formatting lineage to taxonomy file
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4.8 years ago
xioli2013 ▴ 10

Hi,

I am trying to make a taxonomy file like the one provided in qiime for all trnL gene.

What I have done: 1. all trnL sequences 2. all trnL gene accession number 3. all trnL gene tax id

I was able to get the lineage tag from the xml efetch function generated in Python: '1435590': 'cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliophyta; Mesangiospermae; eudicotyledons; Gunneridae; Pentapetalae; rosids; fabids; Rosales; Urticaceae; Urtica',

But I am lost as to how to format it into taxonomy file which has a format: uid k__; p__; etc

I hope I can get some thoughts from the community.

Thank you,

xp

metabarcode trnL taxonomy file formatting • 981 views
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