| Title: | Sequence Manipulation Utilities |
| Version: | 0.1.7 |
| 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). |
| Depends: | R (≥ 3.6.0) |
| Imports: | Biostrings, magrittr, stats, utils, yulab.utils (> 0.1.1) |
| Suggests: | downloader, knitr, rmarkdown, GenomicAlignments, GenomicRanges, IRanges, muscle, Rsamtools, prettydoc |
| VignetteBuilder: | knitr |
| ByteCompile: | true |
| URL: | https://github.com/YuLab-SMU/seqmagick |
| BugReports: | https://github.com/YuLab-SMU/seqmagick/issues |
| License: | Artistic-2.0 |
| Encoding: | UTF-8 |
| RoxygenNote: | 7.2.3 |
| NeedsCompilation: | no |
| Packaged: | 2024-01-09 02:10:27 UTC; HUAWEI |
| Author: | Guangchuang Yu 
[aut, cre] |
| Maintainer: | Guangchuang Yu <guangchuangyu@gmail.com> |
| Repository: | CRAN |
| Date/Publication: | 2024-01-09 03:40:02 UTC |
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)
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)
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)
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