Mercurial > repos > erinija > dnp_binary_strings

annotate shuffle_sequences.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
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3 if test "$#" -ne 3; then
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4
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5 echo ""
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6 echo ""
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7 echo " CALL "
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8 echo " sh shuffle_sequences.sh input.fasta k output.fasta"
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9 echo ""
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10 echo " INPUT"
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11 echo " input.fasta - input fasta file "
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12 echo " k - 'preserve frequency of k letters (dinucleotide k=2)'"
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13 echo ""
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14 echo " OUTPUT"
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15 echo " output.fasta - shuffle fasta file "
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16 echo ""
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17 echo " DESCRIPTION"
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18 echo " Wrapper for ushuffle program Created by M Jiang. Reference PMID: 18405375 ."
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19 echo " The ushuffle shuffles nucleotides in fasta sequence preserving frequency"
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20 echo " of k-mers, a positional order is changed. By default k=2."
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21 echo " A sequence in fasta file is shuffled only once. The output fasta"
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22 echo " in the identifier >line contains the original sequence; a shuffled sequence "
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23 echo " is output on the second line."
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24 echo ""
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25 echo " REQUIREMENT"
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26 echo " ushuffle installed"
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27 echo " conda install -c bioconda ushuffle"
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28 echo ""
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29
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30 exit 1
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31 fi
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32
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33 name=$1
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34 diset=$2
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35 out=$3
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36
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37 # comment for a galaxy tool
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38 call=ushuffle
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39
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40 # prepare fasta into tabular
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41 cat ${name} | awk 'BEGIN{RS=">";OFS="\t"}NR>1{print ">"$1,$2}' > temp.tab.fa
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42
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43 # read the tab file and create shuffled fasta
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44 while read -r line;
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45 do
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46 seq=`echo $line | tr " " "\t" | cut -f2`
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47 useq=`${call} -s ${seq} -k ${diset} -n 1`;
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48 echo $line
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49 echo $useq
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50 done < temp.tab.fa > ${out}
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51 rm temp.tab.fa
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52