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No paradigm format #2

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carlotarp opened this issue Mar 19, 2015 · 0 comments
Open

No paradigm format #2

carlotarp opened this issue Mar 19, 2015 · 0 comments

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@carlotarp
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I am trying to download whole super pathway in xgmml format. However I am not able to do it. I have folllowed the readme steps but it fails here:

./scripts/pathway_db.py build --paradigm > superpathway.pid

usage: pathway_db.py [-h] [-b BASE_DIR]
{build,hugosync,suggest,biopax-format,biopax-convert,library-gmt,library-table,library-compile,library-copy}
...
pathway_db.py: error: unrecognized arguments: --paradigm

I have also tried to convert a superpathway I downloaded from synapse (https://www.synapse.org/#!Synapse:syn1528312/version/1 )
I doesn't work either

./scripts/network_convert.py --in-paradigm 1528312_1528313_pid_1_pathway.tab --in-gmt output.gmt --out-xgmml super.xgmml

usage: network_convert.py [-h] [-etd EDGE_TYPE_DEFAULT]
[-ntd NODE_TYPE_DEFAULT] [-ntf NODE_TYPE_FIELD]
[-etf EDGE_TYPE_FIELD] [-pmf PATHWAY_MEMBER_FIELD]
[--in-xgmml IN_XGMML] [--in-spf IN_SPF]
[--in-gmt IN_GMT] [--in-spf-dir IN_SPF_DIR]
[--strict] [--out-spf OUT_SPF] [--out-sif OUT_SIF]
[--out-xgmml OUT_XGMML] [--out-gmt OUT_GMT]
network_convert.py: error: unrecognized arguments: --in-paradigm 1528312_1528313_pid_1_pathway.tab

I would appreciate if you could solve this problem. Thank you.

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