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Extracting information from pathwaytools using pythoncyc help

Hi I'm a newbie using python and pathwaytools in debian, I have tried to extract some information from the tool using the pythoncyc packages. E.g., pathways, genes and reactions separately. But I could not link them as expected. My expected output should be like this:

Expected output for each organism E.g.,

PTW1   have Gen1,  and that gene in that pathway carry out Rx1
PTW1   have Gen2,  and that gene in that pathway carry out Rx2
PTW1   have Gen3,  and that gene in that pathway carry out Rx3
.                     .                                                                          .
.                    .                                                                          .
PTW2   have Gen4,  and that gene in that pathway carry out Rx4

If anyone could help me, I would appreciate it very much.

pythoncyc python pathwaytools
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updated by Ram Ram • written by fernandeznegreteguillermo • fernandeznegreteguillermo

See the following link to study pythoncyc:

http://brg.ai.sri.com/ptools/pythoncyc.html

Its manual link is inside.

Pathwaytools software:

http://pathwaytools.org/

There are some other ways, see this post below:

Visualizing metabolic models

Note:"PathwayTools - Nice if you have an annotated genome and want to map it to the MetaCyc database but for me personally the software is a pain to work with".

or REACTOME-site:

http://www.reactome.org/

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written by natasha.sernova natasha.sernova

Hi thanks for reply. I have seen before that links but, i'm interested specifically in a code which used pythoncyc package to get the expected output that i couldn't get by myself. thanks again.

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written by fernandeznegreteguillermo • fernandeznegreteguillermo

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