Get MG-RAST Data

A suite of scripts that allow easy retrieval of information from the MG-RAST API.

Requirements

download_mgrast_abundance_tables.pl -- Downloads 'feature' by sample abundance tables, where 'feature' can be from several taxonomic or functional databases.
download_mgrast_sequences.pl -- Downloads sequences associated with each sample.
biom_to_stamp.py -- A multipurpose file to convert BIOM files (with various types of metadata) into a STAMP formatted file.

./download_mgrast_abundance_tables.pl -h
./download_mgrast_sequences.pl -h 
./biom_to_stamp.py -h

Downloads and creates both a BIOM table (KO_function.biom) and tab-delimited table (KO_function.tab)
```
  ./download_mgrast_abundance_tables.pl test_samples.txt
```

Create a STAMP format file

  ./biom_to_stamp.py -m ontology KO_function.biom > KO_function.spf

Download sequences associated with a list of samples

  ./download_mgrast_sequences.pl test_stamples.txt