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1 #!/bin/bash
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2 # mgescan.sh $input $input.name 3 $output L None None None $ltr_gff3 None $sw_rm "$scaffold" $min_dist $max_dist $min_len_ltr $max_len_ltr $ltr_sim_condition $cluster_sim_condition $len_condition $repeatmasker
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3 user_dir=/u/lee212
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4 #script=$user_dir/retrotminer/wazim/MGEScan1.1/run_MGEScan.pl
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5 #script=$user_dir/retrotminer/wazim/MGEScan1.3.1/run_MGEScan2.pl
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6 source $user_dir/virtualenv/retrotminer/bin/activate
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7 script_program=`which python`
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8 script=$user_dir/github/retrotminer/retrotminer/retrotminer.py
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9 input_file=$1
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10 input_file_name=$2
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11 hmmsearch_version=$3
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12 output_file=$4
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13 program=$5 # N is nonLTR, L is LTR and B is both
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14 # Optional output parameters for nonLTR
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15 clade=$6
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16 en=$7
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17 rt=$8
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18 ltr_gff3=$9
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19 nonltr_gff3=${10}
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20 #### for ltr between $11 and $20
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21 sw_rm=${11}
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22 scaffold=${12}
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23 min_dist=${13}
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24 max_dist=${14}
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25 min_len_ltr=${15}
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26 max_len_ltr=${16}
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27 ltr_sim_condition=${17}
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28 cluster_sim_condition=${18}
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29 len_condition=${19}
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30 repeatmasker=${20}
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31
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32 # /nfs/nfs4/home/lee212/retrotminer/galaxy-dist/tools/retrotminer/find_ltr.sh /nfs/nfs4/home/lee212/retrotminer/galaxy-dist/database/files/000/dataset_1.dat /nfs/nfs4/home/lee212/retrotminer/galaxy-dist/database/files/000/dataset_3.dat
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33
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34 #load env?
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35 source $user_dir/.bashrc
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36 source $user_dir/.bash_profile
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37
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38 #set path for transeq
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39 export PATH=$user_dir/retrotminer/EMBOSS/bin:/usr/bin:$PATH
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40
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41 #move to the working directory
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42 work_dir=`dirname $script`
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43 cd $work_dir
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44
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45 #create directory for input and output
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46 mkdir -p input
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47 t_dir=`mktemp -p input -d` #relative path
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48 input_dir="$work_dir/$t_dir/seq" # full path
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49 output_dir="$work_dir/$t_dir/data"
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50 mkdir -p $input_dir
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51 mkdir -p $output_dir
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52
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53 #make a copy of input
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54 /bin/cp $input_file $input_dir/$input_file_name
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55
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56 if [ "2" == "$hmmsearch_version" ]
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57 then
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58 export PATH=$user_dir/retrotminer/HMMER2.0/bin:$PATH
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59 else
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60 export PATH=/usr/bin:$PATH
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61 fi
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62
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63 if [ "$program" == "L" ]
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64 then
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65 program_name="ltr"
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66 else
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67 programname="nonltr"
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68 fi
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69
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70 #run
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71 $script_program $script $program_name $input_dir/ --output=$output_dir/ #-hmmerv=$hmmsearch_version -sw_rm=${11} -scaffold=${12} -min_dist=${13} -max_dist=${14} -min_len_ltr=${15} -max_len_ltr=${16} -ltr_sim_condition=${17} -cluster_sim_condition=${18} -len_condition=${19}
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72 #/usr/bin/perl $script -genome=$input_dir/ -data=$output_dir/ -hmmerv=$hmmsearch_version -program=$program -sw_rm=${11} -scaffold=${12} -min_dist=${13} -max_dist=${14} -min_len_ltr=${15} -max_len_ltr=${16} -ltr_sim_condition=${17} -cluster_sim_condition=${18} -len_condition=${19}
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73
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74 #RES=`ssh -i $user_dir/.ssh/.internal silo.cs.indiana.edu "/usr/bin/perl $script -genome=$input_dir/ -data=$output_dir/ -hmmerv=$hmmsearch_version -program=$program > /dev/null"`
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75
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76 #make a copy of output
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77 if [ "$program" != "N" ]
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78 then
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79 /bin/cp $output_dir/ltr/ltr.out $output_file
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80 if [ "$ltr_gff3" != "None" ]
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81 then
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82 /bin/cp $output_dir/ltr/ltr.gff3 $ltr_gff3
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83 fi
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84
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85 if [ "$repeatmasker" != "None" ]
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86 then
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87 # chr2L.fa.cat.gz chr2L.fa.masked chr2L.fa.out chr2L.fa.out.pos chr2L.fa.tbl
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88 /bin/cp $output_dir/repeatmasker/${input_file_name}.out $repeatmasker
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89 fi
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90 fi
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91 if [ "$program" != "L" ]
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92 then
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93
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94 #compressed_file=$output_dir/$RANDOM.tar.gz
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95 #/bin/tar cvzfP $compressed_file $output_dir/info
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96 #/bin/cp $compressed_file $output_file
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97 /bin/cp $output_dir/info/full/*/* $clade
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98 /bin/cp $output_dir/info/validation/en $en
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99 /bin/cp $output_dir/info/validation/rt $rt
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100 if [ "$nonltr_gff3" != "None" ]
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101 then
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102 /bin/cp $output_dir/info/nonltr.gff3 $nonltr_gff3
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103 # nonltr.gff3
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104 ##gff-version 3
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105 #chr2L.fa MGEScan_nonLTR mobile_genetic_element 19670384 19676921 . . . ID=chr2L.fa_19670384
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106 #chr2L.fa MGEScan_nonLTR mobile_genetic_element 17689430 17695994 . . . ID=chr2L.fa_17689430
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107 #chr2L.fa MGEScan_nonLTR mobile_genetic_element 11897186 11903717 . . . ID=chr2L.fa_11897186
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108 #chr2L.fa MGEScan_nonLTR mobile_genetic_element 49574 56174 . . . ID=chr2L.fa_49574
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109 fi
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110
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111 #else
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112 # Both LTR, nonLTR executed
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113 #compressed_file=$output_dir/$RANDOM.tar.gz
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114 #/bin/tar cvzfP $compressed_file $output_dir
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115 #/bin/cp $compressed_file $output_file
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116 fi
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117
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118 # delete temp directory
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119 if [ $? -eq 0 ]
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120 then
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121 rm -rf $work_dir/$t_dir
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122 #echo
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123 else
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124 #echo cp -pr $work_dir/$t_dir $work_dir/error-cases/
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125 cp -pr $work_dir/$t_dir $work_dir/error-cases/
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126 fi
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