write_sqs: Write out sequences

In ropensci/phylotaR: Automated Phylogenetic Sequence Cluster Identification from 'GenBank'

Write out sequences

Description

Write out sequences, as .fasta, for a given vector of IDs.

Usage

write_sqs(phylota, outfile, sid, sq_nm = sid, width = 80)

Arguments

phylota	Phylota
outfile	Output file
sid	Sequence ID(s)
sq_nm	Sequence name(s)
width	Maximum number of characters in a line, integer

Details

The user can control the output definition lines of the sequences using the sq_nm. By default sequences IDs are used. Note, ensure the sq_nm are in the same order as sid.

See Also

Other tools-public: calc_mad(), calc_wrdfrq(), drop_by_rank(), drop_clstrs(), drop_sqs(), get_clstr_slot(), get_nsqs(), get_ntaxa(), get_sq_slot(), get_stage_times(), get_tx_slot(), get_txids(), is_txid_in_clstr(), is_txid_in_sq(), list_clstrrec_slots(), list_ncbi_ranks(), list_seqrec_slots(), list_taxrec_slots(), plot_phylota_pa(), plot_phylota_treemap(), read_phylota()

Examples

data('aotus')
# get sequences for a cluster and write out
random_cid <- sample(aotus@cids, 1)
sids <- aotus[[random_cid]]@sids
write_sqs(phylota = aotus, outfile = file.path(tempdir(), 'test.fasta'),
          sq_nm = 'my_gene', sid = sids)

ropensci/phylotaR documentation built on July 9, 2023, 3:17 p.m.