diff shuffle_sequences.sh @ 0:b45de206654d draft default tip

"planemo upload commit 1a32efb8343938e8d49190003f251c78b5a58225-dirty"

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/shuffle_sequences.sh	Fri May 01 12:08:23 2020 +0000
@@ -0,0 +1,52 @@
+#!/bin/sh
+
+if test "$#" -ne 3; then
+
+echo ""
+echo ""
+echo " CALL  "
+echo "   sh shuffle_sequences.sh input.fasta k output.fasta"
+echo ""
+echo " INPUT" 
+echo "   input.fasta   - input fasta file "
+echo "   k             - 'preserve frequency of k letters (dinucleotide k=2)'"
+echo ""
+echo " OUTPUT"
+echo "   output.fasta   - shuffle fasta file "
+echo ""
+echo " DESCRIPTION"
+echo "   Wrapper for ushuffle program Created by M Jiang. Reference PMID: 18405375 ."
+echo "   The ushuffle shuffles nucleotides in fasta sequence preserving frequency" 
+echo "   of k-mers, a positional order is changed. By default  k=2." 
+echo "   A sequence in fasta file is shuffled only once. The output fasta"
+echo "   in the identifier >line contains the original sequence; a shuffled sequence "
+echo "   is output on the second line."   
+echo ""
+echo " REQUIREMENT"
+echo "   ushuffle installed"
+echo "   conda install -c bioconda ushuffle"
+echo ""
+
+    exit 1
+fi
+
+name=$1
+diset=$2
+out=$3
+
+# comment for a galaxy tool
+call=ushuffle
+
+# prepare fasta into tabular
+cat ${name} | awk 'BEGIN{RS=">";OFS="\t"}NR>1{print ">"$1,$2}' > temp.tab.fa
+
+# read the tab file and create shuffled fasta
+while read -r line; 
+do 
+   seq=`echo $line | tr " " "\t" | cut -f2` 
+   useq=`${call} -s ${seq} -k ${diset} -n 1`; 
+   echo $line
+   echo $useq 
+done <  temp.tab.fa > ${out}
+rm temp.tab.fa
+