Question

Running gmap tool via gmapR package?

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Thomas Sandmann ▴ 90

@thomas-sandmann-6817

Last seen 15 months ago

USA

Hi Michael,

Thanks a lot for making the gsnap aligner (and associated tools) available through the gmapR package. The vignette mentions that "GMAP integration is scheduled for the near future" as well.

I noticed that there is a gmap-command.R file in the package as well, but it still seems to be a stub since 2012 (last change in the repository). Do you still plan to enable use of the gmap command through the package?

Again, thanks for making these (and many other) tools available to the community,

Thomas

gmapR • 2.2k views

ADD COMMENT • link updated 9.0 years ago by Michael Lawrence ★ 11k • written 9.0 years ago by Thomas Sandmann ▴ 90

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Hi Michael,

thanks a lot for responding to my question.

I would like to map cDNA sequences to a genome, e.g. map an EST sequence to the reference genome of the same or a very highly related species. As described in the original gmap paper, I would be interested in very close matches, e.g. near-identity between a cDNA sequence and its corresponding genomic exons, to learn about the intron-exon structure of the locus.

For example, I would like to start with one (or more) query sequences (fasta files, DNAStrings, DNAStringSeq, whatever makes most sense) and a GmapGenome.

Does this description help?

Thanks, Thomas

ADD REPLY • link 9.0 years ago Thomas Sandmann ▴ 90

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I will put it on the list. Perhaps something in devel by the end of the week. Have to fix R first.

ADD REPLY • link 9.0 years ago Michael Lawrence ★ 11k

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Update: have been working on this, but it's a fairly significant feature addition and will take a couple more days before it is ready to try.

ADD REPLY • link 9.0 years ago Michael Lawrence ★ 11k

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Thanks a lot for spending some of your valuable time to implement this feature. Very much appreciated. Let me know if / when I can help.

ADD REPLY • link 9.0 years ago Thomas Sandmann ▴ 90

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I edited the answer; there is something that might work.

ADD REPLY • link 9.0 years ago Michael Lawrence ★ 11k

score 0 · Answer 1 · 2015-11-15

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Michael Lawrence ★ 11k

@michael-lawrence-3846

Last seen 3.0 years ago

United States

Here is what you can do with gmapR 1.13.4 (after one has a genome and a FASTA file).

gmapParam <- GmapParam(genome=gmapGenome,
                       unique_only=FALSE,
                       suboptimal_score=2L, 
                       npaths=10L,
                       splicing=FALSE,
                       min_intronlength=20L)
output <- gmap("H1993.fasta", params=gmapParam)
gr <- import(output)

I am going to be honest: I did not do much testing of this. Perhaps you could help me there ;)

ADD COMMENT • link 9.0 years ago Michael Lawrence ★ 11k

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Hi Michael,

thanks a ton for for implementing gmapR so quickly. I ran your example code (using the Drosophila dm3 genome and an example fasta file) a few days ago and got nice results. Yet, when I tried again today - to test it more thoroughly - with a fresh download of gmapR 1.13.6, I ran into an error. (I have trouble accessing the BioC SVN repository right now, so I can't check any earlier versions... Dan is helping me get back on track.)

Here's a (hopefully) reproducible example:

library(BSgenome.Dmelanogaster.UCSC.dm3) library(TxDb.Dmelanogaster.UCSC.dm3.ensGene) library(gmapR)

# load Drosophila melanogaster genome and transcriptome annotations genome <- BSgenome.Dmelanogaster.UCSC.dm3 txdb <- TxDb.Dmelanogaster.UCSC.dm3.ensGene seqlevels(txdb) <- "chr2L" tx_seqs <- extractTranscriptSeqs(genome, txdb)

# create fasta file with an example transcript sequence transcriptId <- "FBtr0091487" # a transcript from the pnuts gene stopifnot(transcriptId %in% names(tx_seqs)) temp.file <- tempfile(fileext = ".fasta") writeXStringSet(tx_seqs[transcriptId], temp.file)

# alignment params <- GmapParam(genome=GmapGenome(genome), unique_only=TRUE, suboptimal_score=2L, npaths=10L, splicing=TRUE, min_intronlength=20L) output <- gmap(temp.file, params = params)

Error in params$format : $ operator not defined for this S4 class

Here's the result of calling sessionInfo(). (I currently don't have a separate installation of R devel available to me, so there is a mix of release and development versions of packages here.)

R version 3.2.2 (2015-08-14) Platform: x86_64-apple-darwin13.4.0 (64-bit) Running under: OS X 10.11.1 (El Capitan)

locale: [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8

attached base packages: [1] stats4 parallel stats graphics grDevices datasets utils methods base

other attached packages: [1] gmapR_1.13.6 TxDb.Dmelanogaster.UCSC.dm3.ensGene_3.2.2 [3] GenomicFeatures_1.22.6 AnnotationDbi_1.32.0 [5] Biobase_2.30.0 BSgenome.Dmelanogaster.UCSC.dm3_1.4.0 [7] BSgenome_1.38.0 rtracklayer_1.31.2 [9] Biostrings_2.38.2 XVector_0.10.0 [11] GenomicRanges_1.22.1 GenomeInfoDb_1.6.1 [13] IRanges_2.4.4 S4Vectors_0.8.3 [15] BiocGenerics_0.16.1 BiocInstaller_1.20.1 [17] devtools_1.9.1

loaded via a namespace (and not attached): [1] zlibbioc_1.16.0 GenomicAlignments_1.6.1 BiocParallel_1.4.0 [4] tools_3.2.2 SummarizedExperiment_1.0.1 DBI_0.3.1 [7] lambda.r_1.1.7 futile.logger_1.4.1 digest_0.6.8 [10] futile.options_1.0.0 bitops_1.0-6 biomaRt_2.26.1 [13] RCurl_1.95-4.7 RSQLite_1.0.0 memoise_0.2.1 [16] Rsamtools_1.22.0 XML_3.98-1.3 VariantAnnotation_1.16.3

ADD REPLY • link 9.0 years ago Thomas Sandmann ▴ 90

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Thanks for the testing and reproducible example. Fixed in 1.13.7.

