Tool:biomartian enables querying BioMart from the command line - now all Python!

Question

[Endre Bakken Stovner]

I wrote a script called biomartian to simplify my work (doing data analysis always requires me to find common gene identifiers). Perhaps someone else will find it useful?

biomartian greatly simplifies extracting data from BioMart.

Instead of having to

1. Open an R session
2. Load biomaRt
3. Load a mart and dataset
4. Write the code required to extract the data you need
5. Merge the new data into a dataset

You can simply call a single simple biomartian command!

biomartian also aids BioMart discoverability since you can use standard tools like grep to search BioMart results instead of having to use Rs clunky and verbose ersatz implementation.

Lastly, biomartian caches all queries across sessions (in ~/.biomartian), so that subsequent queries are instantaneous.

Examples

Find the name of mrna ids in BioMart for the common rat

biomartian -d rnorvegicus_gene_ensembl --list-attributes | grep -i mrna
refseq_mrna RefSeq mRNA [e.g. NM_001195597]
refseq_mrna_predicted   RefSeq mRNA predicted [e.g. XM_001125684]

Note that we did not need to write the name of the mart since ensembl is the default.

Get the refseq mrna id for all regular gene names and attach them to an input file

$ head simple.txt
"logFC" "AveExpr"
"Ipcef1"    -2.70987558746701   4.80047582653889
"Sema3b"    2.00143465979322    3.82969788437155
"Rab26" -2.40250648553797   5.57320249609294
"Arhgap25"  -1.84668909768998   3.66617832656769
"Ociad2"    -1.99052684394044   5.26213130909702
"Mmp17" -2.01026790614161   4.88012776225311
"C4a"   2.22003976804983    3.52842041243544
"Gna14" -2.42391191670209   1.56313048066253
"Kcna6" -1.74168813159872   6.54586068659631

$ biomartian -d rnorvegicus_gene_ensembl -c 0 -i external_gene_name -o refseq_mrna simple.txt
index   logFC   AveExpr refseq_mrna
Ipcef1  -2.70987558746701   4.80047582653889    NM_001170799
Sema3b  2.00143465979322    3.82969788437155    NM_001079942
Rab26   -2.40250648553797   5.57320249609294    NM_133580
Arhgap25    -1.84668909768998   3.66617832656769    NM_001109247
Ociad2  -1.99052684394044   5.26213130909702    NM_001271181
Mmp17   -2.01026790614161   4.88012776225311    NM_001105925
C4a 2.22003976804983    3.52842041243544    NM_031504
C4a 2.22003976804983    3.52842041243544    NA
Gna14   -2.42391191670209   1.56313048066253    NM_001013151
Kcna6   -1.74168813159872   6.54586068659631    NM_023954

Install

pip install biomartian

Usage

biomartian

Query biomart from the command line.
For help and examples, visit github.com/endrebak/biomartian

Usage:
    biomartian [--mart=MART] [--dataset=DATA] --mergecol=COL... --intype=IN... --outtype=OUT... [--noheader] FILE
    biomartian [--mart=MART] [--dataset=DATA] --intype=IN --outtype=OUT
    biomartian --list-marts
    biomartian [--mart=MART] --list-datasets
    biomartian [--mart=MART] [--dataset=DATASET] --list-attributes

Arguments:
    FILE                   file with COL(s) to join mart data on (- for STDIN)
    -i IN --intype=IN      the datatype in the column to merge on
    -o OUT --outtype=OUT   the datatype to get (joining on value COL)
    -c COL --mergecol=COL  name or number of the column to join on in FILE

Note:
    Required args --intype, --outtype and --mergecol must be equal in number.

Options:
    -h      --help          show this message
    -m MART --mart=MART     which mart to use [default: ensembl]
    -d DATA --dataset=DATA  which dataset to use [default: hsapiens_gene_ensembl]
    -n --noheader           the input data does not contain a header (must
                            use integers to denote COL)

Lists:
    --list-marts       show all available marts
    --list-datasets    show all available datasets for MART
    --list-attributes  show all kinds of data available for MART and DATASET

See https://github.com/endrebak/biomartian for more info.

[Endre Bakken Stovner]

Woops. Seems there is a teensy bug in the first line for files that contain no header. Will fix.

[Endre Bakken Stovner]

Fixed; the bug was merely that I had hard-coded a header-related bool. TGF unit tests.

[Endre Bakken Stovner]

To fix: pip install -U biomartian

[Malcolm.Cook]

The advertised github repos, https://github.com/endrebak/biomartian, is non-existent.

Instead, I find https://github.com/daler/biomartian

However, the repos does not have issues and I have an issue.

For starters, the example given above does not work and retusns blank values for refesq_mrna.

Otherwise, I love the idea of shell command line interface to biomart.

Answer 1

[Endre Bakken Stovner]

Bumping this since biomartian is now all python, having a dependency on R was a less than optimal solution - the fewer interpreters needed the better :)

pip install -U biomartian