Get MG-RAST Data

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

Requirements

• BIOM Format (http://biom-format.org/)
• Curl
• Perl
• Python

Scripts

• 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.

To get help for each script use the -h option

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

Examples/Testing

• 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