diff --git a/trackHub_generator.py b/trackHub_generator.py index d0e5313..da19ab4 100755 --- a/trackHub_generator.py +++ b/trackHub_generator.py @@ -4,6 +4,9 @@ ## script that parses a local directory structure and maps this to a UCSC trackDB.txt config ## https://github.com/steffenheyne/UCSC_trackHub_generator +## UCSC docu +## https://genome.ucsc.edu/goldenPath/help/trackDb/trackDbHub.html + import argparse import os.path import glob @@ -93,6 +96,8 @@ "itemRgb": "on", "color": "255,0,0", "visibility": "squish", + "maxItems": "100000", + "maxWindowToDraw": "20000000" #"colorByStrand": "255,0,0 0,0,255" } @@ -100,6 +105,7 @@ ## either for multiwig container or individual bigwig tracks ## keys are used as regex pattern against filename/ 'track' key in dict ## more specific patterns should come first in dict as we break loop after first match +## if matching, then the specifc track values are added or overwritten bigwig_specific = { "CD24.*H3K27ac": { "viewLimits": "0:30"}, @@ -149,7 +155,7 @@ super_default = {"track": None, - "superTrack": "on show", + "superTrack": "on", "parent": None, "shortLabel": None, "longLabel": None,