Incorrect handling of hdf5 file for repeated runs of RiboCode

[jdcla]

Ribocode does not correctly handle the hdf5 file it creates to store temperary data, resulting in identical results for multiple runs that are ran from the same folder.

For example, running this script resulted in all identical ORF libraries for each of the datasets.

while IFS= read -r folder; do
    echo "$folder"
    mkdir "$folder/GRCh38_110/ribocode/"
    RiboCode_onestep -g "$assembly/Homo_sapiens.GRCh38.110.gtf" \
                     -f "$assembly/Homo_sapiens.GRCh38.dna.primary_assembly.fa" \
                     -r "${folder}/GRCh38_110/aligned_tran.bam" \
                     -l no \
                     -o "${folder}/GRCh38_110/ribocode/ribo" \
                     -f0_percent 0.5
done < "$1"

I solved this by removing the hdf5 file created after each run

while IFS= read -r folder; do
    echo "$folder"
    mkdir "$folder/GRCh38_110/ribocode/"
    rm aligned_tran_psites.hd5                                               <-- remove file
    RiboCode_onestep -g "$assembly/Homo_sapiens.GRCh38.110.gtf" \
                     -f "$assembly/Homo_sapiens.GRCh38.dna.primary_assembly.fa" \
                     -r "${folder}/GRCh38_110/aligned_tran.bam" \
                     -l no \
                     -o "${folder}/GRCh38_110/ribocode/ribo" \
                     -f0_percent 0.5
done < "$1"