fasta from BED-like file with dashes

dashes-fasta.py

import pybedtools

# This demo uses files that ship with pybedtools
a = pybedtools.example_bedtool('a.bed')
fasta = pybedtools.example_filename('test.fa')

# Use a properly-formatted BED file, and then post-process the resulting fasta.
x = a.sequence(fi=fasta, s=True)
for i, line in enumerate(open(x.seqfn)):
    if line.startswith('>') and i >0:
        print '>\n------------'
    print line,

# Alternative method: use a text file with dashes, without stripping the dashes first.
# First make a version of `a.bed` that has dashes every other line
with open('a-with-dashes.txt', 'w') as fout:
    for i in a:
        fout.write(str(i))
        fout.write('------------\n')

for line in open('a-with-dashes.txt'):
    if line.startswith('------'):
        print('>\n--------')
    else:
        print open(
            pybedtools.BedTool(line, from_string=True)\
            .sequence(fi=fasta, s=True).seqfn
        ).read(),