#!/bin/csh
# get PSI-BLAST output file
mkdir alignments
awk -f parsePSIBLAST_aln2A.awk $1 >$1"A.html"

# make FOM file
awk -f makeFOMout.awk $1"A.html" >FOMtemp.out

# sort based on FOM
sort -k5g FOMtemp.out >FOMtemp.sort
awk -f formatTXT.awk sortBy=1 FOMtemp.sort >resultSUM.txt
#awk -f formatHTML2A.awk FOMtemp.sort >resultSUM.html

# sort based on E-value iteration 2
sort -k3g FOMtemp.out >FOMtemp2.sort
awk -f formatTXT.awk sortBy=2 FOMtemp2.sort >resultSUM2.txt
#awk -f formatHTML2_2A.awk FOMtemp2.sort >resultSUM2.html

# sort based on E-value last iteration
sort -k4g FOMtemp.out >FOMtemp_L.sort
awk -f formatTXT.awk sortBy=3 FOMtemp_L.sort >resultSUM_L.txt
#awk -f formatHTML_L2A.awk FOMtemp_L.sort >resultSUM_L.html