diff tools/scrsh.sh @ 0:c5a812cdf478 draft

planemo upload

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tools/scrsh.sh	Fri Dec 09 10:52:35 2016 -0500
@@ -0,0 +1,56 @@
+#!/bin/bash
+
+#sample_data=(tmp tmp1 tmp2 tmp3)
+sample_data=(`cat $1 | cut -f1 | sed ':a;N;$!ba;s/\n/ /g'`)
+#sample_name=(sample1 sample2 sample3 sample4)
+sample_name=(`cat $1 | cut -f2 | sed ':a;N;$!ba;s/\n/ /g'`)
+#sample_group=(gr1 gr1 gr2 gr2)
+sample_group=(`cat $1 | cut -f3 | sed ':a;N;$!ba;s/\n/ /g'`)
+
+
+group=('#')
+sample=('#Feature')
+
+touch anno.tmp
+touch count.tmp
+
+nsamples=`expr ${#sample_data[@]} - 1`
+
+for i in `seq 0 1 $nsamples`; do
+	group+=(${sample_group[i]}:${sample_group[i]})
+	sample+=(${sample_name[i]})
+
+	cat ${sample_data[i]} | tail -n+3 > dataWithoutHeader 2>> script.log
+
+	cat dataWithoutHeader | sort -k1 > dataWithoutHeader.sorted 2>> script.log
+
+	cat dataWithoutHeader.sorted | awk '{print $1}' > anno.sample 2>> script.log
+	cat dataWithoutHeader.sorted | awk '{print $5}' > count.sample 2>> script.log
+
+	paste -d"\t" count.tmp count.sample > count 2>> script.log
+	paste -d"\t" anno.tmp anno.sample > anno 2>> script.log
+
+	cat count > count.tmp 2>> script.log
+	cat anno > anno.tmp 2>> script.log
+
+done
+
+echo ${group[*]} | sed -e 's/ /\t/g' > count.matrix 2>> script.log
+echo ${sample[*]} | sed -e 's/ /\t/g' >> count.matrix 2>> script.log
+
+cat count | cut -f 2- > count.tmp 2>> script.log
+
+paste -d"\t" anno.sample count.tmp >> count.matrix 2>> script.log
+
+cat anno.tmp | cut -f 2- | awk '{for (i=2; i<=NF; i++){if ($1!=$i){print "error"; break}}}' > control.data 2>> script.log
+
+echo -e "gene_ID\tstart_coord\tend_coord" > annotation 2>> script.log
+cat dataWithoutHeader.sorted | awk '{print $1"\t"$2"\t"$3}' >> annotation 2>> script.log
+
+if [[ -s control.data ]]; then
+	echo "kolumny nie sa w odpowiedniej kolejnosci" > error.log
+	echo "" > count.matrix
+	echo "" > annotation
+else
+	echo "" > error.log
+fi