Regression: run_RF2NA.sh - R:RNA.fa No such file or directory

[SuhasSrinivasan]

There is an issue with run_RF2NA.sh which was caused due to the recent Pull Request https://github.com/uw-ipd/RoseTTAFold2NA/pull/52

This issue occurs when running the provided example command for Protein-RNA prediction.

The Error

 -> Running command: /scratch/rf2na-new/input_prep/make_rna_msa.sh R:RNA.fa /scratch/rf2na-new/example/rna_pred RNA 18 120  

$ cat rna_pred/log/make_msa.RNA.stderr

grep: R:RNA.fa: No such file or directory
cp: cannot stat ‘R:RNA.fa’: No such file or directory

Error: Failed to open sequence file R:RNA.fa for reading

This issue did not exist before the PR.

The lines 79-82 which work

    type=`echo $i | awk -F: '{if (NF==1) {print "P"} else {print $1}}'`
    type=${type^^}
    fasta=`echo $i | awk -F: '{if (NF==1) {print $1} else {print $2}}'`
    tag=`basename $fasta | sed -E 's/\.fasta$|\.fas$|\.fa$//'`

Lines 79-84 from the PR which cause the error

    type=`echo $i | awk -F: '{if (NF==1) {print "P"} else {print $1}}'`
    type=${type^^}
    fasta=`echo $i`
    fasta_name=`echo $fasta | awk -F: '{if (NF==1) {print $1} else {print $2}}'`
    tag=`basename $fasta_name | sed -E 's/\.fasta$|\.fas$|\.fa$//'`
    type=`basename $type`  # extract only the last component after the last '/', so users can pass in an absolute path for each FASTA

This issues exists in both the main and dimaio/new_config branches.

[SuhasSrinivasan]

Submitted a Pull Request #111

[SuhasSrinivasan]

Fixed in PR #111