User: matt.chambers42

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Posts by matt.chambers42

<prev • 15 results • page 1 of 2 • next >
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Issues with .extractEnsemblReleaseFromDbVersion() and get_organism_from_Ensembl_Mart_dataset()
... I found a couple issues testing this with older Ensembl archives: 1. .extractEnsemblReleaseFromDbVersion() should support Ensembl 54 (May 2009), which doesn't have "genes" in its version string. Something like this should work: .extractEnsemblReleaseFromDbVersion <- function (db_version)  {   ...
genomicfeatures written 6 months ago by matt.chambers4210 • updated 6 months ago by Hervé Pagès ♦♦ 13k
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seqlevels/keepSeqLevels should set default pruning.mode by a getOption call
... I had some code that worked in 3.4 that was broken by 3.5 adding 'pruning.mode' and making the default mode be an error. It's fine for the default to change, but we should have a way to override it without making the code incompatible with earlier Bioconductor versions (i.e. I get an error if I set ...
genomeinfodb written 6 months ago by matt.chambers4210 • updated 6 months ago by Hervé Pagès ♦♦ 13k
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Comment: C: Possible error in TxDb.Mmusculus.UCSC.mm10.ensGene_3.4.0?
... Ensembl just released 89 and it broke this again: ftp://ftp.ensembl.org/pub/current_mysql/ contains some .gz file named the same as the core dirs. I'm not sure if those are temporary or not, but non-directories should be excluded from Ensembl_listMySQLCoreDirs. The FTP listing will start with 'd' ...
written 6 months ago by matt.chambers4210
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GenomeInfoDb: where are the genome patches?
... I'm trying to implement a function to convert Ensembl chromosome names to UCSC names for many potential input species (i.e. the intersection of species supported by both sources). I saw the `seqlevelStyles` function in GenomeInfoDb, but only the canonical chromosomes are mapped. Why is that? It's ki ...
genomeinfodb seqnames written 6 months ago by matt.chambers4210 • updated 6 months ago by Hervé Pagès ♦♦ 13k
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Comment: C: Possible error in TxDb.Mmusculus.UCSC.mm10.ensGene_3.4.0?
... Isn't this `found 0 or more than 1 subdir for "mmusculus_gene_ensembl" dataset` error something to fix too? It seems due to the multiple strains of mouse in Ensembl. The shortnames code in .Ensembl_getMySQLCoreDir should be: shortnames <- sub("(\\w)\\w*?_(\\w+?)_core_\\S+", "\\1\\2", core_dirs, ...
written 6 months ago by matt.chambers4210
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Answer: A: GenomicFeatures should support old 'Db type' value
... Ah, I see XJ updated the txdb.sqlite file a couple weeks ago and I just haven't pulled that change. But I still think it's weird for it to fail just based on the 'Db type' string. I did notice there is a slight schematic difference, the tx_type field is new. But in my mm10 UCSC txdb, it's always nul ...
written 7 months ago by matt.chambers4210
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GenomicFeatures should support old 'Db type' value
... The customProDB package has a test txdb built in 2013. Its Db type is 'TranscriptDb'. I see newer databases have 'TxDb' instead. Unless there's some other schema difference making them incompatible, the new version should still support the older name. I got this error when building on Travis CI: ...
genomicfeatures written 7 months ago by matt.chambers4210
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makeTxDbFromUCSC("hg38", "refGene") gives "not supported" error
... Of course this track really exists or I wouldn't post an issue about it. :) > browseUCSCtrack("hg38", "refGene") Easy to reproduce the error: ​> makeTxDbFromUCSC(genome="hg38", tablename="refGene") Error in .tablename2track(tablename, session) : UCSC table "refGene" is not supported ​ &g ...
genomicfeatures written 8 months ago by matt.chambers4210 • updated 8 months ago by Hervé Pagès ♦♦ 13k
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Answer: A: Multiple (variable length) string searching in large text (e.g. Aho-Corasick)?
... I wasn't able to find an amino-acid-friendly existing solution and my parallelized `lapply(peptides, gregexpr, proteins)` approach was still not fast enough, so I learned Rcpp and implemented this myself. Now CRAN has a good general purpose multiple-keyword search package: https://cran.r-project.org ...
written 16 months ago by matt.chambers4210
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Comment: C: Multiple (variable length) string searching in large text (e.g. Aho-Corasick)?
... Oops, I should have added a comment, not an answer. I have a decent standard C++ implementation of Aho Corasick which I use for peptide/protein lookup in my C++ programs. It's templated to work with different keyword types and alphabet sizes. It uses TR1's std::shared_ptr to store the keywords in th ...
written 17 months ago by matt.chambers4210

Latest awards to matt.chambers42

Scholar 19 months ago, created an answer that has been accepted. For A: Multiple (variable length) string searching in large text (e.g. Aho-Corasick)?

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