Missing scripts and programs

[MikelAguirreRodrigo]

I have found certain calls to scripts and programs that do not exist in the spot.pl script:

line 189: $command="java -jar TargetRNA2.jar -a $upstream -b $downstream -l $seedt -y -g $acc_dir/$acc -s $PWD/$rna -d Bacteria -o $PWD/TargetRNA2_$out.txt -p $cutofft"; The TargetRNA2 software are only in web format. Where is the .jar obtained? It does not appear on its official page.

The following calls are made to scripts that do not exist:

line 246 (and the following): $command="$COPRADIR/homology_intaRNA.pl $rnas $upstream $downstream 5utr $acc $copra_genomes &";

line 599 (and the following):

# process intarna output
system "$INTADIR/produce_semicolon_sep_results_from_intarna_out.pl --intarna-out-file predictions.intarna > predictions.csv";
# sort intarna output
system "$INTADIR/sort_intarna_csv_results.pl --intarna-csv-file predictions.csv --column 17 > predictions.sorted.csv";
# omit WARNING for 'N' from IntaRNA raw output. fixes interaction parsing warnings.
system "sed -i '/WARNING/{N;d;}' predictions.intarna"; ## d stands for delete N also deletes one line after. add another N to delete one more ##edit 1.0.1 
# add interactions to table
system "$INTADIR/add_interactions.pl predictions.sorted.csv predictions.intarna"; #writes to: intarna_websrv_table.csv

The absence of these scripts are due to forgetfulness?

Best

[milkcookie]

I had the same question, some script can't be found. Did you solve it? @MikelAguirreRodrigo

[MikelAguirreRodrigo]

I had the same question, some script can't be found. Did you solve it? @MikelAguirreRodrigo

No, sorry. I am developing my own scripts.