 
library(Biostrings)
example(readQualityScaledDNAStringSet, echo=FALSE)
## Warning messages:
## 1: In XStringSet("DNA", x, start = start, end = end, width = width,  :
##   metadata columns on input DNAStringSet object were dropped
## 2: In XStringSet("DNA", x, start = start, end = end, width = width,  :
##   metadata columns on input DNAStringSet object were dropped

This stems from

https://github.com/Bioconductor/Biostrings/blob/35181af7b71c742ec60d36c617328c6e88aa89c4/R/QualityScaledXStringSet.R#L188

but the mcols are not wiped prior to

https://github.com/Bioconductor/Biostrings/blob/35181af7b71c742ec60d36c617328c6e88aa89c4/R/QualityScaledXStringSet.R#L193

which presumably leads to the warning above. Not breaking but it is annoying noise when using reading a FASTQ file.

Session info ``` R Under development (unstable) (2023-11-10 r85507) Platform: x86_64-pc-linux-gnu Running under: Ubuntu 20.04.6 LTS Matrix products: default BLAS: /home/luna/Software/R/trunk/lib/libRblas.so LAPACK: /home/luna/Software/R/trunk/lib/libRlapack.so; LAPACK version 3.11.0 locale: [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C [3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8 [5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8 [7] LC_PAPER=en_US.UTF-8 LC_NAME=C [9] LC_ADDRESS=C LC_TELEPHONE=C [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C time zone: America/Los_Angeles tzcode source: system (glibc) attached base packages: [1] stats4 stats graphics grDevices utils datasets methods [8] base other attached packages: [1] Biostrings_2.71.1 GenomeInfoDb_1.39.2 XVector_0.43.0 [4] IRanges_2.37.0 S4Vectors_0.41.2 BiocGenerics_0.49.1 loaded via a namespace (and not attached): [1] zlibbioc_1.49.0 compiler_4.4.0 tools_4.4.0 [4] GenomeInfoDbData_1.2.11 RCurl_1.98-1.13 crayon_1.5.2 [7] bitops_1.0-7 ```
ahl27 commented 4 months ago

Thanks for the callout -- this is fixed in https://github.com/Bioconductor/Biostrings/pull/110. Just going to do some testing to make sure nothing weird happens before merging.

ahl27 commented 3 days ago

This is merged, should be resolved now.