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3

I'm one of the EMBLmyGFF3 developers. If the compressed annotation is 396MB as mentioned by @terdon it is not a small annotation... In the worse case we have tested we never waited more than few minutes. We haven't done any particular speed test. It would be valuable if you could tell us how long it has taken in your case (If you didn't kill the process ...


3

You have to use command line options, not interactive prompts, like so: subprocess.call(['wordcount', '-sequence', filename, '-wordsize', sys.argv[1]], '-outfile', filename + '.wordcount.txt') Or, using the f-strings or formatted string literals: subprocess.call(f'wordcount -sequence {filename} -wordsize {sys.argv[1]} -outfile {filename}.wordcount.txt') ...


2

To find emboss packages type wossname, then hit enter twice. You will see all the programs. There is one called distmat. Then do tfm distmat, to get the fkn manual for distmat.


2

That error is telling you that the script you were running was killed by signal 9, also known as SIGKILL, while executing the command _seqret "$@". This is the way the operating system will kill processes that are asking for more memory than it can provide. Note that removing _secret "$@" is not the solution since that's what's actually doing the job. $@ ...


1

You're supplying a GTF feature file, but telling it that the features are in GFF3 format. I think you need -fformat gff2. See https://www.ebi.ac.uk/Tools/sfc/emboss_seqret/help/


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