Write multiple UTRs for a gene to a fasta file
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Jake ▴ 90
@jake-7236
Last seen 2.4 years ago
United States

I have a GRangesList with multiple transcripts per gene (see example below).

GRangesList object of length 9216:
$ENSMUSG00000000001.4 
GRanges object with 2 ranges and 4 metadata columns:
                       seqnames                 ranges strand |   exon_id            exon_name exon_rank               geneId
                          <Rle>              <IRanges>  <Rle> | <integer>          <character> <integer>          <character>
  ENSMUST00000000001.4     chr3 [108109403, 108109421]      - |     57602 ENSMUSE00000404895.1         8 ENSMUSG00000000001.4
  ENSMUST00000000001.4     chr3 [108107280, 108109316]      - |     57601 ENSMUSE00000363317.2         9 ENSMUSG00000000001.4

$ENSMUSG00000000028.14 
GRanges object with 4 ranges and 4 metadata columns:
                        seqnames               ranges strand | exon_id            exon_name exon_rank                geneId
  ENSMUST00000000028.13    chr16 [18781896, 18781897]      - |  245213 ENSMUSE00000645072.1        19 ENSMUSG00000000028.14
  ENSMUST00000000028.13    chr16 [18780447, 18780573]      - |  245211 ENSMUSE00000788192.1        20 ENSMUSG00000000028.14
   ENSMUST00000096990.9    chr16 [18781896, 18781897]      - |  245213 ENSMUSE00000645072.1        17 ENSMUSG00000000028.14
   ENSMUST00000096990.9    chr16 [18780453, 18780573]      - |  245212 ENSMUSE00000628024.1        18 ENSMUSG00000000028.14

I'd like to write the nucleotide sequences for all transcripts of a given gene to a fasta file grouped by gene id. Ex)

>ENSMUSG00000000028.14
​[transcript 28 sequence][transcript 96990]

However, extractTranscriptSeqs requires that the exons be ordered by genomic location which would disrupt the sequence of each transcript for overlapping multiexon transcripts. I tried the more generic getSeqs, but it inserts transcript ids into the text and names rather than grouping everything just by gene id. Is there a way to do this? Thanks

 
genomicranges genomicfeatures • 1.4k views
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@michael-lawrence-3846
Last seen 3.1 years ago
United States

Probably easiest to form a GRangesList with exons grouped by transcript and extract those sequences. Then concatenate the sequences from the same gene. This would be easiest / most efficient if the transcripts were sorted by gene. Then it would be something like this?

First, munge the transcripts and gene IDs:

library(Homo.sapiens)
tx <- exonsBy(Homo.sapiens, columns="GENEID", outerMcols=TRUE)
mcols(tx)$GENEID <- drop(mcols(tx)$GENEID)
tx <- tx[!is.na(mcols(tx)$GENEID)]
tx <- tx[order(mcols(tx)$GENEID)]

Extract the transcripts:

txseqs <- extractTranscriptSeqs(Hsapiens, tx)

And this is the key aggregation and regrouping to concatenate the sequences:

gene.widths <- sum(splitAsList(sum(width(tx)), mcols(tx)$GENEID))
relist(unlist(txseqs), PartitioningByWidth(gene.widths))

 
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This looks great. However, when I tried to run it on my own data, I couldn't access the mcols()$geneId in order to sort. Here is my full code.

 

​library('GenomicFeatures')
library('hash')
library('BSgenome.Mmusculus.UCSC.mm10')

# Load genome and annotation files
genome <- BSgenome.Mmusculus.UCSC.mm10
gencode <- loadDb('../gencode_m8_basic.sqlite')

# Get transcript <-> gene annotation
trans <- transcriptsBy(gencode, by='gene')
transcript_gene_hash <- hash(mcols(unlist(trans))$tx_name, names(unlist(trans)))

