In sethiyap/fastaR: Fasta Sequence Manipulation

knitr::opts_chunk$set(
  collapse = TRUE,
  comment = "#>",
  fig.path = "man/figures/README-",
  out.width = "100%"
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fastaR

cat(
badger::badge_devel("sethiyap/fastaR" , color = "blue"),
badger::badge_lifecycle()
)

Fasta sequence manipulation is required while performing gene set or genome-wide analysis in RNASeq and ChIPSeq. Sequences of group of genes belonging to a pathway or biological term helps to determine the motifs/signature sequences associated with those genes. It also helps to predict regulators for differentially enriched genes. fastaR provides different ways to manipulate and gather information from the set of sequences. For instance, summary of input fasta file (fa_summary) or percentage of GC in given sequences (fa_percent_GC). Additionally, gene list specific sequences (fa_some_records) or promoters for given genes can also be fetched (get_promoter_from_feature). Together, fastaR provides easy way to analyze and manipulate sequences with minimal input of a feature file (bed or gff) and/or reference genome file (.fa or .fasta).

Install

if(require("devtools")){
        options(repos = BiocManager::repositories())
        devtools::install_github("sethiyap/fastaR",build = FALSE)
} else{
        options(repos = BiocManager::repositories())
        install.packages("devtools")
        devtools::install_github("sethiyap/fastaR", build = FALSE)
}

faUtils

fa_some_records()

# Input list of genes
myGenelist <- system.file("exdata", "Sc_myGenelist.txt", package = "fastaR")
myGenelist <- scan(myGenelist,  what="character", sep=NULL)
head(myGenelist)

# Reference fasta sequence to be subsetted
ref_fasta <- system.file("exdata", "Sc_nucl_R64-2-1.fasta", package = "fastaR",mustWork = TRUE)

# Function
fastaR::fa_some_records(gene_list=myGenelist, fasta_file=ref_fasta, outfile="sc_myGenelist.fa")

fa_size()

ref_fasta <- system.file("exdata", "Sc_nucl_R64-2-1.fasta", package = "fastaR")
cc <- fastaR::fa_size(fasta_file=ref_fasta)
head(cc)

fa_summary()

ref_fasta <- system.file("exdata", "Sc_nucl_R64-2-1.fasta", package = "fastaR")
fs <- fastaR::fa_summary(fasta_file=ref_fasta)
print(t(fs))

fa_percent_GC()

• for more than 20 sequences

ref_fasta <- system.file("exdata", "Sc_nucl_R64-2-1.fasta", package = "fastaR")
ff <- fastaR::fa_percent_GC(fasta_file=ref_fasta)
head(ff)

• for less than 20 sequences

ref_fasta <- system.file("exdata", "Sc_nucl_subset.fa", package = "fastaR")
ft <- fastaR::fa_percent_GC(fasta_file=ref_fasta)
head(ft)

getUtils

get_fasta_from_bed()

# path to bed (.bed) file
bed_file_in <- system.file("exdata","Sc_ref_genes.bed", package = "fastaR")

# path to reference genome sequence
ref_fasta <- system.file("exdata", "Sc_ref_genome.fasta", package = "fastaR")

fastaR::get_fasta_from_bed(bedFile=bed_file_in, fasta_file=ref_fasta, write_output=FALSE)

get_promoter_from_feature()

# path to reference sequence file
ref_fasta <- system.file("exdata", "Sc_ref_genome.fasta", package = "fastaR")

# for gff as feature file
feature_file_in <- system.file("exdata","Sc_ref_genes.gff", package = "fastaR")
pr <- fastaR::get_promoter_from_feature(feature_file=feature_file_in, fasta_file=ref_fasta, write_outputfasta= FALSE, write_promoterbed= FALSE, upstream_bp= 1000, downstream_bp= 100)
pr

# for bed as feature file
feature_file_in <- system.file("exdata","Sc_ref_genes.bed", package = "fastaR")
pr <- fastaR::get_promoter_from_feature(feature_file=feature_file_in, fasta_file=ref_fasta, write_outputfasta= FALSE, write_promoterbed= FALSE, upstream_bp= 1000, downstream_bp= 100)
pr

get_flank_from_feature()

flanks are different region in gene's structure as illustrated below: 1. sequence upstream of start coordinate 2. sequence downstream of start coordinate 3. sequence downstream of end coordinate 4. upstream and downstream of start coordinate 5. upstream and downstream of end coordinate 6. upstream and downstream of feature/gene coordinates 7. middle region, i.e. distance (in bp) from start and end coordinate Start----->ATGCGGATGCGGTC<------End

# path to reference sequence file
ref_fasta <- system.file("exdata", "Sc_ref_genome.fasta", package = "fastaR")

# for gff as feature file

feature_file_in <- system.file("exdata","Sc_ref_genes.gff", package = "fastaR")
ss <- fastaR::get_flank_from_feature(feature_file = feature_file_in, fasta_file = ref_fasta, flank_type = 2)
ss

# for bed file as feature file

feature_file_in <- system.file("exdata","Sc_ref_genes.bed", package = "fastaR")
ss <- fastaR::get_flank_from_feature(feature_file = feature_file_in, fasta_file = ref_fasta, flank_type = 2)
ss

get_random_sequences_from_fasta()

# load reference fasta
ref_fasta <- system.file("exdata", "Sc_ref_genome.fasta", package = "fastaR")

rr <- fastaR::get_random_sequences_from_fasta(fasta_file = ref_fasta,
                                 numberOfRandomSequences = 100,
                                 lengthOfRandomSequence = 500)

rr

sethiyap/fastaR documentation built on June 16, 2020, 1:41 a.m.