Mercurial > repos > dereeper > haplophyle
annotate Haplophyle.sh @ 2:d6281dc90e20 draft default tip
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author | dereeper |
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date | Wed, 09 Jun 2021 16:54:15 +0000 |
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1 #!/bin/bash |
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2 |
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3 # Config ####### |
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4 maxsizeseq=500 |
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5 maxnumseq=200 |
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6 ################ |
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7 |
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8 tool_path=$(dirname $0) |
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9 |
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10 filein=$1 |
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11 fileout=$2 |
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12 dotfile=$3 |
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13 logfile=$4 |
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14 filein2=$5 |
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15 groups=$6 |
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16 |
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17 nbline=$(sed -n '$=' $filein) |
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18 let "nbseq = $nbline / 2" |
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19 seq=$(sed -n 2p $filein) |
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20 sizeseq=${#seq} |
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21 |
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22 if [ $nbseq -lt $maxnumseq ] |
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23 then |
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24 if [ $sizeseq -lt $maxsizeseq ] |
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25 then |
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26 perl $tool_path/Haplophyle.pl --input $filein --groups $groups --stats $filein2 --dot $dotfile --out $fileout --tool_path $tool_path >>$logfile 2>&1 |
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27 else |
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28 echo "Sequence size: $sizeseq" |
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29 echo "Input Sequences bust have a length < $maxsizeseq" |
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30 exit 1 |
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31 fi |
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32 else |
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33 echo "$nbseq sequences in the file" |
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34 echo "Input file must have less than $maxnumseq sequences" |
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35 exit 1 |
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36 fi |