Mercurial > repos > davidvanzessen > sff_extract_demultiplex

comparison wrapper.sh @ 8:cd56ce86c4bf draft

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author davidvanzessen
date Tue, 04 Nov 2014 09:03:22 -0500
parents 18ede27dc6b0
children 5a886d753c0a
comparison
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7:18ede27dc6b0 8:cd56ce86c4bf
62 cat $file.fastq | awk 'NR%4==1{printf ">%s\n", substr($0,2)}NR%4==2{print}' > $file.fasta 62 cat $file.fastq | awk 'NR%4==1{printf ">%s\n", substr($0,2)}NR%4==2{print}' > $file.fasta
63 python $dir/trim.py --input $file.fasta --output ${file}_trimmed.fasta --start ${trim_start[$barcode]} --end ${trim_end[$barcode]} 63 python $dir/trim.py --input $file.fasta --output ${file}_trimmed.fasta --start ${trim_start[$barcode]} --end ${trim_end[$barcode]}
64 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><td><a href='${file}_trimmed.fasta'>${file}_trimmed.fasta</a></td><td><a href='${name}_${barcode}_fastqc.html'>Report</a></td></tr>" >> $output 64 echo "<tr><td>$barcode</td><td>$count</td><td><a href='$file.fastq'>$file.fastq</a></td><td><a href='$file.fasta'>$file.fasta</a></td><td><a href='${file}_trimmed.fasta'>${file}_trimmed.fasta</a></td><td><a href='${name}_${barcode}_fastqc.html'>Report</a></td></tr>" >> $output
65 done < output.txt 65 done < output.txt
66 echo "</tbody></body></html>" >> $output 66 echo "</tbody></body></html>" >> $output
67
68 :'
69 mids = "mid\tforward\treverse"
70 fal = "file with sequenses on single line (no multiline)"
71 for mid in mids:
72 forwardmids = len([x for x in fal if re.match("^" + mid[1], x)])
73 reversemids = len([x for x in fal if re.match(mid[2] + "$", x)])
74 both = len([x for x in fal if re.match("^" + mid[1] + ".*" + mid[2] + "$", x)])
75 if (forwardmids + reversemids + both) > 0:
76 print "%s: %d - %d - %d" % (mid[0], forwardmids, reversemids, both)
77 '