# Get 5' UTRs and 3' UTRs by transcript
fiveutrByTx <- fiveUTRsByTranscript(gencode, use.names=T)

# Get UTR of each transcript, concatenate together, group by gene

# Get all UTRs, GENEID in mcols
fiveutr <- unlist(fiveutrByTx)
mcols(fiveutr)$geneId <- hash::values(transcript_gene_hash, keys=names(fiveutr))
fiveutr2 <- relist(fiveutr, fiveutrByTx)

problem with mcols: ​

# Order by GENEID
> fiveutr2
GRangesList object of length 36036:
$ENSMUST00000027036.10
GRanges object with 1 range and 4 metadata columns:
                        seqnames             ranges strand |   exon_id            exon_name exon_rank                geneId
                           <Rle>          <IRanges>  <Rle> | <integer>          <character> <integer>           <character>
  ENSMUST00000027036.10     chr1 [4807823, 4807913]      + |        17 ENSMUSE00000792454.1         1 ENSMUSG00000025903.14

$ENSMUST00000150971.7
GRanges object with 1 range and 4 metadata columns:
                       seqnames             ranges strand | exon_id            exon_name exon_rank                geneId
  ENSMUST00000150971.7     chr1 [4807830, 4807913]      + |      18 ENSMUSE00000737251.2         1 ENSMUSG00000025903.14

$ENSMUST00000155020.1
GRanges object with 1 range and 4 metadata columns:
                       seqnames             ranges strand | exon_id            exon_name exon_rank               geneId
  ENSMUST00000155020.1     chr1 [4807892, 4807913]      + |      19 ENSMUSE00000730558.1         1 ENSMUSG00000104217.1

...
<36033 more elements>
-------
seqinfo: 22 sequences (1 circular) from an unspecified genome; no seqlengths
test <- fiveutr[order(mcols(fiveutr2)$geneId)]

Error in fiveutr[order(mcols(fiveutr2)$geneId)] :
  error in evaluating the argument 'i' in selecting a method for function '[': Error in .Method(..., na.last = na.last, decreasing = decreasing) :
  argument 1 is not a vector

> mcols(fiveutr2)$geneId
NULL

 

sessionInfo()
R version 3.2.3 (2015-12-10)
Platform: x86_64-apple-darwin14.5.0 (64-bit)
Running under: OS X 10.11.3 (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 utils     datasets  methods   base     

other attached packages:
[1] BiocInstaller_1.20.1                    BSgenome.Hsapiens.UCSC.hg38_1.4.1       Homo.sapiens_1.3.1                   
[4] TxDb.Hsapiens.UCSC.hg19.knownGene_3.2.2 org.Hs.eg.db_3.2.3                      GO.db_3.2.2                          
[7] RSQLite_1.0.0                           DBI_0.3.1                               OrganismDbi_1.12.1                   
[10] BSgenome.Mmusculus.UCSC.mm10_1.4.0      BSgenome_1.38.0                         rtracklayer_1.30.1                   
[13] Biostrings_2.38.3                       XVector_0.10.0                          hash_2.2.6                           
[16] GenomicFeatures_1.22.12                 AnnotationDbi_1.32.3                    Biobase_2.30.0                       
[19] GenomicRanges_1.22.4                    GenomeInfoDb_1.6.3                      IRanges_2.4.6                        
[22] S4Vectors_0.8.11                        BiocGenerics_0.16.1                    

loaded via a namespace (and not attached):
[1] graph_1.48.0               zlibbioc_1.16.0            GenomicAlignments_1.6.3    BiocParallel_1.4.3      
[5] tools_3.2.3                SummarizedExperiment_1.0.2 lambda.r_1.1.7             futile.logger_1.4.1     
[9] RBGL_1.46.0                futile.options_1.0.0       bitops_1.0-6               RCurl_1.95-4.7          
[13] biomaRt_2.26.1             Rsamtools_1.22.0           XML_3.98-1.3
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Yea, if you don't have an OrganismDbi package available, then things get annoying, since the TxDb methods for exonsBy() etc are frustratingly limited.

