Get Metadata for Biosamples

This tool supports extracting BioSample metadata into a user friendly table. It assumes you will provide a list of valid BioSamples and will write out a table.

If an existing table is provided it will be used to update that table with additional columns as present in the collection of samples provided or added to.

Requirements

• Biopython

Usage

biosample2table.py [ --in sample_list.txt] [--sample sampleid sampleid2 ...] --out result_table.tsv [--update]

Retrieve a single biosample

Lookup a single Biosample and output tab delimited file

./scripts/biosample2table.py -s SAMN12327137 --out result_table.tsv -e yourname@gmail.com

Results will be

BioSample	collection_date	geo_loc_name	host	isolate	sample_type	strain
SAMN12327137	2006	USA:Sierra Nevada Mtns	Rana sierrae	Bd_JAM81	isolate	GPL

Output comma delimited file

./scripts/biosample2table.py -s SAMN12327137 --out result_table.csv -e yourname@gmail.com

BioSample,collection_date,geo_loc_name,host,isolate,sample_type,strain SAMN12327137,2006,USA:Sierra Nevada Mtns,Rana sierrae,Bd_JAM81,isolate,GPL

Lookup a single SRA record and find its BioSample

./scripts/biosample2table.py -s SRR14174621 --sra --out result_table.tsv -e yourname@gmail.com

Results will be

BioSample,SRA_Run,SRA_SampID,Sample No.,age,biomaterial_provider,isolate,sex,tissue,treatment
SAMN18650164,SRR14174621,SRS8658905,17,54,Liverpool Hospital,Diabetic Patient,male,Skin,Midpoint

Lookup list of IDs from a single filename

If you have a list of IDs either SRA or BioSample you can use the --in option

./scripts/biosample2table.py --in samplefile.txt --out result_table.tsv -e yourname@gmail.com

Using STDIN and STDOUT

If you had a list of ids you wanted to pass from another program uyou can pass that in and omit the --in option

echo SAMN18650164 | ./scripts/biosample2table.py --out result_table.tsv -e yourname@gmail.com

Omitting the --out option will print the results out to STDOUT

echo SAMN18650164 | ./scripts/biosample2table.py -e yourname@gmail.com

Mixing --in (or STDIN with no --in) and the -s will prefer sample list input provided by the -s option and ignore any stdin or --in file input.

echo SAMN18650164 | ./scripts/biosample2table.py -e yourname@gmail.com

Command line arguments

Argument	Description
-o/--out	Write out the table to this file, if the file already exists, parse it in and reuse the existing data, and add to it. Will use file extension (.tab/.tsv or .csv) to determine output format (default is tab delimited if extension doesn't match). If --out is omitted will write to STDOUT (but will be unable to use previously cached results of course)
--update	use the existing table for sample ids, but also re-lookup the fields
-i/--in	Input file of biosamples, one per line for the query, if - is provided as filename will read in list from STDIN
-s/--sample	List of samples to query instead of providing as input file
--sra	Instead of BioSamples input IDs are SRR numbers

Assembly Accession to Metadata (assembly2metadata.py)

scripts/assembly2metadata.py fetches BioSample metadata for NCBI Assembly accessions (GCA_* or GCF_*). Each assembly is resolved to its linked BioSample via Entrez, then the full metadata is retrieved and written to a table.

Usage

assembly2metadata.py -e your@email.com [-i assemblies.txt] [-s GCA_... GCF_...] [-o output.tsv] [--update]

Retrieve metadata for a single assembly

./scripts/assembly2metadata.py -s GCA_000001405.15 -o result_table.tsv -e yourname@gmail.com

Results will be a tab-delimited table with assembly_accession as the first column, biosample_accession as the second, followed by all BioSample attribute fields:

assembly_accession	biosample_accession	collection_date	geo_loc_name	...
GCA_000001405.15	SAMN02981236	...	...	...

Retrieve metadata for multiple assemblies

./scripts/assembly2metadata.py -s GCA_000001405.15 GCF_000001635.27 -o result_table.tsv -e yourname@gmail.com

Retrieve from a file list

One assembly accession per line:

./scripts/assembly2metadata.py -i assemblies.txt -o result_table.tsv -e yourname@gmail.com

Output comma-delimited file

Use a .csv extension to switch to comma-delimited output:

./scripts/assembly2metadata.py -s GCA_000001405.15 -o result_table.csv -e yourname@gmail.com

Update existing results

Re-query assemblies already present in the output file:

./scripts/assembly2metadata.py -i assemblies.txt -o result_table.tsv -e yourname@gmail.com --update

Using STDIN and STDOUT

echo GCA_000001405.15 | ./scripts/assembly2metadata.py -e yourname@gmail.com

Omitting -o writes results to stdout.

Command line arguments

Argument	Description
-e/--email	Required. Email address for NCBI Entrez queries.
-o/--output	Output file (.tsv or .csv). If the file already exists, existing records are reused and new ones are appended. Omit to write to stdout.
-i/--input	Input file of assembly accessions, one per line. Omit to read from stdin.
-s/--assemblies	One or more assembly accessions on the command line.
--update	Re-query accessions already present in the output file.
--debug	Print verbose debug information to stderr.

Author(s)

Jason Stajich - jason.stajich[at]ucr.edu, http://lab.stajich.org