import.ofst: Load GRanges / GAlignments object from .ofst

In Roleren/ORFik: Open Reading Frames in Genomics

Load GRanges / GAlignments object from .ofst

Description

A much faster way to store, load and use bam files.
.ofst is ORFik fast serialized object, an optimized format for coverage reads with cigar and replicate number. It uses the fst format as back-end: fst-package.
A .ofst ribo seq file can compress the information in a bam file from 5GB down to a few MB. This new files has super fast reading time, only a few seconds, instead of minutes. It also has random index access possibility of the file.
.ofst is represented as a data.frane format with minimum 4 columns:
1. chromosome
2. start (left most position)
3. strand (+, -, *)
4. width (not added if cigar exists)
5. cigar (not needed if width exists): (cigar # M's, match/mismatch total)
5. score: duplicates of that read
6. size: qwidth according to reference of read

If file is from GAlignmentPairs, it will contain a cigar1, cigar2 instead of cigar and start1 and start2 instead of start

Usage

import.ofst(file, strandMode = 0, seqinfo = NULL)

Arguments

file	a path to a .ofst file
strandMode	numeric, default 0. Only used for paired end bam files. One of (0: strand = *, 1: first read of pair is +, 2: first read of pair is -). See ?strandMode. Note: Sets default to 0 instead of 1, as readGAlignmentPairs uses 1. This is to guarantee hits, but will also make mismatches of overlapping transcripts in opposite directions.
seqinfo	Seqinfo object, defaul NULL (created from ranges). Add to avoid warnings later on differences in seqinfo.

Details

Other columns can be named whatever you want and added to meta columns. Positions are 1-based, not 0-based as .bed. Import with import.ofst

Value

a GAlignment, GAlignmentPairs or GRanges object, dependent of if cigar/cigar1 is defined in .ofst file.

Examples

## GRanges
gr <- GRanges("1:1-3:-")
tmp <- file.path(tempdir(), "path.ofst")
# export.ofst(gr, file = tmp)
# import.ofst(tmp)
## GAlignment
# Make input data.frame
df <- data.frame(seqnames = "1", cigar = "3M", start = 1L, strand = "+")
ga <- ORFik:::getGAlignments(df)
# export.ofst(ga, file = tmp)
# import.ofst(tmp)

Roleren/ORFik documentation built on Oct. 19, 2024, 7:37 a.m.