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comparison uniqprimer.sh @ 5:e57b034c1fae draft

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author dereeper
date Mon, 03 Jan 2022 10:07:20 +0000
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4:1306b28be7c3 5:e57b034c1fae
1 #!/bin/bash
2 include=$1
3 exclude=$2
4 product_size_range=$3
5 primer_size=$4
6 min_size=$5
7 max_size=$6
8 crossvalidate=$7
9 outfile=$8
10 log=$9
11 fasta=${10}
12
13 directory=`dirname $0`
14 other_inputs_line=""
15
16 j=1
17 for i in $*
18 do
19 if [[ $j -ge 11 ]]
20 then other_inputs_line=${other_inputs_line}" "$i
21 fi
22 j=$((j+1))
23 done
24
25
26 if [[ $crossvalidate == "Yes" ]]
27 then python $directory/uniqprimer-0.5.0/uniqprimer.py -i $include -x $exclude --productsizerange $product_size_range --primersize $primer_size --minprimersize $min_size --crossvalidate --keeptempfiles --maxprimersize $max_size -o $outfile -f $fasta -l $log $other_inputs_line >>$log 2>&1
28 elif [[ $crossvalidate = "No" ]]
29 then python $directory/uniqprimer-0.5.0/uniqprimer.py -i $include -x $exclude --productsizerange $product_size_range --primersize $primer_size --minprimersize $min_size --keeptempfiles --maxprimersize $max_size -o $outfile -f $fasta -l $log $other_inputs_line >>$log 2>&1
30 fi
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