fetchseq: Fetch sequences from UIDs recovered from a GenBank search...

In lizandropf/ncbiRtools: Tools for searching and retrieving data from NCBI sequence databases

Description

This function fetch sequences from the NCBI GenBank into fasta or GenBank files. The elements can be a result from function searchGB or a vector with UIDs or GenBank accession numbers.

Usage

fetchseq(ids, db="nuccore", rettype="fasta", retmode="text")

Arguments

ids	data recovered from function searchGB or a vector with UIDs or GenBank accession numbers.
db	The database to retrieve sequences from. It uses UIDs or GenBank Accession numbers. It can be any of available options in NCBI databases. Set to "nuccore" as default. It retrieves data from two databases, genbank (any database) or pubmed.
rettype	either "fasta" or "gb". Set to "fasta" as default (best for retrieving data from a vector of UIDs or Accession numbers with known taxa). "gb" option retrieves more data information for each sequence (recommended when retrieving data from a search with function searchGB). New options added for db="pubmed", either rettype="docsum" for summary records or rettype="abstract" for complete records.

Note

Warning for extensive data retrieving: connection to server would be interrupted by NCBI. Function offers a 1 seconds delay every 3 records retrieved.

Author(s)

L.N. Peraza-Flores

References

For details on database visit: https://ncbi.nlm.nih.gov

See Also

searchGB, read_fasta, read_gb, read_PubMedRec, write2fas

Examples

# load example data:
# from a vector of NCBI Accession numbers
seqs_data <- c("KP168671", "EU140072", "AY008665", "EU140235", "EU139932")
retr_seqs <- fetchseq(seqs_data, rettype="fasta")
# from results of function searchGB
sear_seqs <- searchGB("Cattleya crispata", retmax=5)
retr_seqsSgb <- fetchseq(sear_seqs)

lizandropf/ncbiRtools documentation built on May 14, 2019, 8:02 a.m.