Mercurial > repos > davidvanzessen > sff_extract_demultiplex
changeset 2:afddfd016ba6 draft
Uploaded
| author | davidvanzessen |
|---|---|
| date | Thu, 08 May 2014 07:50:42 -0400 |
| parents | 4f50fd2821a6 |
| children | 79be0752711d |
| files | r_wrapper.sh |
| diffstat | 1 files changed, 3 insertions(+), 2 deletions(-) [+] |
line wrap: on
line diff
--- a/r_wrapper.sh Thu May 08 04:23:45 2014 -0400 +++ b/r_wrapper.sh Thu May 08 07:50:42 2014 -0400 @@ -32,8 +32,9 @@ break fi file=$name"_"$barcode - cat $file.fastq | perl -e '$i=0;while(< >){if(/^\@/&&$i==0){s/^\@/\>/;print;}elsif($i==1){print;$i=-3}$i++;}' > $file.fasta - cat $file.fastq + cat $file.fastq | awk 'NR%4==1{printf ">%s\n", substr($0,2)}NR%4==2{print}' > $file.fasta + #cat $file.fastq | perl -e '$i=0;while(< >){if(/^\@/&&$i==0){s/^\@/\>/;print;}elsif($i==1){print;$i=-3}$i++;}' > $file.fasta + #cat $file.fastq echo "<tr><td>$barcode</td><td>$count</td><td><a href='$file.fastq'>$file.fastq</a></td><td><a href='$file.fasta'>$file.fasta</a></td></tr>" >> $output done < output.txt echo "</tbody></body></html>" >> $output