Title:	Basic Sequence Processing Tool for Biological Data
Version:	0.1.4
Description:	Primarily created as an easy and understanding way to do basic sequences surrounding the central dogma of molecular biology.
License:	GPL-3
URL:	https://github.com/ambuvjyn/baseq
BugReports:	https://github.com/ambuvjyn/baseq/issues
Encoding:	UTF-8
RoxygenNote:	7.2.3
NeedsCompilation:	no
Packaged:	2023-05-02 19:07:38 UTC; ambuv
Author:	Ambu Vijayan [aut, cre], J. Sreekumar [aut] (Principal Scientist, ICAR - Central Tuber Crops Research Institute)
Maintainer:	Ambu Vijayan <ambuvjyn@gmail.com>
Repository:	CRAN
Date/Publication:	2023-05-03 11:40:02 UTC

Clean DNA file

Description

This function reads a multi FASTA file containing DNA sequences, removes any characters other than A, T, G, and C, and writes the cleaned sequences to a new multi FASTA file. The output file name is generated from the input file name with the suffix '_clean.fasta'.

Usage

clean_DNA_file(input_file, output_dir = "")

Arguments

Value

A character string specifying the path to the output FASTA file.

Examples

#sample_file_path_three <- system.file("extdata", "sample2_fa.fasta", package = "baseq")
#tempdir <- tempdir()
#temp_file_path <- file.path(tempdir, basename(sample_file_path_three))
#file.copy(sample_file_path_three, temp_file_path, overwrite = TRUE)
#clean_DNA_file(temp_file_path, output_dir = tempdir)

# Write to working directory
# clean_DNA_file(file_path)

# Write to custom directory
# clean_DNA_file(file_path, output_dir = "/path/to/directory/")

Clean DNA sequence

Description

This function takes a DNA sequence as input and removes any characters other than A, C, G, and T.

Usage

clean_DNA_sequence(sequence)

Arguments

Value

Cleaned DNA sequence

Examples

clean_DNA_sequence("ATGTCGTAGCTAGCTN")
# Output: "ATGTCGTAGCTAGCT"

Clean RNA file

Description

This function reads a multi FASTA file containing RNA sequences, removes any characters other than A, T, G, and C, and writes the cleaned sequences to a new multi FASTA file. The output file name is generated from the input file name with the suffix '_clean.fasta'.

Usage

clean_RNA_file(input_file, output_dir = "")

Arguments

Value

A character string specifying the path to the output FASTA file.

Examples

#sample_file_path_three <- system.file("extdata", "sample2_fa.fasta", package = "baseq")
#tempdir <- tempdir()
#temp_file_path <- file.path(tempdir, basename(sample_file_path_three))
#file.copy(sample_file_path_three, temp_file_path, overwrite = TRUE)
#clean_RNA_file(temp_file_path, output_dir = tempdir)

# Write to working directory
# clean_RNA_file(file_path)

# Write to custom directory
# clean_RNA_file(file_path, output_dir = "/path/to/directory/")

Clean RNA sequence

Description

This function takes a RNA sequence as input and removes any characters other than A, C, G, and T.

Usage

clean_RNA_sequence(sequence)

Arguments

Value

Cleaned RNA sequence

Examples

clean_RNA_sequence("AUGUCGTAGCTAGCTN")
# Output: "AUGUCGAGCAGC"

Clean DNA or RNA sequence

Description

This function takes a DNA or RNA sequence as input and removes any characters that are not A, C, G, T (for DNA) or A, C, G, U (for RNA).

Usage

clean_sequence(sequence, type = "DNA")

Arguments

Value

A character string containing the cleaned DNA or RNA sequence.

Examples

clean_sequence("atgcNnRYMK") # Returns "ATGC"
clean_sequence("auggcuuNnRYMK", type = "RNA") # Returns "AUGGCUU"

Count the number of A's, C's, G's, and T's in a DNA sequence

Description

This function takes a single argument, a DNA sequence as a character string, and counts the number of A's, C's, G's, and T's in the sequence. The counts are returned as a named vector.

Usage

count_bases(sequence)

Arguments

Value

a named integer vector containing the counts of A's, C's, G's, and T's

Examples

sequence <- "ATCGAGCTAGCTAGCTAGCTAGCT"
count_bases(sequence)
# A  C  G  T
# 6  6  6  6

Count frequency of a pattern in a sequence

Description

This function counts the frequency of a specific character or pattern in a given sequence.

