Commands so far:

-convert fimo to bed using fimo2bed.py (input is motif_alignments_flyFactor_dm6.2L.txt, output adds a "._bed" to end of file name) -slop gives gene_only_slop: bedtools slop: bedtools slop -i dmel-all-r6.12.gene_only.chr.gff -g ChromInfo.txt -l 1000 -r 0 -s -bedtools intersect -a motif_alignments_flyFactor_dm6.2L_BED.bed -b dmelr6.12.gene_only_slop.txt -wb > bedtoolsintersect_out.txt -phastcons steps:

* wig2bed < dm6.27way.phastCons.wigFix > dm6_phastcons.bed
* grep "chr2L" dm6_phastcons.bed > small.bed
* bedtools intersect -a bedtoolsintersect_out.txt -b small.bed -wo > dm6_phastcons_intersect.txt
* python phastcons_table.py --input /Users/bergeric/data/dm6_phastcons_intersect.txt --output practiceoutfile.txt