running GapSeq with customized pathways about gapseq HOT 2 CLOSED

Dear Weizhi,

thank you for using GapSeq and your question. We will add a documentation on how to analyse a user-defined pathway soon. But here is what you can do right away:

Like you already said, you can add a user-defined pathway in the dat/custom_pwy.tbl file.

The columns are:
id - An unique Identifier for the new Pathway
name and altname - Name and alternative name the new pathway.
hierachy - This corresponds to the pathway-hierarchy / ontologie as in MetaCyc. In case you are unsure, simply use |THINGS| here.
taxrange - Corresponds to the taxonomic ranges as defined in MetaCyc. For bacteria enter |TAX-2|
reaId - comma-separated list of the reaction identifiers (you can freely define new identifieres)
recEc - comma-separated list of reactions' EC-numbers. Should be the same length and in the same order as reaId. If no EC number is defined for a reaction, leave this field free (e.g. "1.1.1.1,,1.9.1.3", in case there is no EC-number for the second reaction")
keyRea - Identifier of the key-reaction of the pathway. Leave empty if you do not want to specifiy/know the key reaction. Can also be multiple key-reactions (separated by comma).
reaName - semicolon-separated list of reaction names. You are free to choose names here, but its recommended to use the Enzyme Commission Primary Name if available. Same length and order as reaId

You can ignore the last four columns (without headers). I think there are some entries there by mistake. I'll have a look at this :)

Once you have entered your user-defined pathway in dat/custom_pwy.tbl you can specifically analyse your pathway in a genome using:

./gapseq find -l custom -p {NEW-PWY-ID} genome.fna.gz

In this way you don't need to delete the other pathway-database files "kegg_pwy.tbl" or "seed_pwy.tbl"

Hope this helpfs. Please let us know if this works for your case.

Best,
Silvio

from gapseq.

Thanks for your detailed description, Silvio!!
I'll prepare the pwy file as you suggested here.
Weizhi

from gapseq.