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biocore / American-Gut

American Gut open-access data and IPython notebooks
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Added sample/accession mappings for r1-14 #129

Closed wasade closed 9 years ago

wasade commented 9 years ago

Constructed with:

from json import dumps
sample_to_accession = dumps({l.split('\t')[0]:f.split('.')[0] for f in glob.glob('ERP*.txt') for l in open(f).readlines()[1:]})
accession_to_sample = dumps({f.split('.')[0]:[l.split('\t')[0] for l in open(f).readlines()[1:]] for f in glob.glob('ERP*.txt')})

cc @madprime

adamrp commented 9 years ago

I think this looks good :+1:

wasade commented 9 years ago

Able to merge? I don't think this warrants dual review IMO

adamrp commented 9 years ago

I'm checking one more thing actually; not yet finding barcode 000011080 in accession ERP005651 (this is the first entry in accession_to_sample.json)

adamrp commented 9 years ago

I think I was just missing it on their interface (which for some reason does not permit sorting by name). Just spot-checked several barcodes that are on their list against the lists here, and they all check out, so I'm going to merge this.

wasade commented 9 years ago

Thanks!

On Tue, Feb 24, 2015 at 10:38 AM, adamrp notifications@github.com wrote:

Merged #129 https://github.com/biocore/American-Gut/pull/129.

— Reply to this email directly or view it on GitHub https://github.com/biocore/American-Gut/pull/129#event-241088191.