write_sqs | R Documentation |
Write out sequences, as .fasta, for a given vector of IDs.
write_sqs(phylota, outfile, sid, sq_nm = sid, width = 80)
phylota |
Phylota |
outfile |
Output file |
sid |
Sequence ID(s) |
sq_nm |
Sequence name(s) |
width |
Maximum number of characters in a line, integer |
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.
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()
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)
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