Mercurial > repos > biomonika > primer_tester
annotate primer_tester.sh @ 0:1e22519d75ac draft
Uploaded
| author | biomonika |
|---|---|
| date | Fri, 25 Jul 2014 17:09:47 -0400 |
| parents | |
| children |
| rev | line source |
|---|---|
| 0 | 1 #!/bin/bash |
| 2 primers_file=$1; | |
| 3 results=$2; | |
| 4 | |
| 5 cat $primers_file | cut -f1 >primers_names; | |
| 6 echo "primer Gorilla_female human_Y chimp_Y" >$results; | |
| 7 | |
| 8 while read primer | |
| 9 do | |
| 10 echo -n $primer >>$results; | |
| 11 for dataset in ${@:3} | |
| 12 do | |
| 13 search=$(cat $dataset| grep -B 1 "Amplimer 1" | grep "Primer" | grep $primer) | |
| 14 if [ "$search" == "" ] | |
| 15 then | |
| 16 echo -n " NO" >>$results; | |
| 17 else | |
| 18 echo -n " YES" >>$results; | |
| 19 fi | |
| 20 done | |
| 21 echo >>$results; | |
| 22 done < primers_names |