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Added taxon to RefSeq genome FASTA files example #21

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Added taxon to RefSeq genome FASTA files example #21

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Added taxon to RefSeq genome FASTA files example
ucpete Aug 26, 2017
eb7f6d4
Merge pull request #1 from ucpete/ucpete/taxon-refseq
ucpete Aug 26, 2017
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15 changes: 15 additions & 0 deletions README.md
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Expand Up @@ -387,3 +387,18 @@ efetch -format xml | \
xtract -pattern PubmedArticle -element MedlineCitation/PMID \
-block PubDate -sep " " -element Year,Month MedlineDate
```

### Given a taxon name, retrieve all RefSeq genomes for that taxon in FASTA format

Description (optional): Takes in the scientific name of a taxon on the command line (should usually be species or strain level to keep number of results manageable), retrieves taxID using `esearch | efetch | xtract`, which is nested by process substitution into `elink | efilter | efetch`.
Written by: Peter Skewes-Cox (8/25/2017)
Confirmed by:
Databases: taxonomy, nuccore

```
elink -db taxonomy -id $( esearch -db taxonomy -query "Hepatitis C virus" | \
efetch -format docsum | \
xtract -pattern DocumentSummary -element TaxId ) -target nuccore | \
efilter -query "refseq" | \
efetch -format fasta
```