#1 geneBody_coverage.py , bedfile split on space

[malte herold]

when running the script geneBody_coverage.py I kept getting the error:
"[NOTE:input bed must be 12-column] skipped this line:"

This was due to the fact that in line 100 of the script:
fields = line.split()
splits on space and not on tab
after replacing the line with:
fields = line.split("\t")

the script worked with my file

[Liguo Wang]

This is weird. In Python, "tab" is also considered as "space" (not vice versa).

[malte herold]

I had entries in my bed file that also contained spaces, that was the problem

[Zehan Dai]

hello,I have the same problem as you do. But the replacement of "fields = line.split()" to "fields = line.split("\t")" does not work for me. I still ecounter lots of "[NOTE:input bed must be 12-column] skipped this line:" while running geneBody_coverage.py

[Fabrice Leclerc]

I have the same problem using a UCSC formatted BED file: it contains 8 columns. All the lines are skipped. Any idea ?

[Liguo Wang]

The BED fie must have 12-column (standard BED format, https://genome.ucsc.edu/FAQ/FAQformat.html#format1). Otherwise, all non-standard BED lines will be skipped.