extractTranscriptSeqs(x, transcripts, ...)

## S4 method for signature 'DNAString'
extractTranscriptSeqs(x, transcripts, strand="+")

## S4 method for signature 'ANY'
extractTranscriptSeqs(x, transcripts, ...)

## ---------------------------------------------------------------------
## 1. A TOY EXAMPLE
## ---------------------------------------------------------------------

library(Biostrings)

## A chromosome of length 30:
x <- DNAString("ATTTAGGACACTCCCTGAGGACAAGACCCC")

## 2 transcripts on 'x':
tx1 <- IRanges(1, 8)            # 1 exon
tx2 <- c(tx1, IRanges(12, 30))  # 2 exons
transcripts <- IRangesList(tx1=tx1, tx2=tx2)
extractTranscriptSeqs(x, transcripts)

## By default, all the exons are considered to be on the plus strand.
## We can use the 'strand' argument to tell extractTranscriptSeqs()
## to extract them from the minus strand.

## Extract all the exons from the minus strand:
extractTranscriptSeqs(x, transcripts, strand="-")

## Note that, for a transcript located on the minus strand, the exons
## should typically be ordered by descending position on the reference
## genome in order to reflect their rank in the transcript:
extractTranscriptSeqs(x, IRangesList(tx1=tx1, tx2=rev(tx2)), strand="-")

## Extract the exon of the 1st transcript from the minus strand:
extractTranscriptSeqs(x, transcripts, strand=c("-", "+"))

## Extract the 2nd exon of the 2nd transcript from the minus strand:
extractTranscriptSeqs(x, transcripts, strand=list("-", c("+", "-")))

## ---------------------------------------------------------------------
## 2. A REAL EXAMPLE
## ---------------------------------------------------------------------

## Load a genome:
library(BSgenome.Hsapiens.UCSC.hg19)
genome <- BSgenome.Hsapiens.UCSC.hg19

## Load a TxDb object:
txdb_file <- system.file("extdata", "hg19_knownGene_sample.sqlite",
                         package="GenomicFeatures")
txdb <- loadDb(txdb_file)

## Check that 'txdb' is based on the hg19 assembly:
txdb

## Extract the exon ranges grouped by transcript from 'txdb':
transcripts <- exonsBy(txdb, by="tx", use.names=TRUE)

## Extract the transcript sequences from the genome:
tx_seqs <- extractTranscriptSeqs(genome, transcripts)
tx_seqs

## A sanity check:
stopifnot(identical(width(tx_seqs), unname(sum(width(transcripts)))))

## Note that 'tx_seqs' can also be obtained with:
extractTranscriptSeqs(genome, txdb, use.names=TRUE)

## ---------------------------------------------------------------------
## 3. USING extractTranscriptSeqs() TO EXTRACT CDS SEQUENCES
## ---------------------------------------------------------------------

cds <- cdsBy(txdb, by="tx", use.names=TRUE)
cds_seqs <- extractTranscriptSeqs(genome, cds)
cds_seqs

## A sanity check:
stopifnot(identical(width(cds_seqs), unname(sum(width(cds)))))

## Note that, alternatively, the CDS sequences can be obtained from the
## transcript sequences by removing the 5' and 3' UTRs:
tx_lens <- transcriptLengths(txdb, with.utr5_len=TRUE, with.utr3_len=TRUE)
stopifnot(identical(tx_lens$tx_name, names(tx_seqs)))  # sanity
## Keep the rows in 'tx_lens' that correspond to a sequence in 'cds_seqs'
## and put them in the same order as in 'cds_seqs':
m <- match(names(cds_seqs), names(tx_seqs))
tx_lens <- tx_lens[m, ]
utr5_width <- tx_lens$utr5_len
utr3_width <- tx_lens$utr3_len
cds_seqs2 <- narrow(tx_seqs[m],
                    start=utr5_width+1L, end=-(utr3_width+1L))
stopifnot(identical(as.character(cds_seqs2), as.character(cds_seqs)))

## ---------------------------------------------------------------------
## 4. TRANSLATE THE CDS SEQUENCES
## ---------------------------------------------------------------------

prot_seqs <- translate(cds_seqs, if.fuzzy.codon="solve")

## Note that, by default, translate() uses The Standard Genetic Code to
## translate codons into amino acids. However, depending on the organism,
## a different genetic code might be needed to translate CDS sequences
## located on the mitochodrial chromosome. For example, for vertebrates,
## the following code could be used to correct 'prot_seqs':
SGC1 <- getGeneticCode("SGC1")
chrM_idx <- which(all(seqnames(cds) == "chrM"))
prot_seqs[chrM_idx] <- translate(cds_seqs[chrM_idx], genetic.code=SGC1,
                                 if.fuzzy.codon="solve")