Hi
I have used PEPPAN on my own .gff data files which were generated from prokka and there were no errors. I subsequently used PEPPAN_parser and again no errors were generated.
I now have the following files and dir:
peppan.allele.fna PEPPAN_OUT
peppan.clust.exemplar peppan.PEPPAN.gene_CGAV.dist
peppan.clust.npy peppan.PEPPAN.gene_CGAV.nwk
peppan.clust.tab peppan.PEPPAN.gene_CGAV.profile
peppan.encode.csv peppan.PEPPAN.gene_content.curve
peppan.genes peppan.PEPPAN.gene_content.fas
peppan.global.npy peppan.PEPPAN.gene_content.nwk
peppan.map_bsn.conflicts.npz peppan.PEPPAN.gff
peppan.map_bsn.mat.npz peppan.Prediction
peppan.map_bsn.seq.npz peppan.self_bsn.npy
peppan.map_bsn.tab.npz peppan.synteny.Prediction
peppan.old_prediction.npz
However, a number of files were not generated (eg summary statistics, gene_presence_absence.csv, gene_presence_absence.Rtab).
I have used the same commands used in the example test file but with path to my .gff files.
Hi I have used PEPPAN on my own .gff data files which were generated from prokka and there were no errors. I subsequently used PEPPAN_parser and again no errors were generated.
I now have the following files and dir: peppan.allele.fna PEPPAN_OUT peppan.clust.exemplar peppan.PEPPAN.gene_CGAV.dist peppan.clust.npy peppan.PEPPAN.gene_CGAV.nwk peppan.clust.tab peppan.PEPPAN.gene_CGAV.profile peppan.encode.csv peppan.PEPPAN.gene_content.curve peppan.genes peppan.PEPPAN.gene_content.fas peppan.global.npy peppan.PEPPAN.gene_content.nwk peppan.map_bsn.conflicts.npz peppan.PEPPAN.gff peppan.map_bsn.mat.npz peppan.Prediction peppan.map_bsn.seq.npz peppan.self_bsn.npy peppan.map_bsn.tab.npz peppan.synteny.Prediction peppan.old_prediction.npz
However, a number of files were not generated (eg summary statistics, gene_presence_absence.csv, gene_presence_absence.Rtab).
I have used the same commands used in the example test file but with path to my .gff files.
Advise appreciated