Package 'seqmagick'

Title: Sequence Manipulation Utilities
Description: Supports reading and writing sequences for different formats (currently interleaved and sequential formats for 'FASTA' and 'PHYLIP'), file conversion, and manipulation (e.g. filter sequences that contain specify pattern, export consensus sequence from an alignment).
Authors: Guangchuang Yu [aut, cre]
Maintainer: Guangchuang Yu <[email protected]>
License: Artistic-2.0
Version: 0.1.7
Built: 2024-11-03 04:36:14 UTC
Source: https://github.com/yulab-smu/seqmagick

Help Index

bam2DNAStringSet

Description

convert bam file to aligned fasta file

Usage

bam2DNAStringSet(bamfile, refseq)

Arguments

bamfile

bam file
refseq

refseq, DNAStringSet object

Value

DNAStringSet object

Author(s)

Guangchuang Yu

bam2DNAStringSet2

Description

convert bam file to aligned fasta file

Usage

bam2DNAStringSet2(bamfile, refseq)

Arguments

bamfile

bam file
refseq

refseq, DNAStringSet object

Value

DNAStringSet object

Author(s)

Guangchuang Yu

bs_aln

Description

sequence alignment

Usage

bs_aln(x, method = "muscle", ...)

Arguments

x

XStringSet object
method

alignment method
...

additional parameter

Value

aligned sequences, XStringSet object

Author(s)

Guangchuang Yu

Examples

## Not run: 
fa_file <- system.file("extdata/HA.fas", package="seqmagick")
x <- fa_read(fa_file)
bs_aln(x)

## End(Not run)

bs_filter

Description

biological sequence filter by searching pattern

Usage

bs_filter(x, pattern, by = "description", ignore.case = FALSE)

Arguments

x

BStringSet object
pattern

keyword for filter
by

one of 'description' and 'sequence'
ignore.case

logical

Value

BStringSet object

Author(s)

Guangchuang Yu

Examples

fa_file <- system.file("extdata/HA.fas", package="seqmagick")
x <- fa_read(fa_file)
bs_filter(x, 'ATGAAAGTAAAA', by='sequence')

bs_hamming

Description

hamming distances of sequences

Usage

bs_hamming(x, count_indel = FALSE, ...)

Arguments

x

BStringSet object
count_indel

whether count indel or not
...

additional parameters

Value

hamming distance

Author(s)

Guangchuang Yu

Examples

## Not run: 
fa_file <- system.file("extdata/HA.fas", package="seqmagick")
x <- fa_read(fa_file)
## align first 5 sequences, use `bs_aln(x)` to align all sequences
aln <- bs_aln(x[1:5])
bs_hamming(aln)

## End(Not run)

bs_rename

Description

rename sequence

Usage

bs_rename(x, mapping, position, sep, mode)

Arguments

x

BStringSet object
mapping

two column data.frame
position

rename token at specific position
sep

sepator to divide token
mode

one of 'replace', 'prefix' or 'suffix'

Value

BStringSet

Author(s)

Guangchuang Yu

consensus

Description

consensus of aligned sequences

consensus of aligned sequences

Usage

consensus(x, type = "DNA")

bs_consensus(x, type = "DNA", r = 1)

Arguments

x

BStringSet object
type

currently, only DNA supported
r

if any NT > r, it will be selected as representative base

Value

consensus sequence string

consensus sequence string

Author(s)

Guangchuang Yu

Examples

## Not run: 
fa_file <- system.file("extdata/HA.fas", package="seqmagick")
x <- fa_read(fa_file)
## align first 5 sequences, use `bs_aln(x)` to align all sequences
aln <- bs_aln(x[1:5])
## or bs_consensus(aln)
consensus(aln)

## End(Not run)

download_genbank

Description

download genbank or fasta file by accession number

Usage

download_genbank(acc, db = "nuccore", format = "genbank", outfile = NULL, ...)

Arguments

acc

accession number(s)
db

supported db, currently 'nuccore'
format

one of 'genbank' or 'fasta'
outfile

output file, by default, acc.gb or acc.fa
...

additional parameters for download.file

Value

output file vector

Author(s)

Guangchuang Yu

Examples

## Not run: 
tmpgb <- tempfile(fileext = '.gb')
tmpfa <- tempfile(fileext = '.fa')
download_genbank(acc='AB115403', format='genbank', outfile=tmpgb)
download_genbank(acc='AB115403', format='fasta', outfile=tmpfa)

## End(Not run)

fa_combine

Description

combine 2 fasta files into 1

Usage

fa_combine(file1, file2, outfile = NULL, type = "interleaved")

Arguments

file1

fasta file 1
file2

fasta file 2
outfile

output file
type

one of interleaved and sequential

Value

BStringSet

Author(s)

Guangchuang Yu

Examples

fa_file <- system.file("extdata/HA.fas", package="seqmagick")
x <- fa_read(fa_file)
fa1 <- tempfile(fileext=".fa")
fa2 <- tempfile(fileext=".fa")
fa_write(x[1:5], fa1)
fa_write(x[6:10], fa2)
fa_combine(fa1, fa2)

fa_filter

Description

fasta filter by searching pattern

Usage

fa_filter(
  fasfile,
  pattern,
  by = "description",
  ignore.case = FALSE,
  outfile = NULL,
  type = "interleaved"
)

Arguments

fasfile

input fasta file
pattern

keyword for filter
by

one of 'description' and 'sequence'
ignore.case

logical
outfile

output file
type

one of 'interleaved' and 'sequential'

