Mercurial > repos > marpiech > rnaseq_pro_workflow_tools
comparison tools/scrsh.sh @ 0:c5a812cdf478 draft
planemo upload
| author | marpiech |
|---|---|
| date | Fri, 09 Dec 2016 10:52:35 -0500 |
| parents | |
| children |
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| -1:000000000000 | 0:c5a812cdf478 |
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| 1 #!/bin/bash | |
| 2 | |
| 3 #sample_data=(tmp tmp1 tmp2 tmp3) | |
| 4 sample_data=(`cat $1 | cut -f1 | sed ':a;N;$!ba;s/\n/ /g'`) | |
| 5 #sample_name=(sample1 sample2 sample3 sample4) | |
| 6 sample_name=(`cat $1 | cut -f2 | sed ':a;N;$!ba;s/\n/ /g'`) | |
| 7 #sample_group=(gr1 gr1 gr2 gr2) | |
| 8 sample_group=(`cat $1 | cut -f3 | sed ':a;N;$!ba;s/\n/ /g'`) | |
| 9 | |
| 10 | |
| 11 group=('#') | |
| 12 sample=('#Feature') | |
| 13 | |
| 14 touch anno.tmp | |
| 15 touch count.tmp | |
| 16 | |
| 17 nsamples=`expr ${#sample_data[@]} - 1` | |
| 18 | |
| 19 for i in `seq 0 1 $nsamples`; do | |
| 20 group+=(${sample_group[i]}:${sample_group[i]}) | |
| 21 sample+=(${sample_name[i]}) | |
| 22 | |
| 23 cat ${sample_data[i]} | tail -n+3 > dataWithoutHeader 2>> script.log | |
| 24 | |
| 25 cat dataWithoutHeader | sort -k1 > dataWithoutHeader.sorted 2>> script.log | |
| 26 | |
| 27 cat dataWithoutHeader.sorted | awk '{print $1}' > anno.sample 2>> script.log | |
| 28 cat dataWithoutHeader.sorted | awk '{print $5}' > count.sample 2>> script.log | |
| 29 | |
| 30 paste -d"\t" count.tmp count.sample > count 2>> script.log | |
| 31 paste -d"\t" anno.tmp anno.sample > anno 2>> script.log | |
| 32 | |
| 33 cat count > count.tmp 2>> script.log | |
| 34 cat anno > anno.tmp 2>> script.log | |
| 35 | |
| 36 done | |
| 37 | |
| 38 echo ${group[*]} | sed -e 's/ /\t/g' > count.matrix 2>> script.log | |
| 39 echo ${sample[*]} | sed -e 's/ /\t/g' >> count.matrix 2>> script.log | |
| 40 | |
| 41 cat count | cut -f 2- > count.tmp 2>> script.log | |
| 42 | |
| 43 paste -d"\t" anno.sample count.tmp >> count.matrix 2>> script.log | |
| 44 | |
| 45 cat anno.tmp | cut -f 2- | awk '{for (i=2; i<=NF; i++){if ($1!=$i){print "error"; break}}}' > control.data 2>> script.log | |
| 46 | |
| 47 echo -e "gene_ID\tstart_coord\tend_coord" > annotation 2>> script.log | |
| 48 cat dataWithoutHeader.sorted | awk '{print $1"\t"$2"\t"$3}' >> annotation 2>> script.log | |
| 49 | |
| 50 if [[ -s control.data ]]; then | |
| 51 echo "kolumny nie sa w odpowiedniej kolejnosci" > error.log | |
| 52 echo "" > count.matrix | |
| 53 echo "" > annotation | |
| 54 else | |
| 55 echo "" > error.log | |
| 56 fi |