Mercurial > repos > dereeper > uniqprimer
changeset 5:e57b034c1fae draft
Uploaded
| author | dereeper |
|---|---|
| date | Mon, 03 Jan 2022 10:07:20 +0000 |
| parents | 1306b28be7c3 |
| children | 8218425fda1d |
| files | uniqprimer.sh |
| diffstat | 1 files changed, 33 insertions(+), 0 deletions(-) [+] |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/uniqprimer.sh Mon Jan 03 10:07:20 2022 +0000 @@ -0,0 +1,33 @@ +#!/bin/bash +include=$1 +exclude=$2 +product_size_range=$3 +primer_size=$4 +min_size=$5 +max_size=$6 +crossvalidate=$7 +outfile=$8 +log=$9 +fasta=${10} + +directory=`dirname $0` +other_inputs_line="" + +j=1 +for i in $* +do + if [[ $j -ge 11 ]] + then other_inputs_line=${other_inputs_line}" "$i + fi + j=$((j+1)) +done + + +if [[ $crossvalidate == "Yes" ]] +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 +elif [[ $crossvalidate = "No" ]] +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 +fi + + +