Biostrings (version 2.40.2)

PairwiseAlignments-io: Write a PairwiseAlignments object to a file

Description

The writePairwiseAlignments function writes a PairwiseAlignments object to a file. Only the "pair" format is supported at the moment.

Usage

writePairwiseAlignments(x, file="", Matrix=NA, block.width=50)

Arguments

x

A PairwiseAlignments object, typically returned by the pairwiseAlignment function.

file

A connection, or a character string naming the file to print to. If "" (the default), writePairwiseAlignments prints to the standard output connection (aka the console) unless redirected by sink. If it is "|cmd", the output is piped to the command given by cmd, by opening a pipe connection.

Matrix

A single string containing the name of the substitution matrix (e.g. "BLOSUM50") used for the alignment. See the substitutionMatrix argument of the pairwiseAlignment function for the details. See ?substitution.matrices for a list of predefined substitution matrices available in the Biostrings package.

block.width

A single integer specifying the maximum number of sequence letters (including the "-" letter, which represents gaps) per line.

Details

The "pair" format is one of the numerous pairwise sequence alignment formats supported by the EMBOSS software. See http://emboss.sourceforge.net/docs/themes/AlignFormats.html for a brief (and rather informal) description of this format.

References

http://emboss.sourceforge.net/docs/themes/AlignFormats.html

See Also

• pairwiseAlignment
• PairwiseAlignments-class
• substitution.matrices

Examples

## ---------------------------------------------------------------------
## A. WITH ONE PAIR
## ---------------------------------------------------------------------
pattern <- DNAString("CGTACGTAACGTTCGT")
subject <- DNAString("CGTCGTCGTCCGTAA")
pa1 <- pairwiseAlignment(pattern, subject)
pa1
writePairwiseAlignments(pa1)
writePairwiseAlignments(pa1, block.width=10)
## The 2 bottom-right numbers (16 and 15) are the lengths of
## the original pattern and subject, respectively.

pa2 <- pairwiseAlignment(pattern, subject, type="global-local")
pa2  # score is different!
writePairwiseAlignments(pa2)
## By just looking at the file, we can't tell the length of the
## original subject! Could be 13, could be more...

pattern <- DNAString("TCAACTTAACTT")
subject <- DNAString("GGGCAACAACGGG")
pa3 <- pairwiseAlignment(pattern, subject, type="global-local",
                         gapOpening=-2, gapExtension=-1)
writePairwiseAlignments(pa3)

## ---------------------------------------------------------------------
## B. WITH MORE THAN ONE PAIR (AND NAMED PATTERNS)
## ---------------------------------------------------------------------
pattern <- DNAStringSet(c(myp1="ACCA", myp2="ACGCA", myp3="ACGGCA"))
pa4 <- pairwiseAlignment(pattern, subject)
pa4
writePairwiseAlignments(pa4)

## ---------------------------------------------------------------------
## C. REPRODUCING THE ALIGNMENT SHOWN AT
##    http://emboss.sourceforge.net/docs/themes/alnformats/align.pair
## ---------------------------------------------------------------------
pattern <- c("TSPASIRPPAGPSSRPAMVSSRRTRPSPPGPRRPTGRPCCSAAPRRPQAT",
             "GGWKTCSGTCTTSTSTRHRGRSGWSARTTTAACLRASRKSMRAACSRSAG",
             "SRPNRFAPTLMSSCITSTTGPPAWAGDRSHE")
subject <- c("TSPASIRPPAGPSSRRPSPPGPRRPTGRPCCSAAPRRPQATGGWKTCSGT",
             "CTTSTSTRHRGRSGWRASRKSMRAACSRSAGSRPNRFAPTLMSSCITSTT",
             "GPPAWAGDRSHE")
pattern <- unlist(AAStringSet(pattern))
subject <- unlist(AAStringSet(subject))
pattern  # original pattern
subject  # original subject
data(BLOSUM62)
pa5 <- pairwiseAlignment(pattern, subject,
                         substitutionMatrix=BLOSUM62,
                         gapOpening=9.5, gapExtension=0.5)
pa5
writePairwiseAlignments(pa5, Matrix="BLOSUM62")