Strand not extracting from .bed

[daler]

Strand not extracting from .bed

[arq5x]

Strand should always be the 6th column. In this case, your strand is being populated in the name column.

[daler]

One solution is to pad lines with empty fields (by convention, "." is used to fill a field) so that strand is in the 6th column (http://genome.ucsc.edu/FAQ/FAQformat.html#format1).

Another solution is to just access the 4th field, name, where you have strand stored. You can do this in 2 ways -- by attribute lookup or by indexing into the fields, e.g.,

print txpt.name
print txpt[3]

[olgabot]

Thank you! I made the file from using mergeBed on the command line and
didn't know it would screw up the column order so much.
Olga

www.olgabotvinnik.com
blog.olgabotvinnik.com

2012/3/18 Ryan Dale <
[email protected]

One solution is to pad lines with empty fields (by convention, "." is used
to fill a field) so that strand is in the 6th column (
http://genome.ucsc.edu/FAQ/FAQformat.html#format1).

Another solution is to just access the 4th field, name, where you have
strand stored. You can do this in 2 ways -- by attribute lookup or by
indexing into the fields, e.g.,

print txpt.name
print txpt[3]

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