Mercurial > repos > erinija > dnp_correlation_between_profiles
annotate dnp-binary-strings.sh @ 0:b45de206654d draft default tip
"planemo upload commit 1a32efb8343938e8d49190003f251c78b5a58225-dirty"
author | erinija |
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date | Fri, 01 May 2020 12:08:23 +0000 |
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b45de206654d
"planemo upload commit 1a32efb8343938e8d49190003f251c78b5a58225-dirty"
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1 #!/bin/sh |
b45de206654d
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2 if test "$#" -ne 3; then |
b45de206654d
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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" |
b45de206654d
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7 echo "" |
b45de206654d
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8 echo " INPUT" |
b45de206654d
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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 |