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Parse VFDB #2

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JFsanchezherrero opened this issue Feb 19, 2020 · 0 comments

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bug enhancement ToDo

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JFsanchezherrero commented Feb 19, 2020

Fix VFDB parsing results in virulence_resistance.py

https://github.com/JFsanchezherrero/BacterialTyper/blob/900aba422e2bfcf4ef0888cbdae360712f93cdf3/BacterialTyper/virulence_resistance.py#L27

https://github.com/JFsanchezherrero/BacterialTyper/blob/900aba422e2bfcf4ef0888cbdae360712f93cdf3/BacterialTyper/virulence_resistance.py#L153

Correctly retrieved VFDB ID:

VF: Virulence factor
VFG: Virulence factor gene

Additionally, add to excel direct link to entries in VFDB website.

VF: Virulence factor:: "http://www.mgc.ac.cn/cgi-bin/VFs/gene.cgi?GeneID="
e.g.: http://www.mgc.ac.cn/cgi-bin/VFs/gene.cgi?GeneID=VFG001358
VFG: Virulence factor gene:: "http://mgc.ac.cn/cgi-bin/VFs/vfs.cgi?VFID="
e.g.: http://mgc.ac.cn/cgi-bin/VFs/vfs.cgi?VFID=VF0143

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