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Sheikhizadeh / pantools

PanTools
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Examples ? #3

Open colindaven opened 7 years ago

colindaven commented 7 years ago

Hi,

this is highly interesting software, and easy to use being Java.

However, a great number of sub commands using various different formats are available. I think it would be highly beneficial to put an example set onto github detailing example commands and example file formats.

For example, I successfully build pangenomes but cannot annotate them successfully - (0 genes annotated, no errors or warnings) and query also failed (using the 1st query from the paper adapted to my data).

So I think you have examples - e.g. the Ecoli or HIV would be perfect - and it would be great to see that posted when you have a moment.

Just my 2 cents.

Thanks, Colin

Sheikhizadeh commented 7 years ago

Dear Colin,

Thank you for your useful comments, I just commit a new version with sample input files, data, and an easy-to-follow Readme file. Please let me know if you feel something still needs to be there.

Cheers,

Siavash

Siavash Sheikhizadeh Anari Bioinformatics Group Wageningen University Droevendaalsesteeg 1, 6708PB Building/Room: 107/W1.Ad.054

From: colindaven notifications@github.com Sent: 19 September 2016 12:58 To: Sheikhizadeh/pantools Subject: [Sheikhizadeh/pantools] Examples ? (#3)

Hi,

this is highly interesting software, and easy to use being Java.

However, a great number of sub commands using various different formats are available. I think it would be highly beneficial to put an example set onto github detailing example commands and example file formats.

For example, I successfully build pangenomes but cannot annotate them successfully - (0 genes annotated, no errors or warnings) and query also failed (using the 1st query from the paper adapted to my data).

So I think you have examples - e.g. the Ecoli or HIV would be perfect - and it would be great to see that posted when you have a moment.

Just my 2 cents.

Thanks, Colin

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colindaven commented 7 years ago

Dear Siavash,

thanks a lot, that looks very helpful. I'll have another go at the annotation part.

cheers, Colin