Supported file formats | Sequence I/O | FASTA | PHYLIP | CLUSTAL and STOCKHOLM | MEGA | GenBank | Download sequences from NCBI | Format conversion | fasta and phylip conversion | interleaved and sequential format conversion | Sequence manipulation | Filtering, alignment and consensus | Renaming sequences | Summary statistics | Bugs/Feature requests | Session info | References
Package: seqmagick 0.1.9
Guangchuang Yu
seqmagick: Sequence Manipulation Utilities
Tools for reading and writing biological sequences in multiple formats, including 'FASTA', 'PHYLIP', 'CLUSTAL', 'STOCKHOLM', 'MEGA' and 'GenBank'. Supports interleaved and sequential layouts where applicable, and reads or writes gzip, bzip2 and xz compressed files transparently. Converts between formats, renames sequences via a two-column mapping, summarizes sequence counts, lengths, GC content and ambiguous characters, and manipulates sequence sets (e.g., filtering by patterns and computing consensus sequences from alignments). Also includes functions to download nucleotide records from NCBI by accession.
Authors:
seqmagick_0.1.9.tar.gz
seqmagick_0.1.9.zip(r-4.7-any)seqmagick_0.1.9.zip(r-4.6-any)seqmagick_0.1.9.zip(r-4.5-any)
seqmagick_0.1.9.tgz(r-4.6-any)seqmagick_0.1.9.tgz(r-4.5-any)
seqmagick_0.1.9.tar.gz(r-4.7-any)seqmagick_0.1.9.tar.gz(r-4.6-any)
seqmagick_0.1.9.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
seqmagick/json (API)
| # Install 'seqmagick' in R: |
| install.packages('seqmagick', repos = c('https://yulab-smu.r-universe.dev', 'https://cloud.r-project.org')) |
Bug tracker:https://github.com/yulab-smu/seqmagick/issues
Last updated from:17f392cbd7. Checks:9 OK. Indexed: yes.
| Target | Result | Time | Files | Syslog |
|---|---|---|---|---|
| linux-devel | OK | 179 | ||
| source / vignettes | OK | 194 | ||
| linux-release | OK | 152 | ||
| macos-release | OK | 125 | ||
| macos-oldrel | OK | 158 | ||
| windows-devel | OK | 192 | ||
| windows-release | OK | 150 | ||
| windows-oldrel | OK | 193 | ||
| wasm-release | OK | 126 |
Exports:bam2DNAStringSetbam2DNAStringSet2bs_alnbs_consensusbs_filterbs_hammingbs_renameclw_readconsensusdownload_genbankfa_combinefa_filterfa_readfa_renamefa_summaryfa_to_interleavedfa_to_sequentialfa_writefas2phygb_readget_idmega_readncbi_fa_readphy_readphy_writephy2fasrenameTXTreplaceInsideseqlensth_read
Dependencies:BiocGenericsBiostringsclicrayondigestfsgenericsIRangesrappdirsrlangS4VectorsSeqinfoXVectoryulab.utils
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| bam2DNAStringSet | bam2DNAStringSet |
| bam2DNAStringSet2 | bam2DNAStringSet2 |
| bs_aln | bs_aln |
| bs_filter | bs_filter |
| bs_hamming | bs_hamming |
| bs_rename | bs_rename |
| consensus | bs_consensus consensus |
| download_genbank | download_genbank |
| fa_combine | fa_combine |
| fa_filter | fa_filter |
| fa_rename | fa_rename |
| fa_summary | fa_summary |
| fa_to_interleaved | fa_to_interleaved fa_to_sequential |
| fa_write | fa_write |
| fas2phy | fas2phy |
| gb_read | gb_read |
| get_id | get_id |
| read sequence alignment file | clw_read fa_read mega_read sth_read |
| ncbi_fa_read | ncbi_fa_read |
| phy_read | phy_read |
| phy_write | phy_write |
| phy2fas | phy2fas |
| renameTXT | renameTXT |
| replaceInside | replaceInside |
| seqlen | seqlen |