Open johnnytam100 opened 2 months ago
Hi this is more of a tensorflow error rather than Biopython. Try the installation as I recommended here and let me know if it resolves the issue
To take care of Biopython inability to parse header of PDB I am using the following trick:
ls -1 /data/foldseek/af/*.pdb.gz | while read p;
do
name=$(echo $p | xargs -n 1 basename | cut -f 2 -d '-');
python predict.py -pdb $p -ont bp -v;
python predict.py -pdb $p -ont mf -v;
python predict.py -pdb $p -ont cc -v;
python predict.py -pdb $p -ont ec -v;
sed -i "s/query_prot/${name}/g" DeepFRI_BP_predictions.csv;
sed -i "s/query_prot/${name}/g" DeepFRI_CC_predictions.csv;
sed -i "s/query_prot/${name}/g" DeepFRI_MF_predictions.csv;
sed -i "s/query_prot/${name}/g" DeepFRI_EC_predictions.csv;
mv DeepFRI_BP_predictions.csv ${name}.BP.csv;
mv DeepFRI_CC_predictions.csv ${name}.CC.csv;
mv DeepFRI_MF_predictions.csv ${name}.MF.csv;
mv DeepFRI_EC_predictions.csv ${name}.EC.csv;
done
Hi @Rohit-Satyam ! Thank you for helping out! May I know where should I run this trick?
ls -1 /data/foldseek/af/*.pdb.gz | while read p;
do
name=$(echo $p | xargs -n 1 basename | cut -f 2 -d '-');
python predict.py -pdb $p -ont bp -v;
python predict.py -pdb $p -ont mf -v;
python predict.py -pdb $p -ont cc -v;
python predict.py -pdb $p -ont ec -v;
sed -i "s/query_prot/${name}/g" DeepFRI_BP_predictions.csv;
sed -i "s/query_prot/${name}/g" DeepFRI_CC_predictions.csv;
sed -i "s/query_prot/${name}/g" DeepFRI_MF_predictions.csv;
sed -i "s/query_prot/${name}/g" DeepFRI_EC_predictions.csv;
mv DeepFRI_BP_predictions.csv ${name}.BP.csv;
mv DeepFRI_CC_predictions.csv ${name}.CC.csv;
mv DeepFRI_MF_predictions.csv ${name}.MF.csv;
mv DeepFRI_EC_predictions.csv ${name}.EC.csv;
done
Hi this is more of a tensorflow error rather than Biopython. Try the installation as I recommended here and let me know if it resolves the issue
By the way, this solution didn't work.
Hi DeepFRI! Do you have idea how to troubleshoot this
BiopythonParserWarning: 'HEADER' line not found
error as follows?