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suggestion: output lineage tax id instead of full name #17

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mewu3 opened this issue Oct 5, 2021 · 5 comments
Open

suggestion: output lineage tax id instead of full name #17

mewu3 opened this issue Oct 5, 2021 · 5 comments

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@mewu3
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mewu3 commented Oct 5, 2021

If it's possible to have lineage tax id instead of full name ?

taxid	kindom	phylum	class	order	family	genus	species
11138	10239	2732408	2732506	76804	11118	694002	694005
123595	10239	2732408	2732506	76804	11118	694002	694005
11138	10239	2732408	2732506	76804	11118	694002	694005
11138	10239	2732408	2732506	76804	11118	694002	694005
11128	10239	2732408	2732506	76804	11118	694002	694003
160235	10239	2732408	2732506	76804	11118	694013	694014
11120	10239	2732408	2732506	76804	11118	694013	694014
249065	10239	2732408	2732506	76804	11118	694002	694009
249069	10239	2732408	2732506	76804	11118	694002	694009
258508	10239	2732408	2732506	76804	11118	694002	694009
11120	10239	2732408	2732506	76804	11118	694013	694014
270642	10239	2732408	2732506	76804	11118	693996	277944
267385	10239	2732408	2732506	76804	11118	694002	694009
31631	10239	2732408	2732506	76804	11118	694002	694003
11120	10239	2732408	2732506	76804	11118	694013	694014
694009	10239	2732408	2732506	76804	11118	694002	694009
@zyxue
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zyxue commented Oct 5, 2021 •
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Feel free to send a pull request. You may add an option like --output-tax_id.

@zyxue zyxue changed the title suggestion suggestion: output lineage tax id instead of full name Jan 26, 2022
@Xueliang24
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where can I know more option about ncbitax2lin
The help information is simple

@Xueliang24
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Feel free to send a pull request. You may add an option like --output=tax_id.

I used the option --output=tax_id, it just changed the name of output file to "tax_id"

@Xueliang24
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If it's possible to have lineage tax id instead of full name ?

taxid	kindom	phylum	class	order	family	genus	species
11138	10239	2732408	2732506	76804	11118	694002	694005
123595	10239	2732408	2732506	76804	11118	694002	694005
11138	10239	2732408	2732506	76804	11118	694002	694005
11138	10239	2732408	2732506	76804	11118	694002	694005
11128	10239	2732408	2732506	76804	11118	694002	694003
160235	10239	2732408	2732506	76804	11118	694013	694014
11120	10239	2732408	2732506	76804	11118	694013	694014
249065	10239	2732408	2732506	76804	11118	694002	694009
249069	10239	2732408	2732506	76804	11118	694002	694009
258508	10239	2732408	2732506	76804	11118	694002	694009
11120	10239	2732408	2732506	76804	11118	694013	694014
270642	10239	2732408	2732506	76804	11118	693996	277944
267385	10239	2732408	2732506	76804	11118	694002	694009
31631	10239	2732408	2732506	76804	11118	694002	694003
11120	10239	2732408	2732506	76804	11118	694013	694014
694009	10239	2732408	2732506	76804	11118	694002	694009

Could you use ncbitax2lin --nodes-file taxdump/nodes.dmp --names-file taxdump/names.dmp? Or could you share your code?

@zyxue
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zyxue commented Dec 2, 2022

@Xueliang24 , sorry for confusion. I meant --output-tax-id instead, but it isn't implemented yet, so not expected to work.

@zyxue zyxue closed this as completed Dec 2, 2022
@zyxue zyxue reopened this Dec 2, 2022
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@zyxue @Xueliang24 @mewu3