#############################################################################
# muPIT protein map track (DONE - 2014-10-30 - Hiram)

specific locations received in email:
-rw-r--r-- 1 19041 Oct  2 12:21 mupit_ebola_pos.txt

mkdir /hive/data/genomes/eboVir3/bed/muPIT
cd /hive/data/genomes/eboVir3/bed/muPIT

# turn those positions into a bed file:

awk '{printf "KM034562v1\t%d\t%d\t%d\n", $1-1,$1,$1}' mupit_ebola_pos.txt \
  > muPIT.bed

# process this bed file into three bases per item, and add
# sequence/AA names to items:

~/kent/src/hg/makeDb/doc/eboVir3/threeBaseAATrack.pl > nameVersion.bed

# load table
hgLoadBed eboVir3 muPIT nameVersion.bed

featureBits -countGaps eboVir3 muPIT
# 3666 bases of 18957 (19.339%) in intersection


#############################################################################