deltaBS for pairwise comparisons

There is a script to run pairwise comparisons of EMBL formatted assembly annotations. This Github repository has some test data included so you can run a test analysis.

When running deltaBS, the option -hp specifies the path to HMMER3, and -hd specifies the directory that the Pfam HMMs have been downloaded to.

To test

./src/deltaBS.pl -f embl -f1 data/tests/FQ312003.embl -f2 data/tests/AE014613.embl 
    --verbose -o /tmp -hp /usr/local/bin/ -hd <hmm_file.hmm> -t /tmp

If re-running the analysis, you can skip the hmmscan step by specifying the names of the files that were created in the first run. These follow the format [sequence filename]-pfam_hmmscan1.tbl:

./src/deltaBS.pl -f embl -f1 data/tests/FQ312003.embl -f2 data/tests/AE014613.embl 
    --verbose --dirty -o data/tests/salmonella -hp /usr/local/bin -hd 
    [path to deltaBS.hmmlib] -t data/tests/salmonella 
    -pa1 data/tests/FQ312003.embl-pfam_hmmscan1.tbl 
    -pa2 data/tests/AE014613.embl-pfam_hmmscan1.tbl

Options

-f [embl, genbank, fasta] file format for reference/query files

-f1 [filename] your reference genome/proteome file

-f2 [filename] your query genome/proteome file

-o [directory] directory you would like the results to go in

-ol [filename] (optional) ortholog list

-pa1 [filename] (optional) hmmscan results for genome 1

-pa2 [filename] (optional) hmmscan results for genome 2

-hp [directory] directory where HMMER3 has been installed (e.g. /usr/local/bin/)

-c [number] number of cpus to be used by HMMER

-hd [directory] directory where HMM directory has been downloaded

-v (optional) use this if you would like updates on what the script is doing while its running