seqrec_gen: Generate sequence record

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

Generate sequence record

Description

Creates an S4 SeqRec

Usage

seqrec_gen(
  accssn,
  nm,
  txid,
  sq,
  dfln,
  orgnsm,
  ml_typ,
  rec_typ,
  vrsn,
  age,
  lctn = NULL
)

Arguments

accssn	Accession ID
nm	Sequence name
txid	Taxonomic ID of source organism
sq	Sequence
dfln	Definition line
orgnsm	Source organism name
ml_typ	Molecule type
rec_typ	Sequence record type
vrsn	Accession version
age	Number of days since upload
lctn	Location numbers for features, e.g. '1..200'

Value

SeqRec

See Also

Other run-private: batcher(), blast_clstr(), blast_filter(), blast_setup(), blast_sqs(), blastcache_load(), blastcache_save(), blastdb_gen(), blastn_run(), cache_rm(), cache_setup(), clade_select(), clstr2_calc(), clstr_all(), clstr_direct(), clstr_sqs(), clstr_subtree(), clstrarc_gen(), clstrarc_join(), clstrrec_gen(), clstrs_calc(), clstrs_join(), clstrs_merge(), clstrs_renumber(), clstrs_save(), cmdln(), descendants_get(), download_obj_check(), error(), gb_extract(), hierarchic_download(), info(), ncbicache_load(), ncbicache_save(), obj_check(), obj_load(), obj_save(), outfmt_get(), parameters_load(), parameters_setup(), parent_get(), progress_init(), progress_read(), progress_reset(), progress_save(), rank_get(), rawseqrec_breakdown(), safely_connect(), search_and_cache(), searchterm_gen(), seeds_blast(), seq_download(), seqarc_gen(), seqrec_augment(), seqrec_convert(), seqrec_get(), sids_check(), sids_get(), sids_load(), sids_save(), sqs_count(), sqs_save(), stage_args_check(), stages_run(), tax_download(), taxdict_gen(), taxtree_gen(), txids_get(), txnds_count(), warn()

ropensci/phylotaR documentation built on July 21, 2024, 1:01 a.m.