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#!/bin/csh
# Block Processor script
# process.csh <multiple alignment>
# m.a. must be in FASTA, CLUSTAL, MSF or STOCKHOLM format
setenv BLIMPS_DIR ../..
set bin = $BLIMPS_DIR/bin
# 1. mablock carves ungapped regions in all sequences out of m.a.
# Set min and max width of blocks
# Creates files $1.blks and $1.seqs
set minwidth=10
set maxwidth=60
$bin/mablock $1 $1 B $minwidth $maxwidth
# 2. Calibrate blocks for searching with blimps program
./calibrate.csh $1.blks $1.cblks > /dev/null
# 3. Add sequence weights to calibrated blocks
$bin/blweight $1.cblks $1.wblks P M > /dev/null
echo "Final blocks are in $1.wblks"
exit
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