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Adding a recipe to get all assemblies associated with a bioproject #51

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Better version
linsalrob Jan 11, 2018
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Merge branch 'master' of github.com:NCBI-Hackathons/EDirectCookbook
linsalrob Jun 8, 2020
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Adding a recipe to get all assemblies associated with a bioproject
linsalrob Jun 8, 2020
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22 changes: 20 additions & 2 deletions README.md
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Expand Up @@ -64,13 +64,15 @@ esearch -db taxonomy -query "vertebrata[orgn]" | efetch -db taxonomy -format doc
```

### Get all SRA runs for a BioProject based on an SRA Run ID
Description: Given an SRA Run ID (e.g. SRR532256) that is a member of a BioProject that has additional runs, retrieve all the other run IDs. This is a variant of the BioProject call below.
Description: Given an SRA Run ID (e.g. SRR5088933) that is a member of a BioProject that has additional runs, retrieve all the other run IDs. This is a variant of the BioProject call below. The example run is from [PRJNA356544](https://www.ncbi.nlm.nih.gov/bioproject/PRJNA356544) which has 12 experiments, each with a single run, and we should return 12 runs.
Written by: Rob Edwards (1/11/2018)
Confirmed by:
Databases: SRA, BioProject

```
esearch -db sra -query "SRR532256" | efetch -format docsum | xtract -pattern Runs -ACC @acc -element "&ACC"
esearch -db sra -query "SRR5088933" | efetch -format docsum | xtract -pattern Bioproject -element Bioproject | \
xargs -i esearch -db bioproject -query "{}" | elink -target sra | efetch -format docsum | \
xtract -pattern Runs -ACC @acc -element "&ACC"
```

### Get all SRA runs for a given BioProject
Expand All @@ -84,6 +86,22 @@ esearch -db bioproject -query "PRJNA356464" | elink -target sra | efetch -format
xtract -pattern DocumentSummary -ACC @acc -block DocumentSummary -element "&ACC"
```

### Get all assemblies associated with a bioproject
Description (optional): Metagenome-assembled-genomes (MAGs) are being deposited as assemblies in bioprojects, and often include thousands of genomes. In order to extract them for computing, you probably want to download all the genomes. For example, bioproject [PRJEB26432](https://www.ncbi.nlm.nih.gov/bioproject/PRJEB26432/) has 1,962 assemblies. This bioproject does not include annotated sequences, and so this recipe downloads the fasta file, but you should check other assemblies.
Written by: Rob Edwards (8/6/2020)
Confirmed by:
Databases: BioProject, Assembly

```
esearch -db bioproject -query "PRJEB26432" | \
elink -target assembly | efetch -format docsum | \
xtract -pattern DocumentSummary -element FtpPath_GenBank | \
awk -F"/" '{print $0"/"$NF"_genomic.fna.gz"}' | xargs wget
```




### Get latitiude and longitude for SRA Datasets (e.g. outbreaks and metagenomes)
Description (optional):
Written by: BB, Mike D, Rob Edwards (4/12/2017)
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