Usage

count_seq_pattern(seq, pattern)

Arguments

Value

An integer representing the count of the pattern in the sequence.

Examples

seq <- "ATGGTGCTCCGTGCGCGCGCGCGCGCGCGCGCGCGCGCGCGCGCGCGCGCGCGCGCGCGCGCGCGCGCGCGCTACGTAG"
count_seq_pattern(seq, "CG")
# [1] 31

Translation of a DNA sequence

Description

This function takes a DNA sequence as input and translates it in all six reading frames.

Usage

dna_to_protein(sequence)

Arguments

Value

A list of character strings representing the translated protein sequences in all six frames.

Examples

sequence <- "ATCGAGCTAGCTAGCTAGCTAGCT"
dna_to_protein(sequence)
# Returns a list containing the translated protein sequences in all six frames:
# $`Frame F1`
# [1] "IELAS"
#
# $`Frame F2`
# [1] "SS"
#
# $`Frame F3`
# [1] "RAS"
#
# $`Frame R1`
# [1] "S"
#
# $`Frame R2`
# [1] "AS"
#
# $`Frame R3`
# [1] "LAS"

Transcription of a DNA sequence

Description

This function takes a DNA sequence as input and returns its RNA transcript.

Usage

dna_to_rna(sequence)

Arguments

Value

A character string representing the RNA transcript of the input DNA sequence.

Examples

sequence <- "ATCGAGCTAGCTAGCTAGCTAGCT"
dna_to_rna(sequence)
# Returns "AUCGAGCUAGCUAGCUAGCUAGCU"

Convert a FASTQ file to a FASTA file

Description

This function converts a FASTQ file to a FASTA file. The output file has the same name as the input FASTQ file, but with the extension changed to .fasta. This function removes the @ symbol at the beginning of FASTQ sequence names and replaces it with the > symbol for the FASTA format.

Usage

fastq_to_fasta(fastq_file)

Arguments

Value

A character string specifying the path to the output FASTA file.

Examples

#sample_file_path_two <- system.file("extdata", "sample_fq.fastq", package = "baseq")
#tempdir <- tempdir()
#temp_file_path <- file.path(tempdir, basename(sample_file_path_two))
#file.copy(sample_file_path_two, temp_file_path, overwrite = TRUE)
#fastq_to_fasta(temp_file_path)

# Output: "path/to/Temp/tempfoldername/sample_fq.fasta"

Calculate GC content of a DNA sequence

Description

Calculates the percentage of nucleotides in a DNA sequence that are either guanine (G) or cytosine (C).

Usage

gc_content(sequence)

Arguments

Value

A numeric value representing the percentage of nucleotides in the sequence that are G or C.

Examples

sequence <- "ATCGAGCTAGCTAGCTAGCTAGCT"
gc_content(sequence)
50

GC content of sequences in a multi FASTA file

Description

Function to calculate GC content of sequences in a multi FASTA file and write the results to a new FASTA file

Usage

gc_content_file(input_file)

Arguments

Examples

#sample_file_path <- system.file("extdata", "sample_fa.fasta", package = "baseq")
#clean_DNA_file(sample_file_path)

Read a fasta file into a dataframe and assign to the environment

Description

This function reads a fasta file and creates a dataframe with two columns: Header and Sequence. The dataframe is then assigned to the environment with the name same as the fasta file name but without the .fasta extension.

Usage

read.fasta_to_df(fasta_file)

Arguments

Value

This function does not return anything. It assigns the resulting dataframe to the environment.

Examples

# Read in sequences from a FASTA file

sample_file_path <- system.file("extdata", "sample_fa.fasta", package = "baseq")
read.fasta_to_df(sample_file_path)

Read a fasta file into a list and assign to the environment

Description

This function reads a fasta file and creates a list with two columns: Header and Sequence. The list is then assigned to the environment with the name same as the fasta file name but without the .fasta extension.

Usage

read.fasta_to_list(fasta_file)

Arguments

Value

This function does not return anything. It assigns the resulting list to the environment.

