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1 #!/bin/bash
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2 #SrcFolder='/data/zhang/wuj/scripts/SpliceTrap.0.8'
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3 InputFileName=$1
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4 faorfq=$2
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5 DatabasePrefix=$3
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6 Outputfolder=$4
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7 SrcFolder=$5
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8 Threads=$6
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9 DatabaseFolder=$SrcFolder'/../db/'$DatabasePrefix'/btw/TXdb'
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10 TmpFolderName=`basename $1`
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11 #fasta or fastq
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12
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13 cd $Outputfolder;
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14 #prepare the folder
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15 if [ -d $TmpFolderName.result ];then
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16 echo "MAPPING: !!!Error, there is already a folder named "$TmpFolderName".result !"
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17 echo "MAPPING: !!!change the name of that folder first in case I erase them..."
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18 exit
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19 fi
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20 echo "MAPPING: Start mapping $InputFileName...Creating cache folder $TmpFolderName.result"
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21 mkdir $TmpFolderName".result"
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22 mkdir $TmpFolderName".result"/cache
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23
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24 cd $TmpFolderName".result"
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25 cd cache
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26 echo "MAPPING: Split to pieces ..."
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27 split -l 1000000 $InputFileName
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28 for name in x*
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29 do
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30
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31 if [ $faorfq == "fasta" ];then
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32 add="-f"
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33 fi
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34 # if [ $name != $InputFileName ];then
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35 echo "bowtie -p $Threads -a -v 2 $DatabaseFolder $name $add >$name.btw; perl $SrcFolder/bowtie2eland.pl $name.btw $name $name.eland;rm $name.btw ;perl $SrcFolder/mark.mt.4eland.pl $name.eland >$name.nomt;rm $name.eland">>map.sh
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36 echo $name >>checklist
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37 # fi
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38 done
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39
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40 echo "MAPPING: submit scripts..."
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41 perl $SrcFolder/batchqsub.pl map.sh
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42
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43 tasknum=`wc -l map.sh |tr -d "\n"`
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44 #checking..
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45
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46 echo "MAPPING: mapping $InputFileName to TXdb done...start to check.."
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47 while [ 1 ]
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48 do
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49 if [ -f mapcheck.sh ];then
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50 rm mapcheck.sh
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51 fi
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52 while read checklist
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53 do
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54
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55 name=`echo $checklist |tr -d "\n"`
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56 echo "MAPPING: checking $name...."
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57 readnum=`wc -l $name | cut -f1 -d" "`
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58 if [ $faorfq == "fasta" ];then
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59 readnum=`echo "$readnum/2"|bc`
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60 else
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61 readnum=`echo "$readnum/4"|bc`
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62 fi
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63 if [ -f $name.nomt ];then
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64 bowtienum=`wc -l $name.nomt | cut -f1 -d" "`
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65 else
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66 bowtienum=0
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67 fi
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68 if [ $bowtienum != $readnum ];then
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69 echo "bowtie -p $Threads -a -v 2 $DatabaseFolder $name $add >$name.btw; perl $SrcFolder/bowtie2eland.pl $name.btw $name $name.eland;rm $name.btw ;perl $SrcFolder/mark.mt.4eland.pl $name.eland >$name.nomt;rm $name.eland">>mapcheck.sh
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70
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71 fi
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72 done <checklist
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73 if [ -f mapcheck.sh ];then
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74 checktasknum=`wc -l mapcheck.sh |tr -d "\n"`
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75 if [ $checktasknum == $tasknum ];then
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76 echo "MAPPING: warning! none of the mapping tasks properly finished!"
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77 fi
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78 echo "MAPPING: resubmit TASKS...."
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79 perl $SrcFolder/batchqsub.pl mapcheck.sh
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80 else
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81 break
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82 fi
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83 done
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84 echo "MAPPING: Done.....merging files..."
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85 cat *.nomt >$Outputfolder/$TmpFolderName.nomt
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86 cd ../../
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87 rm $TmpFolderName.result -rf
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88 #/data/zhang/wuj/tools/bowtie-0.12.3/bowtie -a $DatabaseFolderTXdb -f
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89
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