Question

antiSMASH output

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3.3 years ago

kirankumareripogu ▴ 10

Hello. Can someone help me to interpret the antiSMASH output and the count number of BGCs by using command line. It would be great to receive your help.

Thank you

RESULTS antiSMASH • 2.1k views

ADD COMMENT • link updated 2.6 years ago by timothy.kirkwood ▴ 140 • written 3.3 years ago by kirankumareripogu ▴ 10

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Can you provide some sample output?

ADD REPLY • link 3.3 years ago by Nitin Narwade ★ 1.6k

score 0 · Answer 1 · 2021-08-10

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3.3 years ago

kirankumareripogu ▴ 10

Hi Nitin,

Thank you for your kind response.

I have sent you the screenshot of one of the output data. If you could kindly tell me how to proceed further then it would be great. Thank you.

enter image description here

ADD COMMENT • link 3.3 years ago by kirankumareripogu ▴ 10

score 0 · Answer 2 · 2022-04-26

Each gbk file with the 'region' suffix is basically a BGC (although check the antiSMASH docs for the specific differences between regions, protoclusters etc). In python you can just use os to get filenames with the region suffix then count them, if you just want the number of regions - more detailed parsing would need you to start parsing each region gbk or, for maximal information, the json file (which has all the clusterblast data etc).