Mercurial > repos > erinija > dnp_compute_composite
view dnp-binary-strings.sh @ 0:92b1f9bacad7 draft default tip
"planemo upload commit 1a32efb8343938e8d49190003f251c78b5a58225-dirty"
author | erinija |
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date | Fri, 01 May 2020 12:12:16 +0000 |
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#!/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