I'm trying to automatically obtain fasta files from the NCBI nucleotide database for a list of taxonomy IDs. I know I can use Entrez's efetch but it expects a GI number, which I do not have a list of. Is there a way to fetch by taxonomy ID or a straight-forward and non-manual way to get GI numbers from taxonomy IDs?
Thanks much for any help!
This is really simple with Entrez Direct
epost -db taxonomy -id 63221 | elink -target nuccore | efetch -format uid 196123578 677001457 634744538 634744524 2286205 584458899 513134556 398637208 315623200 270209679 270209678 270209677 262527002 253947345 253947331 253947317 253947303 253947289 222350099 222350097 195972535 158958247 158251955 158251954 111035029 91075865 28557455 11141613 11141612 7769684 4927255
Also works with -target nucgss if that's what you're interested in. You can also skip the gi part and efetch -format fasta
Haven't found a great solution for this. But the work-around I am using now is downloading /pub/taxonomy/gi_taxid_nucl.dmp.gz from the NCBI ftp server. The file maps GI numbers to taxonomy id, and I search it to get the GI numbers for a given taxonomy ID.
The elink util will turn up cross-references between NCBI databases.
In this case you want to find links between the taxonomy and nucleotide databases. Here's a demo using the R pacakge rentrez (there are similar libraries for pretty much all popular scripting languages, and even command line utils for this):
## find sequenced linked to a taxid
tax_seqs <- entrez_link(db = "nuccore", dbfrom = "taxonomy", id=5911)
#elink result with ids from 2 databases:
#[1] taxonomy_nuccore taxonomy_nucleotide_exp
grab them
tmp <- tempfile()
recs <- entrez_fetch(db="nuccore", id=tax_seqs$taxonomy_nuccore[1:3], rettype="fasta")
cat(recs, file=tmp)
ape::read.dna(tmp, format="fasta")
#3 DNA sequences in binary format stored in a list.
#
# Mean sequence length: 1493
# Shortest sequence: 1137
# Longest sequence: 1779
#
# Labels: gi|697738807|gb|KM406498.1| Tetrahymena thermophila Pat2 mRNA, complete cds #gi|697738801|gb|KM406497.1| #Tetrahymena thermophila Tpt1 mRNA, complete cds #gi|697738796|gb|KM406496.1| Tetrahymena thermophila Pat1 mRNA, complete #cds
It's much simplier - see http://www.bioperl.org/wiki/HOWTO:EUtilities_Cookbook.
Good luck!
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Duplicate of How To Retrieve All Sequences, From Ncbi, That Belong To A Specific Txid And Its Sub Txids?