pmfe-findmfe not returning results

[spoznan]

When I try now

./RunPMFECommand.sh pmfe-findmfe --sequence /projects/rna/rnatope/Data/tRNA_50/fasta/Aquifex.aeolicus.VF5_AE000657.fasta -a 3.4 -b 0 -c 0.4 -d 1

The only output I get is

[PMFE-WRAPPER-SCRIPT] Changing current working directory to "/projects/rna/PMFEUpdated-2020.09.10-MDS-mschmidt34/GTDMMBSoftware2020/pmfe" ...

and the code seems to take a very long time to return a result.

[maxieds]

@spoznan
There appears to have been another problem with my changes to the function to handle trailing zeros. Is this the correct output:

./RunPMFECommand.sh pmfe-findmfe --sequence /projects/rna/rnatope/Data/tRNA_50/fasta/Aquifex.aeolicus.VF5_AE000657.fasta -a 3.4 -b 0 -c 0.4 -d 1
   >> [PMFE-WRAPPER-SCRIPT] Changing current working directory to "/projects/rna/PMFEUpdated-2020.09.10-MDS-mschmidt34/GTDMMBSoftware2020/pmfe" ...
(((((((...((.((.(((..((.(.(((((.......))))).)))..))).))))........)))))))>	0	0	0	-311/10	-311/10

If so, let me know so I can file the new code as a part of the existing pull request I started last week:

Rational get_rational_from_word(std::string word) {
        Rational result;
        std::size_t decimalpoint = word.find('.');
        bool negative = (word.find('-') != std::string::npos);
        if (decimalpoint != std::string::npos) {
            std::string intpart = word.substr(0, decimalpoint);
            std::string fracpart = word.substr(decimalpoint+1);

            if (intpart == "") intpart = "0";
            Integer theint (intpart, 10);
            theint = abs(theint);

            // Carve out the fractional part. Surprisingly fiddly!
            // Handle a corner case where the fractional part is all zeros:
            int fracdenom = 1;
            int lastNonZeroPos = fracpart.find_last_of("0");
            if(lastNonZeroPos != std::string::npos) {
                 while(lastNonZeroPos > 0 && lastNonZeroPos != std::string::npos) {
                      fracpart = fracpart.substr(0, lastNonZeroPos);
                      lastNonZeroPos = fracpart.find_last_of("0");
                 }
                 if(lastNonZeroPos == 0) {
                      fracpart = "";
                 }
                 fracdenom = pow(10, fracpart.length());
            }
            if(fracpart.size() == 0) {
                 fracpart = "0";
            }
            Integer fracval (fracpart, 10);
            Rational thefrac (fracval, fracdenom);
            thefrac.canonicalize();

            result = theint + thefrac;
            if (negative) result *= -1;
        } else {
            Rational thevalue (word);
            result = thevalue;
        }
        result.canonicalize();
        return result;
    };

[spoznan]

The output I get with the old code is
(((((((><((((........))))>(((((.......)))))>...<(((((.......))))))))))))> 1 8 4 -397/10 -347/10

[maxieds]

@spoznan
Confirming that the new output I get is

(((((((><((((........))))>(((((.......)))))>...<(((((.......))))))))))))>	1	8	4	-397/10	-347/10