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Update needed to modelVis rule for models reconstructed using CarveMe version>=1.5.0
Hello, again Francisco!
I think I figured out the problem with the modelVis rule. Just small corrections are needed for users working with a carveme >1.5.0.
Changes (In the Snakefile): In lines 1511 to 1518:
while read model;do
id=$(echo $(basename $model)|sed 's/.xml//g');
mets=$(less $model| grep "species id="|cut -d ' ' -f 8|sed 's/..$//g'|sort|uniq|wc -l);
rxns=$(less $model|grep -c 'reaction id=');
genes=$(less $model|grep 'fbc:geneProduct fbc:id='|grep -vic spontaneous);
echo "Model: $id has $mets mets, $rxns reactions, and $genes genes ... "
echo "$id $mets $rxns $genes" >> GEMs.stats;
done< <(find . -name "*.xml")
- species id ----->species metaid
- reaction id ------>reaction metaid
- fbc:geneProduct fbc:id ------>fbc:geneProduct metaid
These changes are reflected in a smooth run of this rule!
I hope this helps!
P.S.: I am still trying to figure out the multiple job submission on an OGE cluster and the memote errors. I will keep you posted if I find something!
Thanks and regards, Shreyansh
Hey Shreyansh,
Thank you for bringing this up, I would not have found this bug myself since I am using v1.4.1 of CarveMe. Will implement your suggested changes soon :)
Best wishes, Francisco