Tests on arguments not performed when using Python API

[dputhier]

When using the code below file formats (and more) are not tested as these tests are embedded in the argument parser...

	from pygtftk.plugins.ologram import ologram

	ologram(
	    inputfile="hg38_chr1.gtf.gz",
	    peak_file="ENCFF112BHN_H3K4me3_chr1.bed",
	    chrom_info="hg38_chr1.genome",
	    upstream=1500,
	    downstream=1500,
	    sort_features="summed_bp_overlaps_pvalue",
	    nb_threads=8
	)

[dputhier]

Here is another solution. Maybe not totally convincing. However its ensure that all arguments are tested by the parser dedicated classes (e.g. arg_formatter.FormattedFile())

	from pygtftk.plugins.ologram import ologram
	from pygtftk.plugins.ologram import make_parser

	myparser = make_parser()

	args = myparser.parse_args(['--inputfile', "hg38_chr1.gtf.gz",
                                    '--peak-file', "ENCFF112BHN_H3K4me3_chr1.bed",
                                    '--chrom-info', "hg38_chr1.genome",
                                    '--upstream', "1500",
                                    '--downstream', "1500",
                                    '--sort-features', "summed_bp_overlaps_pvalue"])
	args = dict(args.__dict__)
	ologram(**args)

[dputhier]

Here is another solution with 8 threads and increased verbosity

	from pygtftk.plugins.ologram import ologram
	from pygtftk.plugins.ologram import make_parser
	import pygtftk.utils 

	pygtftk.utils.VERBOSITY = 3

	myparser = make_parser()

	args = myparser.parse_args(['--inputfile', "hg38_chr1.gtf.gz",
	                                '--peak-file', "ENCFF112BHN_H3K4me3_chr1.bed",
	                                '--chrom-info', "hg38_chr1.genome",
	                                '--upstream', "1500",
	                                '--downstream', "1500",
	                                '--sort-features', "summed_bp_overlaps_pvalue",
	                                '--nb-threads', "8"])
	args = dict(args.__dict__)
	ologram(**args)	

[dputhier]

Note that VERBOSITY is normally controlled by the main parser (the parser below behaving normally as a sub_parser).