ADD REPLY • link 9.0 years ago Michael Lawrence ★ 11k

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Hi Michael,

thanks again for fixing the small bug so quickly. I have aligned a number of Drosophila transcripts by now and e.g. visualized the results with the Gviz package. Things work great and I am very grateful that you make it so easy to use gmap through R.

I noticed that the import method for the GmapOutput object wasn't able to parse the gff3 file I generated. Specifying the gff3 format explicitly helped e.g. in the example pasted below.

Now, I will need some more reading on gmap's command line options to understand the different parameters better (and how to specify them via the GmapParam function).

library(gmapR) library(BSgenome.Dmelanogaster.UCSC.dm3) library(TxDb.Dmelanogaster.UCSC.dm3.ensGene) library(Gviz)

# load genome and transcriptome annotations genome <- BSgenome.Dmelanogaster.UCSC.dm3 txdb <- TxDb.Dmelanogaster.UCSC.dm3.ensGene tx_seqs <- extractTranscriptSeqs(genome, txdb)

# create fasta file with annotated transcripts sequences for the Dmef2 gene geneId <- "FBgn0011656" # Dmef2 gene transcriptIds <- transcriptsBy(txdb, by = "gene")[[geneId]]$tx_name # all Dmef2 transcripts temp.file <- tempfile(fileext = ".fasta") writeXStringSet(tx_seqs[transcriptIds], temp.file)

# alignment params <- GmapParam(genome=GmapGenome(genome), unique_only=TRUE, suboptimal_score=2L, npaths=10L, splicing=TRUE, min_intronlength=20L, format = "gff3_gene") output <- gmap(temp.file, params = params) gr <- import(output) # error gr <- import.gff3(path(output), format = "gff3") # works

# visualization with GViz gff.file <- sub("fasta$", "gff3", basename(temp.file)) stopifnot(file.exists(gff.file))

gaTrack <- GenomeAxisTrack() grTrack <- GeneRegionTrack(txdb, name = "Flybase", showId = TRUE, fill = "#FDAE6B", col="#7F2704") gmTrack <- GeneRegionTrack(gff.file, name = "gmap", showId = TRUE, fill = "#6BAED6", col="#08306B") plotTracks(list(gaTrack, grTrack, gmTrack), chromosome = chromosome(gmTrack), from = min(start(gr)-1000), to = max(end(gr)+1000))

SessionInfo() output:

R version 3.2.2 (2015-08-14) Platform: x86_64-apple-darwin13.4.0 (64-bit) Running under: OS X 10.11.1 (El Capitan)

locale: [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8

attached base packages: [1] grid parallel stats4 stats graphics grDevices datasets utils [9] methods base

other attached packages: [1] Gviz_1.14.0 TxDb.Dmelanogaster.UCSC.dm3.ensGene_3.2.2 [3] GenomicFeatures_1.22.6 AnnotationDbi_1.32.0 [5] Biobase_2.30.0 BSgenome.Dmelanogaster.UCSC.dm3_1.4.0 [7] BSgenome_1.38.0 rtracklayer_1.31.2 [9] Biostrings_2.38.2 XVector_0.10.0 [11] gmapR_1.13.7 GenomicRanges_1.22.1 [13] GenomeInfoDb_1.6.1 IRanges_2.4.4 [15] S4Vectors_0.8.3 BiocGenerics_0.16.1 [17] BiocInstaller_1.20.1 devtools_1.9.1

loaded via a namespace (and not attached): [1] SummarizedExperiment_1.0.1 VariantAnnotation_1.16.3 reshape2_1.4.1 [4] splines_3.2.2 lattice_0.20-33 colorspace_1.2-6 [7] XML_3.98-1.3 survival_2.38-3 foreign_0.8-66 [10] DBI_0.3.1 BiocParallel_1.4.0 RColorBrewer_1.1-2 [13] lambda.r_1.1.7 matrixStats_0.15.0 plyr_1.8.3 [16] stringr_1.0.0 zlibbioc_1.16.0 munsell_0.4.2 [19] gtable_0.1.2 futile.logger_1.4.1 memoise_0.2.1 [22] latticeExtra_0.6-26 biomaRt_2.26.1 proto_0.3-10 [25] Rcpp_0.12.2 acepack_1.3-3.3 scales_0.3.0 [28] Hmisc_3.17-0 gridExtra_2.0.0 Rsamtools_1.22.0 [31] ggplot2_1.0.1 digest_0.6.8 stringi_1.0-1 [34] biovizBase_1.18.0 tools_3.2.2 bitops_1.0-6 [37] magrittr_1.5 RCurl_1.95-4.7 RSQLite_1.0.0 [40] dichromat_2.0-0 Formula_1.2-1 cluster_2.0.3 [43] futile.options_1.0.0 MASS_7.3-45 rpart_4.1-10 [46] GenomicAlignments_1.6.1 nnet_7.3-11