write_sqs: Write out sequences

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

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)

phylotaR documentation built on May 1, 2019, 9:26 p.m.