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#!/bin/sh
################
# example that runs psisearch2_msa.pl iteratively through 5 iterations.
# Equivalent to:
# psisearch2_msa.pl --query CL0238_emb.fa --num_iter 5 --db /slib2/fa_dbs/rpd3_pfam28_lib.lseg
#
PS_BIN=/usr/share/fasta3/psisearch2
Q_DIR=/usr/share/doc/fasta3/examples/
FA_DB=/slib2/fa_dbs/qfo78.lseg
BL_DB=/slib2/bl_dbs/qfo78
DB=$FA_DB
OUT_SUFF='qm8CB'
M_FORMAT='m8CB'
ITERS='2 3 4 5'
for q_file_p in $*; do
q_file=${q_file_p##*/}
echo $q_file
# iteration 1:
$PS_BIN/psisearch2_msa.pl --query $Q_DIR/$q_file --num_iter 1 --db $DB --int_mask query --end_mask query --out_suffix $OUT_SUFF --m_format $M_FORMAT
# iteration 2 - 5
for it in $ITERS; do
prev=$(($it-1))
$PS_BIN/psisearch2_msa.pl --query $Q_DIR/$q_file --num_iter 1 --db $DB --int_mask query --end_mask query --out_suffix $OUT_SUFF --this_iter $it --prev_m89res $q_file.it${prev}.$OUT_SUFF --m_format $M_FORMAT
done
done
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