Examples

# Read in sequences from a FASTA file

sample_file_path <- system.file("extdata", "sample_fa.fasta", package = "baseq")
read.fasta_to_list(sample_file_path)

# Access a specific sequence by name
# sample_fa[["sample_seq.1"]]

Read a Fastq file and store it as a dataframe

Description

This function reads a Fastq file and stores it as a dataframe with three columns: Header, Sequence, and QualityScore.

Usage

read.fastq_to_df(fastq_file)

Arguments

Value

This function returns a dataframe with three columns: Header, Sequence, and QualityScore.

Examples

# Read in sequences from a FASTQ file

#sample_file_path_two <- system.file("extdata", "sample_fq.fastq", package = "baseq")
#read.fastq_to_df(sample_file_path_two)

Read a Fastq file and store it as a list

Description

This function reads a Fastq file and stores it as a list with three columns: Header, Sequence, and QualityScore.

Usage

read.fastq_to_list(fastq_file)

Arguments

Value

This function returns a list with three columns: Header, Sequence, and QualityScore.

Examples

# Read in sequences from a FASTQ file

sample_file_path_two <- system.file("extdata", "sample_fq.fastq", package = "baseq")
read.fastq_to_list(sample_file_path_two)

Generate Reverse Complement of DNA sequence

Description

Given a DNA sequence, the function generates the reverse complement of the sequence and returns it.

Usage

reverse_complement(sequence)

Arguments

Value

A character string containing the reverse complement of the input DNA sequence

Examples

sequence <- "ATCGAGCTAGCTAGCTAGCTAGCT"
reverse_complement(sequence)
# [1] "AGCTAGCTAGCTAGCTAGCTCGAT"

Generate Reverse Complement of DNA sequence

Description

Given a DNA sequence, the function generates the reverse complement of the sequence and returns it.

Usage

rna_reverse_complement(sequence)

Arguments

Value

A character string containing the reverse complement of the input DNA sequence

Examples

sequence <- "AUCGAGCUAGCUAGCUAGCUAGCU"
rna_reverse_complement(sequence)
# [1] "AGCUAGCUAGCUAGCUAGCUCGAU"

Reverse Transcription of a RNA sequence

Description

This function takes a RNA sequence as input and returns its DNA transcript.

Usage

rna_to_dna(sequence)

Arguments

Value

A character string representing the RNA transcript of the input RNA sequence.

Examples

sequence <- "AUCGAGCUAGCUAGCUAGCUAGCU"
rna_to_dna(sequence)
# Returns "ATCGAGCTAGCTAGCTAGCTAGCT"

Translation of a RNA sequence

Description

This function takes a RNA sequence as input and translates it in all six reading frames.

Usage

rna_to_protein(sequence)

Arguments

Value

A list of character strings representing the translated protein sequences in all six frames.

Examples

sequence <- "AUCGAGCUAGCUAGCUAGCUAGCU"
rna_to_protein(sequence)
# Returns a list containing the translated protein sequences in all six frames:
# $`Frame F1`
# [1] "IELAS"
#
# $`Frame F2`
# [1] "SS"
#
# $`Frame F3`
# [1] "RAS"
#
# $`Frame R1`
# [1] "S"
#
# $`Frame R2`
# [1] "AS"
#
# $`Frame R3`
# [1] "LAS"

Write a data frame to a fasta file

Description

This function writes a data frame to a fasta file with the same name as the data frame. The data frame is assumed to have two columns, "Header" and "Sequence", which represent the header and sequence lines of each fasta record, respectively.

Usage

write.df_to_fasta(df, output_dir = getwd())

Arguments

Value

This function does not return a value, but writes a fasta file to the specified output directory or the working directory.

Examples

#sample_file_path <- system.file("extdata", "sample_fa.fasta", package = "baseq")
#tempdir <- tempdir()
#temp_file_path <- file.path(tempdir, basename(sample_file_path))
#file.copy(sample_file_path, temp_file_path, overwrite = TRUE)
#read.fasta_to_df(sample_file_path)
#write.df_to_fasta(sample_fa, output_dir = tempdir)

# Write to working directory
# write.df_to_fasta(sample_fa)

# Write to custom directory
# write.df_to_fasta(sample_fa, output_dir = "/path/to/directory/")

Write a FASTQ file from a dataframe of reads

Description

Write a FASTQ file from a dataframe of reads

Usage

write.df_to_fastq(df, output_dir = getwd())

Arguments

Value

A FASTQ file with the same name as the input dataframe.

