david: split gene ids (merged from cufflinks)

[setempler]

Add option --split-id SEPARATOR:

• split and expand gene list values by the supplied separator if -g option is used
• default None means no splitting
• problem/use case: cufflinks creates merged XLOC, thus merged gene symbols, which are not matching gtf file gene_names

See also https://github.com/mpg-age-bioinformatics/htseq-tools/blob/master/aDiff

[jorgeboucas]

use XLOC to retrieved old gene id

[setempler]

XLOC can contain list of genes.

So, for one XLOC

1) split list and duplicate lines per element?

e.g.

gene_id     log2fc pvalue
geneA;geneB 3.1    0.034

to

gene_id log2fc pvalue
geneA   3.1    0.034
geneB   3.1    0.034

or

2) use first gene only (as aDiff did)?

[jorgeboucas]

do 1) as aDiff does.