Produces sliceable
-inheriting objects to query "in situ" FASTA files.
track.fasta.multi
is designed to handle a single multi-FASTA file aggregating all the chromosomes of an organism. An index as generated by the HTSlib (formerly "SAMtools") faidx
command is required.
track.fasta.collection
is designed to handle a collection of standard FASTA files, one per chromosome.
track.fasta.multi(fastaFile, indexFile, .name, .organism, .assembly,
.parameters, warn = TRUE)
track.fasta.collection(files, chromosomes, .name, .organism, .assembly,
.parameters, warn = TRUE)
An object of class track.fasta
.
Single character value, the file name and path to a multi-FASTA file (.fa) to build a track upon.
Single character value, the file name and path to a multi-FASTA index file (.fai) corresponding to fastaFile
. This index file is supposd to be produced by the faidx
command from SAMtools.
Single character value, to fill the name
field inherited from drawable
.
Single character value, to fill the organism
field of the object.
Single character value, to fill the assembly
field of the object.
A list
of drawing parameters, to fill the parameters
field of the object.
Single logical value, to be passed to the appropriate check
method. Other conversion warnings rely on this value too in track.table
.
Character vector, file names and paths to multiple single-FASTA file (.fa) to build a track upon (one per chromosome).
Character vector, chromosomes names to attribute to each file in files
.
Sylvain Mareschal
Both functions suppose the FASTA files to respect the following :
They begin with a single line of comment, after a '>' sign.
All sequence lines have the same length (whatever it is).
The line separator (\n, \r\n) is always the same in a file.
No empty line.
Returned sequences may be wrong (without error or notice !) if any of these is not fullfilled. Standard sources (see below) usually enforce these conditions.
Example of FASTA file collection (human assembly 'hg19'), from UCSC : http://hgdownload.soe.ucsc.edu/goldenPath/hg19/bigZips/chromFa.tar.gz
Example of single multi-FASTA file (human assembly 'hg19'), from 1000 genomes : ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/technical/reference/human_g1k_v37.fasta.gz
The faidx documentation, from the HTSlib project.
track-constructors
, Annotation
tk.browse
, browsePlot