elmaffo
commented
4 years ago Addendum: the bed file is in format chr# start stop, not # start stop
Open elmaffo opened 4 years ago
elmaffo
commented
4 years ago Addendum: the bed file is in format chr# start stop, not # start stop
I am trying to set up msings on a custom analysis. When I try to create the msi intervals file, target BED file sorting works but then the creation of the intervals file fails (the intervals file is empty) with the following messages:
Making MSI intervals file scripts/custom_regions.msi_intervals Traceback (most recent call last): File "/home/elmaffo/msings/msings-env/bin/msi", line 4, in
import('pkg_resources').run_script('msings==191.302893', 'msi')
File "/home/elmaffo/msings/msings-env/local/lib/python2.7/site-packages/pkg_resources/init.py", line 658, in run_script
self.require(requires)[0].run_script(script_name, ns)
File "/home/elmaffo/msings/msings-env/local/lib/python2.7/site-packages/pkg_resources/init.py", line 1438, in run_script
exec(code, namespace, namespace)
File "/home/elmaffo/msings/msings-env/lib/python2.7/site-packages/msings-191.302893-py2.7.egg/EGG-INFO/scripts/msi", line 7, in
sys.exit(main(sys.argv[1:]))
File "/home/elmaffo/msings/msings-env/local/lib/python2.7/site-packages/msings-191.302893-py2.7.egg/msings/scripts/script.py", line 32, in main
return action(arguments)
File "/home/elmaffo/msings/msings-env/local/lib/python2.7/site-packages/msings-191.302893-py2.7.egg/msings/subcommands/formatter.py", line 57, in action
chr, beg, end = coords(row)
File "/home/elmaffo/msings/msings-env/local/lib/python2.7/site-packages/msings-191.302893-py2.7.egg/msings/subcommands/formatter.py", line 32, in coords
return row[chromosome], int(row[start]), int(row[stop])
ValueError: invalid literal for int() with base 10: 'Start'
Created scripts/custom_regions.msi_intervals