Mercurial > repos > davidvanzessen > mutation_analysis

comparison wrapper.sh @ 47:099cc1254f74 draft

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Uploaded
author davidvanzessen
date Mon, 09 Nov 2015 07:21:09 -0500
parents 7304b91757a8
children 5c6b9e99d576
comparison
equal deleted inserted replaced
46:42e39033514b 47:099cc1254f74
7 outdir=$4 7 outdir=$4
8 title=$5 8 title=$5
9 include_fr1=$6 9 include_fr1=$6
10 functionality=$7 10 functionality=$7
11 unique=$8 11 unique=$8
12 naive_output=$9
12 mkdir $outdir 13 mkdir $outdir
13 14
14 type="`file $input`" 15 type="`file $input`"
15 if [[ "$type" == *"Zip archive"* ]] ; then 16 if [[ "$type" == *"Zip archive"* ]] ; then
16 echo "Zip archive" 17 echo "Zip archive"
23 tar -xJf $input -C $PWD/files/$title 24 tar -xJf $input -C $PWD/files/$title
24 fi 25 fi
25 26
26 cat $PWD/files/*/1_* > $PWD/summary.txt 27 cat $PWD/files/*/1_* > $PWD/summary.txt
27 cat $PWD/files/*/3_* > $PWD/sequences.txt 28 cat $PWD/files/*/3_* > $PWD/sequences.txt
29 cat $PWD/files/*/5_* > $PWD/aa.txt
28 cat $PWD/files/*/6_* > $PWD/junction.txt 30 cat $PWD/files/*/6_* > $PWD/junction.txt
29 cat $PWD/files/*/7_* > $PWD/mutationanalysis.txt 31 cat $PWD/files/*/7_* > $PWD/mutationanalysis.txt
30 cat $PWD/files/*/8_* > $PWD/mutationstats.txt 32 cat $PWD/files/*/8_* > $PWD/mutationstats.txt
31 cat $PWD/files/*/10_* > $PWD/hotspots.txt 33 cat $PWD/files/*/10_* > $PWD/hotspots.txt
32 34
132 done < $outdir/transitions.txt 134 done < $outdir/transitions.txt
133 echo "</table>" >> $output 135 echo "</table>" >> $output
134 136
135 echo "</html>" >> $output 137 echo "</html>" >> $output
136 138
139
140 #optional output for naive
141
142 if [[ "$naive_output" != "None" ]]
143 then
144 echo "naive_output: $naive_output"
145 python $dir/imgt_loader.py --summ $PWD/summary.txt --aa $PWD/aa.txt --junction $PWD/junction.txt --output $naive_output
146 Rscript $dir/naive_output.r $naive_output $outdir/merged.txt $naive_output 2>&1
147 fi
148
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137 #rm $outdir/HS12RSS.txt 159 #rm $outdir/HS12RSS.txt
138 #rm $outdir/HS23RSS.txt 160 #rm $outdir/HS23RSS.txt