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#!/bin/sh
################
# example that runs psisearch2_msa.pl iteratively through 5 iterations using psiblast instead of ssearch
# Equivalent to:
# psisearch2_msa.pl --pgm psiblast --query query.aa --num_iter 5 --db /slib2/bl_dbs/qfo78
#
PS_BIN=/usr/share/fasta3/psisearch2
q_file=$1
db=/slib2/bl_dbs/pir1
pssm_eval=1e-10
m_format='m8CB'
SRC_QDIR=../hum_1dom200_queries
iters='2 3 4 5'
# iters=''
for q_file_p in $*; do
q_file=${q_file_p##*/}
echo $q_file
# iteration 1:
# echo "$PS_BIN/psisearch2_msa.pl --pgm psiblast --query $SRC_QDIR/$q_file --num_iter 1 --db $db --int_mask query --end_mask query --out_suffix q_pblt --m_format $m_format --save_list asnbin"
$PS_BIN/psisearch2_msa.pl --pgm psiblast --query $q_file --num_iter 1 --pssm_eval $pssm_eval --db $db --int_mask query --end_mask query --out_suffix q_pblt --m_format $m_format --save_list asntxt
# iteration 2 - 5
for it in $iters; do
prev=$(($it-1))
$PS_BIN/psisearch2_msa.pl --pgm psiblast --query $q_file --num_iter 1 --pssm_eval $pssm_eval --db $db --int_mask query --end_mask query --out_suffix q_pblt --this_iter $it --prev_m89res $q_file.it${prev}.q_pblt --m_format $m_format --save_list asntxt
done
done
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