Mercurial > repos > ryotas > export2sam

annotate export2sam.sh @ 0:61f3089ddc74 default tip

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author ryo_tas <yamanaka@genome.rcast.u-tokyo.ac.jp>
date Tue, 30 Dec 2014 18:53:23 +0900
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ryo_tas <yamanaka@genome.rcast.u-tokyo.ac.jp>
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1 #!/bin/sh
ryo_tas <yamanaka@genome.rcast.u-tokyo.ac.jp>
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2 # SET TOOL DIRECTORY
ryo_tas <yamanaka@genome.rcast.u-tokyo.ac.jp>
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3
ryo_tas <yamanaka@genome.rcast.u-tokyo.ac.jp>
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4 CMDNAME=`basename $0`
ryo_tas <yamanaka@genome.rcast.u-tokyo.ac.jp>
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5
ryo_tas <yamanaka@genome.rcast.u-tokyo.ac.jp>
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6 while getopts a:b:o:gr OPT
ryo_tas <yamanaka@genome.rcast.u-tokyo.ac.jp>
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7 do
ryo_tas <yamanaka@genome.rcast.u-tokyo.ac.jp>
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8 case $OPT in
ryo_tas <yamanaka@genome.rcast.u-tokyo.ac.jp>
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9 "a" ) FLG_A="TRUE" ; VALUE_A="$OPTARG" ;;
ryo_tas <yamanaka@genome.rcast.u-tokyo.ac.jp>
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10 "b" ) FLG_B="TRUE" ; VALUE_B="$OPTARG" ;;
ryo_tas <yamanaka@genome.rcast.u-tokyo.ac.jp>
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11 "o" ) FLG_O="TRUE" ; VALUE_O="$OPTARG" ;;
ryo_tas <yamanaka@genome.rcast.u-tokyo.ac.jp>
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12 "g" ) FLG_G="TRUE" ;;
ryo_tas <yamanaka@genome.rcast.u-tokyo.ac.jp>
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13 "r" ) FLG_R="TRUE" ;;
ryo_tas <yamanaka@genome.rcast.u-tokyo.ac.jp>
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14 * ) echo "Usage: $CMDNAME [-a VALUE] [-b] [-o VALUE] [-gr]" 1>&2
ryo_tas <yamanaka@genome.rcast.u-tokyo.ac.jp>
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15 exit 1 ;;
ryo_tas <yamanaka@genome.rcast.u-tokyo.ac.jp>
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16 esac
ryo_tas <yamanaka@genome.rcast.u-tokyo.ac.jp>
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17 done
ryo_tas <yamanaka@genome.rcast.u-tokyo.ac.jp>
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18
ryo_tas <yamanaka@genome.rcast.u-tokyo.ac.jp>
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19 # SINGLE END OR PAIR END
ryo_tas <yamanaka@genome.rcast.u-tokyo.ac.jp>
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20 if [ ! $FLG_B ] ; then
ryo_tas <yamanaka@genome.rcast.u-tokyo.ac.jp>
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21 ARGS="--read1=$VALUE_A"
ryo_tas <yamanaka@genome.rcast.u-tokyo.ac.jp>
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22 else
ryo_tas <yamanaka@genome.rcast.u-tokyo.ac.jp>
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23 ARGS="--read1=$VALUE_A --read2=$VALUE_B"
ryo_tas <yamanaka@genome.rcast.u-tokyo.ac.jp>
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24 fi
ryo_tas <yamanaka@genome.rcast.u-tokyo.ac.jp>
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25
ryo_tas <yamanaka@genome.rcast.u-tokyo.ac.jp>
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26 # GZIPPED OR NOT
ryo_tas <yamanaka@genome.rcast.u-tokyo.ac.jp>
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27 if [ $FLG_G ] ; then
ryo_tas <yamanaka@genome.rcast.u-tokyo.ac.jp>
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28 CMD1="./illumina_export2sam_gz.pl $ARGS"
ryo_tas <yamanaka@genome.rcast.u-tokyo.ac.jp>
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29 else
ryo_tas <yamanaka@genome.rcast.u-tokyo.ac.jp>
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30 CMD1="./illumina_export2sam.pl $ARGS"
ryo_tas <yamanaka@genome.rcast.u-tokyo.ac.jp>
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31 fi
ryo_tas <yamanaka@genome.rcast.u-tokyo.ac.jp>
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32
ryo_tas <yamanaka@genome.rcast.u-tokyo.ac.jp>
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33 # MODIFY ACCORDING TO THE REFERENCE
ryo_tas <yamanaka@genome.rcast.u-tokyo.ac.jp>
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34 if [ $FLG_R ] ; then
ryo_tas <yamanaka@genome.rcast.u-tokyo.ac.jp>
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35 CMD2='$tmp=$_;$tmp=~s/chr_fragments\.fa\///g;$tmp=~s/(chr\w+)\.fa/$1/g;print $tmp;'
ryo_tas <yamanaka@genome.rcast.u-tokyo.ac.jp>
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36 CMD="$CMD1 | perl -ne '$CMD2'"
ryo_tas <yamanaka@genome.rcast.u-tokyo.ac.jp>
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37 else
ryo_tas <yamanaka@genome.rcast.u-tokyo.ac.jp>
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38 CMD=$CMD1
ryo_tas <yamanaka@genome.rcast.u-tokyo.ac.jp>
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39 fi
ryo_tas <yamanaka@genome.rcast.u-tokyo.ac.jp>
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40
ryo_tas <yamanaka@genome.rcast.u-tokyo.ac.jp>
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41 echo $CMD
ryo_tas <yamanaka@genome.rcast.u-tokyo.ac.jp>
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42 eval $CMD > $VALUE_O