Does anyone familiar with downloading data from MG-RAST? I have more than 100 metagenome ids that need to be downloaded in an efficient way. I found this link at MG-RAST (http://api.metagenomics.anl.gov/1/api.html#download) but couldn't manage to download those 100 metagenomes using their ids (e.g. 4441908.3). I dont want to download one by one with individual ids as it will take ages..!!
I did something like this a while back:
cat keywordTableSortedUniqueIds.txt mgm4440036.3 mgm4440037.3 mgm4440038.3 mgm4440039.3 mgm4440040.3 mgm4440041.3 mgm4440055.3 mgm4440056.3 .. while read line do curl http://api.metagenomics.anl.gov/1/download/"$line"?file=425.1 > $line.gz done
The "file=XXX" part specifies what exactly you want to download from the given metagenome, e.g. 425.1 here specifies predicted rRNA.
I have a question... I have downloaded project files using MG-RAST tools mg-download.py --project projectid
But, now I want metadata for particular project (which file corresponds to which sample type?). How to download metadata?