Gtf files should allow "." in phase column (parse.py)

[benbfly]

Column 7 of GTF files are only allowed values "0", "1", or "2". But they often have "." for non-coding features. This is in the UCSC spec:
https://genome.ucsc.edu/FAQ/FAQformat.html#format3

[dpryan79]

Do you have an example of a GTF file that's getting parse incorrectly? The phase is ignored by deeptools_intervals.

[benbfly]

In the end actually I think I had another problem with my GTF. I opened the issue because of the function description for seemsLikeGTF, which seemed to say that it could only be 0,1, or 2. But when I look down at the code, i see it actually takes '.' as well. I would recommend changing the function description comment just to avoid confusion:

deeptools_intervals/deeptoolsintervals/parse.py

Line 33 in 2070277

7: 0, 1 or 2

Thanks!

[dpryan79]

@benbfly That's just a comment, the code checks for .:

deeptools_intervals/deeptoolsintervals/parse.py

Lines 42 to 43 in 2070277

	if cols[7] != '.':
	int(cols[7]) in [0, 1, 2]