Examples

#sample_file_path_two <- system.file("extdata", "sample_fq.fastq", package = "baseq")
#tempdir <- tempdir()
#temp_file_path <- file.path(tempdir, basename(sample_file_path_two))
#file.copy(sample_file_path_two, temp_file_path, overwrite = TRUE)
#read.fastq_to_df(sample_file_path_two)
#write.df_to_fastq(sample_fq, output_dir = tempdir)

# Write to working directory
# write.df_to_fastq(sample_fq)

# Write to custom directory
# write.df_to_fastq(sample_fq, output_dir = "/path/to/directory/")

Convert DNA file to RNA file

Description

This function reads a multi FASTA file containing DNA sequences, converts each DNA sequence to RNA sequence, and writes the RNA sequences to a new multi FASTA file. The output file name is generated from the input file name with the suffix '_rna.fasta'.

Usage

write.dna_to_rna(input_file, output_dir = "")

Arguments

Value

A character string specifying the path to the output FASTA file.

Examples

#sample_file_path <- system.file("extdata", "sample_fa.fasta", package = "baseq")
#tempdir <- tempdir()
#temp_file_path <- file.path(tempdir, basename(sample_file_path))
#file.copy(sample_file_path, temp_file_path, overwrite = TRUE)
#write.dna_to_rna(temp_file_path, output_dir = tempdir)

# Write to working directory
# write.dna_to_rna(file_path)

# Write to custom directory
# write.dna_to_rna(file_path, output_dir = "/path/to/directory/")

Write a list of sequences to a FASTA file

Description

This function takes a list of sequences and writes them to a FASTA file. The name of the list is used as the base name for the output file with the .fasta extension. Each sequence in the list is written to the output file in FASTA format with the sequence name as the header.

Usage

write.list_to_fasta(sequence_list, output_dir = getwd())

Arguments

Examples

sequences <- list("ACGT", "ATCG")
tempdir <- tempdir()
write.list_to_fasta(sequences, output_dir = tempdir)

# Write to working directory
# write.list_to_fasta(sequences)

# Write to custom directory
# write.list_to_fasta(sequences, output_dir = "/path/to/directory/")

Write a list of sequence_bases and quality scores to a FASTQ file

Description

This function takes a list of sequence_bases and quality scores and writes them to a FASTQ file. The name of the list is used as the base name for the output file with the .fastq extension. Each sequence in the list is written to the output file in FASTQ format with the sequence name as the header and the quality scores on the following line.

Usage

write.list_to_fastq(sequence_list, output_dir = getwd())

Arguments

Examples

sequence_bases <- list("ACGT", "ATCG")
quality_scores <- list("IIII", "JJJJ")
sequences <- list(seq1=list(Sequence=sequence_bases[[1]], QualityScore=quality_scores[[1]]),
                       seq2=list(Sequence=sequence_bases[[2]], QualityScore=quality_scores[[2]]))
tempdir <- tempdir()
write.list_to_fastq(sequences, output_dir = tempdir)

# Write to working directory
# write.list_to_fastq(sequences)

# Write to custom directory
# write.list_to_fastq(sequences, output_dir = "/path/to/directory/")

Convert RNA file to DNA file

Description

This function reads a multi FASTA file containing RNA sequences, converts each RNA sequence to DNA sequence, and writes the DNA sequences to a new multi FASTA file. The output file name is generated from the input file name with the suffix '_rna.fasta'.

Usage

write.rna_to_dna(input_file, output_dir = "")

Arguments

Value

A character string specifying the path to the output FASTA file.

Examples

#sample_file_path <- system.file("extdata", "sample3_fa.fasta", package = "baseq")
#tempdir <- tempdir()
#temp_file_path <- file.path(tempdir, basename(sample_file_path))
#file.copy(sample_file_path, temp_file_path, overwrite = TRUE)
#write.rna_to_dna(temp_file_path, output_dir = tempdir)

# Write to working directory
# write.rna_to_dna(file_path)

# Write to custom directory
# write.rna_to_dna(file_path, output_dir = "/path/to/directory/")