.sequence() only works when from_string=True about pybedtools HOT 4 CLOSED

This one doesn't work because there's no support for creation from a tuple (e.g., try printing loc -- TypeError is raised). This should be supported, so I'll add it.

# ...
# no content in .seqfn
loc = BedTool([(chrom, start, end)])
print open(loc.sequence(fi=fa).seqfn).read()

This one doesn't work because there's no newline at the end of the file. The latest versions use the full line, plus the "\n", as the definition of a feature; using the from_string kwarg adds the newlines. I'll add some more checks on this so that it's supported as well.

# ...
# no content in .seqfn
out = open('t.fa', 'w')
out.write("%s\t%i\t%i" % (chrom, start, end))
out.close()
loc = BedTool(out.name)
print open(loc.sequence(fi=fa).seqfn).read()

Adding a newline to the created file makes it work:

from pybedtools import BedTool
import pybedtools
chrom, start, end = "chr1", 1, 10
fa = pybedtools.example_filename('test.fa')
out = open('t.fa', 'w')

# add newline too
out.write("%s\t%i\t%i\n" % (chrom, start, end))

out.close()
loc = BedTool(out.name)
print open(loc.sequence(fi=fa).seqfn).read()

from pybedtools.

ah, thanks for looking into it. Yes, the docs do say you can create from a tuple.
I missed that about having a newline. doh!

from pybedtools.

Turns out it's BEDTools that doesn't support a one-feature BED file with no newline -- with your original example,

$ bedtools getfasta -bed t.fa -fi pybedtools/test/data/test.fa -fo res.fa
$ wc -l res.fa
0 res.fa

Maybe because it doesn't know if it's in the middle of a stream? Should hit EOF though . . . anyway, it's a corner case, and not sure if it should be supported or not by BEDTools.

Also, I just opened a separate issue for the creation from tuple . . . so closing this one for now.

from pybedtools.

Hmm, BEDTools should handle this. I suspect it's an untested corner case that arose from my latest restructuring of the API. I'll ook into this soon.

from pybedtools.