Maybe something like this will work?

library(TxDb.Hsapiens.UCSC.hg19.knownGene)
library(BSgenome.Hsapiens.UCSC.hg19)

txdb <- TxDb.Hsapiens.UCSC.hg19.knownGene

tx <- transcripts(txdb, columns=c("tx_id", "gene_id"))
exons <- exonsBy(txdb)
mcols(exons)$gene_id <- tx$gene_id[match(names(exons), tx$tx_id)]
cds <- cdsBy(txdb)
utrs <- psetdiff(exons[names(cds)], cds)

mcols(utrs)$gene_id <- drop(mcols(utrs)$gene_id)
utrs <- utrs[!is.na(mcols(utrs)$gene_id)]
utrseqs <- extractTranscriptSeqs(Hsapiens, utrs)

resplit <- function(x, f) {
    widths <- rowsum(lengths(x), f)
    widths <- setNames(as.integer(widths), rownames(widths))
    relist(unlist(x[order(f)], use.names=FALSE), PartitioningByWidth(widths))
}

resplit(utrseqs, mcols(utrs)$gene_id)

 

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If you want to keep the 3' and 5' UTRs separate, then maybe this code (3' UTR only, repeat for 5'):

tx <- transcripts(txdb, columns=c("tx_name", "gene_id"))
utrs <- threeUTRsByTranscript(txdb, use.names=TRUE)
mcols(utrs)$gene_id <- drop(tx$gene_id[match(names(utrs), tx$tx_name)])
utrseqs <- extractTranscriptSeqs(Hsapiens, utrs)
resplit(utrseqs, mcols(utrs)$gene_id) # resplit defined in previous answer

 

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Yep, that will do it.

A few more things:

Instead of using resplit(), you can just do unstrsplit(split(utrseqs, mcols(utrs)$gene_id)) for concatenating the UTRs sequences from the same gene. There is one difference though: resplit() will concatenate together all the transcripts that are not linked to a gene (orphan transcripts) but the unstrsplit(split()) solution will drop them:

sum(is.na(mcols(utrs)$gene_id))  # number of orphan transcripts
## [1] 988

answer1 <- resplit(utrseqs, mcols(utrs)$gene_id)
## Warning message:
## In rowsum.default(lengths(x), f) : missing values for 'group'

answer2 <- unstrsplit(split(utrseqs, mcols(utrs)$gene_id))

length(answer1)
## [1] 19189
length(answer2)
## [1] 19188

tail(answer1, n=4)
##   A DNAStringSet instance of length 4
##      width seq                                              names
## [1]  15498 ACGGCCTGGCCTGTACCCCAACG...TAAACTTGTGTTCCGGAAGAGG 9993
## [2]   1883 GTGTTGCTGAATTCCTGGGACTC...AACCATGTAAAGTTTTGTTGTA 9994
## [3]    172 GCCACTGCAGTCTGGGCCCCATC...TCATTAAACGGGCTGCGTTTAA 9997
## [4] 867733 CTCTCGCCTCACTGCGGCCTCCC...TGGAGGAGCTTTAGGACGCGGG <NA>

tail(answer2, n=3)
##   A DNAStringSet instance of length 3
##     width seq                                               names
## [1] 15498 ACGGCCTGGCCTGTACCCCAACG...ATAAACTTGTGTTCCGGAAGAGG 9993
## [2]  1883 GTGTTGCTGAATTCCTGGGACTC...AAACCATGTAAAGTTTTGTTGTA 9994
## [3]   172 GCCACTGCAGTCTGGGCCCCATC...ATCATTAAACGGGCTGCGTTTAA 9997

The additional sequence in answer1 is from all the orphan transcripts.

all(head(answer1, n=-1) == answer2)
## [1] TRUE

If you want the unstrsplit(split()) solution to keep them:

mcols(utrs)$gene_id[is.na(mcols(utrs)$gene_id)] <- "NA"
answer3 <- unstrsplit(split(utrseqs, mcols(utrs)$gene_id))
all(answer1 == answer3)
## [1] TRUE

Finally, in your original question you say that "extractTranscriptSeqs requires that the exons be ordered by genomic location" which is not correct. From its man page:

        Note that, for each transcript, the exons must be ordered by
        ascending rank, that is, by their position in the transcript.

See ?extractTranscriptSeqs for more information.

Cheers,
H.

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