How to create dictionary by reading lines from a file and find exact values inside another file through looping a defined path?
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4.5 years ago
Promi ▴ 10

Hello,

I have a file containing gi's

103485576

**298489615**

103485741

10348579

And there is a directory

home/documents/all.ptt/_Nostoc_azollae__0708_uid**49725**/**NC_014249**.ptt

home/documents/all.ptt/_Ruminococcus__obeum_uid197165/NC_021022.ptt

Inside the ptt file for example of _Nostoc_azollae__0708_uid49725/NC_014249.ptt

'Nostoc azollae' 0708 chromosome, complete genome - 1..5354700

3589 proteins

Location    Strand  Length  PID Gene    Synonym Code    COG Product

2007..2231  +   74  **298489615**   -   Aazo_0002   -   -   hypothetical protein

2814..2942  +   42  298489616   -   Aazo_0003   -   -   hypothetical protein

Desired ouput is:

gi accession taxid (where gi is the key and accession and taxid are the values or features)

298489615 NC_014249 49725

Can anyone tell me how to read a file of gi's and look for matching value in the PID Gene column of each ptt file looping over mentioned working directory?

Thanks.

ptt python bash linux dictionary • 976 views
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