Hello,
I tried to use CASPER with a draft genome assembly consisting of around 1029 contigs (named contig_1, contig_2 etc).
I initially had a problem with the bioservices package. I did installed it but when I was running Run_CASPER.py I was still getting an error that there is no module named 'bioservices'.
However, since I was using the specific region and not the KEGG code, I decided to edit CASPERQuick file and remove lines 27-29 and line 65. After these, the script run but I got no sequences in my "sequences" output folder while in a file named sequencesquickresults.txt I only get the position that I entered in the Run_CASPER.py file (1008,46300,46800).
By looking the script, I am assuming that the problem is the naming of the contigs or something like that, is that right? Could I have any help on that matter please?
Thank you in advance.
/Katerina
Hello,
I tried to use CASPER with a draft genome assembly consisting of around 1029 contigs (named contig_1, contig_2 etc).
I initially had a problem with the bioservices package. I did installed it but when I was running Run_CASPER.py I was still getting an error that there is no module named 'bioservices'.
However, since I was using the specific region and not the KEGG code, I decided to edit CASPERQuick file and remove lines 27-29 and line 65. After these, the script run but I got no sequences in my "sequences" output folder while in a file named sequencesquickresults.txt I only get the position that I entered in the Run_CASPER.py file (1008,46300,46800).
By looking the script, I am assuming that the problem is the naming of the contigs or something like that, is that right? Could I have any help on that matter please?
Thank you in advance.
/Katerina