Value

BStringSet object

Author(s)

Guangchuang Yu

fa_rename

Description

rename fasta sequence name

Usage

fa_rename(fasfile, mapping_file, position, sep, mode, outfile)

Arguments

fasfile

fasta file
mapping_file

mapping file
position

rename token at specific position
sep

sepator to divide token
mode

one of 'replace', 'prefix' or 'suffix'
outfile

output file

Value

BStringSet object

Author(s)

Guangchuang Yu

fa_to_interleaved

Description

convert fasta file to interleaved format

convert fasta file to sequential format

Usage

fa_to_interleaved(file, outfile)

fa_to_sequential(file, outfile)

Arguments

file

fasta file
outfile

output file

Value

None

None

Author(s)

Guangchuang Yu

Examples

fa_file <- system.file("extdata/HA.fas", package="seqmagick")
fa1 <- tempfile(fileext = '.fa')
fa2 <- tempfile(fileext = '.fa')
fa_to_interleaved(fa_file, fa1)
fa_to_sequential(fa_file, fa2)

fa_write

Description

write fasta file

Usage

fa_write(x, outfile, type = "interleaved")

Arguments

x

XStringSet object
outfile

output file
type

one of interleaved and sequential

Value

None

Author(s)

Guangchuang Yu

References

https://phylipweb.github.io/phylip/

Examples

phy_file <- system.file("extdata/HA.phy", package="seqmagick")
x <- phy_read(phy_file)
fa_file <- tempfile(fileext = '.fas')
fa_write(x, fa_file)

fas2phy

Description

convert fasta (aligned sequences) to phylip format

Usage

fas2phy(fasfile, outfile = "out.phy", type = "sequential")

Arguments

fasfile

aligned sequences in fasta format
outfile

output file
type

one of interleaved and sequential

Value

None

Author(s)

Guangchuang Yu fa_file <- system.file("extdata/HA.fas", package="seqmagick") phy_file <- tempfile(fileext = ".phy") fas2phy(fa_file, phy_file)

gb_read

Description

extract accession number and sequence from genbank file

Usage

gb_read(file)

Arguments

file

input genbank file

Value

sequence object

Author(s)

Guangchuang Yu

get_id

Description

get id at specific position

Usage

get_id(x, sep = " ", position)

Arguments

x

sequence description line
sep

separator to split x
position

id position

Value

id

Author(s)

Guangchuang Yu

Examples

fa_file <- system.file("extdata/HA.fas", package="seqmagick")
x <- fa_read(fa_file)
get_id(names(x)[1:5], sep = " ", position=1)

read sequence alignment file

Description

read sequence alignment file

Usage

mega_read(file)

fa_read(file, type = "auto")

clw_read(file, type = "auto")

sth_read(file, type = "auto")

Arguments

file

multiple sequence file
type

one of 'DNA', 'RNA', 'AA', 'Protein', 'unknown' or 'auto'

Value

BStringSet object

Author(s)

Guangchuang Yu

Examples

fa_file <- system.file("extdata/HA.fas", package="seqmagick")
fa_read(fa_file)

mega_file <- system.file("extdata/mega/Crab_rRNA.meg", package="seqmagick")
mega_read(mega_file)

phy_read

Description

read aligned sequences in phylip format

Usage

phy_read(file)

Arguments

file

phylip file

Value

BStringSet object

Author(s)

Guangchuang Yu

Examples

phy_file <- system.file("extdata/HA.phy", package="seqmagick")
phy_read(phy_file)

phy_write

Description

write phylip file

Usage

phy_write(x, outfile, type = "sequential")

Arguments

x

XStringSet object
outfile

output file
type

one of interleaved and sequential

Value

None

Author(s)

Guangchuang Yu

Examples

## Not run: 
fa_file <- system.file("extdata/HA.fas", package="seqmagick")
x <- fa_read(fa_file)
aln <- bs_aln(x[1:5])
phy_file <- tempfile(fileext = '.phy')
phy_write(aln, phy_file)

## End(Not run)

phy2fas

Description

convert phylip file to fasta file

Usage

phy2fas(phyfile, outfile = "out.fas", type = "interleaved")

Arguments

phyfile

phylip file
outfile

output file
type

one of interleaved and sequential

Value

None

Author(s)

Guangchuang Yu

Examples

phy_file <- system.file("extdata/HA.phy", package="seqmagick")
fa_file <- tempfile(fileext = '.fas')
phy2fas(phy_file, fa_file)

renameTXT

Description

rename txt file (eg Description line of fasta file) according to first token (eg accession number)

Usage

renameTXT(txt_file, name_file, sep = "_", split = TRUE)

Arguments

txt_file

txt file
name_file

name file
sep

separator
split

logical, split result or not

Value

None

Author(s)

Guangchuang Yu

replaceInside

Description

replace character for example from '-' to 'N' of fasta sequence that only applied inside sequence any '-' character at start/end of the sequence (aligned seqs may contains '-' at prefix/suffix) will not be replaced

Usage

replaceInside(fasfile, from = "-", to = "N", outfile = NULL)

Arguments

fasfile

fasta file
from

character to be replaced, '-' by default
to

replace 'from' to 'to', 'N' by default
outfile

output file

Value

DNAStringSet

Author(s)

Guangchuang Yu

seqlen

Description

sequence length

Usage

seqlen(fasfile)

Arguments

fasfile

fasta file

Value

numeric vector

Author(s)

Guangchuang Yu