We're trying to determine if there are repeats near genomic probems.

The first pass file had a large number of repeats in it.

high_genomic_signal_fewer_repeats.txt had those stripped out.

I created a fasta file with the following python code

data = [ x.strip().split('\t') for x in open('high_genomic_signal_fewer_repeats.txt','r')]
open('high_genomic_signal_fewer_repeats.fa','w').writelines([ ">%s|%s\n%s\n" % (x[2],x[0],x[3]) for x in data])

ok yeah I shouldn't do that in so few lines.

Hopefully the following

blastall -p blastn -e 0.000001 -d mouse_34.0.fa -i high_genomic_signal_fewer_repeats.fa -m 7 | tee high_genomic_signal_fewer_repeats.blast.xml

command will generate a new, smaller xml results file.