Mercurial > repos > erinija > dnp_binary_strings

annotate dnp-binary-strings.sh @ 0:611156829647 draft default tip

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"planemo upload commit 1a32efb8343938e8d49190003f251c78b5a58225-dirty"
author erinija
date Fri, 01 May 2020 12:07:46 +0000
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1 #!/bin/sh
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2 if test "$#" -ne 3; then
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3
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4 echo ""
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5 echo " CALL "
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6 echo " sh binary_strings.sh input.fasta dinucleotides output.file"
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7 echo ""
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8 echo " INPUT"
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9 echo " input.fasta - input fasta file "
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10 echo " dinucleotides - 'AA AC AG AT ...'"
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11 echo ""
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12 echo " OUTPUT"
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13 echo " output.file - name of tabular format output file "
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14 echo ""
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15 echo " DESCRIPTION"
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16 echo " Convert fasta sequences to a binary sequence of 01 "
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17 echo " in which 1(ones) indicate a presence of a given"
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18 echo " dinucleotide at that position and 0 everywhere else."
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19 echo " Each fasta sequence in the input file has a "
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20 echo " corresponding row with four tab separated columns"
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21 echo " binary_string dinucleotide fasta_string times_occurred"
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22 echo ""
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23 echo " REQUIREMENT"
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24 echo " dnp-binstrings installed"
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25 echo " conda install -c bioconda dnp-binstrings"
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26 echo ""
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27 exit 1
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28 fi
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29
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30 name=$1
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31 diset=$2
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32 out=$3
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33
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34 call=dnp-binstrings
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35
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36 cp ${name} ${name}.fa
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37
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38 for di in ${diset}
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39 do
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40 ${call} ${name}.fa -di ${di} >> ${out}
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41 done;
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42 rm ${name}.fa
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43 exit 0