diff dnp-binary-strings.sh @ 0:b45de206654d draft default tip

"planemo upload commit 1a32efb8343938e8d49190003f251c78b5a58225-dirty"

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/dnp-binary-strings.sh	Fri May 01 12:08:23 2020 +0000
@@ -0,0 +1,43 @@
+#!/bin/sh
+if test "$#" -ne 3; then
+
+echo ""
+echo " CALL  "
+echo "   sh binary_strings.sh input.fasta dinucleotides output.file"
+echo ""
+echo " INPUT" 
+echo "   input.fasta   - input fasta file "
+echo "   dinucleotides - 'AA AC AG AT ...'"
+echo ""
+echo " OUTPUT"
+echo "   output.file   - name of tabular format output file "
+echo ""
+echo " DESCRIPTION"
+echo "   Convert fasta sequences to a binary sequence of 01 "
+echo "   in which 1(ones) indicate a presence of a given" 
+echo "   dinucleotide at that position and 0 everywhere else." 
+echo "   Each fasta sequence in the input file has a "
+echo "   corresponding row with four tab separated columns" 
+echo "   binary_string dinucleotide fasta_string times_occurred"
+echo ""
+echo " REQUIREMENT"
+echo "   dnp-binstrings installed"
+echo "   conda install -c bioconda dnp-binstrings"
+echo ""
+  exit 1
+fi
+
+name=$1
+diset=$2
+out=$3
+
+call=dnp-binstrings
+
+cp ${name} ${name}.fa
+
+for di in ${diset}
+do
+    ${call} ${name}.fa -di ${di} >> ${out}
+done;
+rm ${name}.fa
+exit 0