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comparison mgescan.sh @ 7:b14f55bb20be draft

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author hyungrolee
date Mon, 15 Feb 2016 03:33:48 -0500
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children 1a143426370c
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6:f65687bfdc0a 7:b14f55bb20be
1 #!/bin/bash
2 # mgescan.sh $input $input.name 3 $output L None None None $ltr_gff3 None None $sw_rm "$scaffold" $min_dist $max_dist $min_len_ltr $max_len_ltr $ltr_sim_condition $cluster_sim_condition $len_condition $repeatmasker
3 if [ "" == "$MGESCAN_SRC" ]
4 then
5 echo "\$MGESCAN_SRC is not defined."
6 exit
7 fi
8
9 script_program=`which python`
10 script=$MGESCAN_SRC/mgescan/cmd.py
11 input_file=$1
12 #input_file_name=$2
13 input_file_name=`basename $input_file`
14 hmmsearch_version=$3
15 output_file=$4
16 program=$5 # N is nonLTR, L is LTR and B is both
17 # Optional output parameters for nonLTR
18 clade=$6
19 en=$7
20 rt=$8
21 ltr_gff3=$9
22 nonltr_gff3=${10}
23 both_gff3=${11}
24 #### for ltr between $11 and $20
25 if [ "$program" == "L" ]
26 then
27 sw_rm=${12}
28 scaffold=${13}
29 min_dist=${14}
30 max_dist=${15}
31 min_len_ltr=${16}
32 max_len_ltr=${17}
33 ltr_sim_condition=${18}
34 cluster_sim_condition=${19}
35 len_condition=${20}
36 repeatmasker=${21}
37 fi
38
39 #elif [ "$program" == "B" ]
40 if [ $# -eq 12 ]
41 then
42 nmpi=${12}
43 if [ ! -z $nmpi ] && [ $nmpi -ge 1 ]
44 then
45 mpi_enabled="--mpi=$nmpi"
46 fi
47
48 fi
49
50 # /nfs/nfs4/home/lee212/mgescan/galaxy-dist/tools/mgescan/find_ltr.sh /nfs/nfs4/home/lee212/mgescan/galaxy-dist/database/files/000/dataset_1.dat /nfs/nfs4/home/lee212/mgescan/galaxy-dist/database/files/000/dataset_3.dat
51
52 #set path for transeq
53 #export PATH=$user_dir/mgescan/EMBOSS/bin:/usr/bin:$PATH
54 transeq --version 2> /dev/null
55 res=$?
56 if [ 0 -ne $res ]
57 then
58 echo "EMBOSS is not available."
59 exit
60 fi
61
62 #move to the working directory
63 work_dir=`dirname $script`
64 cd $work_dir
65
66 #create directory for input and output
67 mkdir -p input
68 t_dir=`mktemp -p input -d` #relative path
69 input_dir="$work_dir/$t_dir/seq" # full path
70 output_dir="$work_dir/$t_dir/data"
71 mkdir -p $input_dir
72 mkdir -p $output_dir
73
74 #make a copy of input
75 #/bin/cp $input_file $input_dir/$input_file_name
76
77 # Check tar.gz
78 tar tf $input_file &> /dev/null
79 ISGZ=$?
80 if [ 0 -eq $ISGZ ]
81 then
82 # It seems pre_process.pl creates ./data/genome directory and makes a copy of a genome file.
83 # Due to this reason, extracts compressed inputs to output directory.
84 tar xzf $input_file -C $input_dir 2> /dev/null
85 if [ $? -ne 0 ]
86 then
87 tar xf $input_file -C $input_dir 2> /dev/null
88 fi
89 else
90 /bin/ln -s $input_file $input_dir/$input_file_name
91 fi
92
93 VERSION2=`hmmsearch -h|grep "HMMER 2" 2> /dev/null`
94 VERSION3=`hmmsearch -h|grep "HMMER 3" 2> /dev/null`
95 if [ "2" == "$hmmsearch_version" ] && [ "" != "$VERSION2" ]
96 then
97 echo $VERSION2 selected.
98 elif [ "3" == "$hmmsearch_version" ] && [ "" != "$VERSION3" ]
99 then
100 echo $VERSION3 selected.
101 else
102 echo HMMER is not available.
103 exit
104 fi
105
106 if [ "$program" == "L" ]
107 then
108 program_name="ltr"
109 elif [ "$program" == "N" ]
110 then
111 program_name="nonltr"
112 else
113 program_name="both"
114 fi
115
116 #run
117 $script_program $script $program_name $input_dir/ --output=$output_dir/ $mpi_enabled #-hmmerv=$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}
118 #/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}
119
120 #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=$program > /dev/null"`
121
122 #make a copy of output
123 if [ "$program" != "N" ]
124 then
125 /bin/cp $output_dir/ltr/ltr.out $output_file
126 if [ "$ltr_gff3" != "None" ]
127 then
128 /bin/cp $output_dir/ltr/ltr.gff3 $ltr_gff3
129 fi
130
131 if [ "$repeatmasker" != "None" ] && [ "$repeatmasker" != "" ]
132 then
133 # chr2L.fa.cat.gz chr2L.fa.masked chr2L.fa.out chr2L.fa.out.pos chr2L.fa.tbl
134 /bin/cp $output_dir/repeatmasker/${input_file_name}.out $repeatmasker
135 fi
136 fi
137 if [ "$program" != "L" ]
138 then
139
140 tmp=`mktemp`
141 RANDOM=`basename $tmp`
142 compressed_file=$output_dir/$RANDOM.tar.gz
143 /bin/tar czfP $compressed_file $output_dir/info
144 #/bin/cp $compressed_file $output_file
145 #RES=`/bin/cp $output_dir/info/full/*/* $clade 2> /dev/null`
146 RES=`/bin/cp $compressed_file $clade 2> /dev/null`
147 RES=`/bin/cp $output_dir/info/validation/en $en 2> /dev/null`
148 RES=`/bin/cp $output_dir/info/validation/rt $rt 2> /dev/null`
149 if [ "$nonltr_gff3" != "None" ]
150 then
151 /bin/cp $output_dir/info/nonltr.gff3 $nonltr_gff3
152 # nonltr.gff3
153 ##gff-version 3
154 #chr2L.fa MGEScan_nonLTR mobile_genetic_element 19670384 19676921 . . . ID=chr2L.fa_19670384
155 #chr2L.fa MGEScan_nonLTR mobile_genetic_element 17689430 17695994 . . . ID=chr2L.fa_17689430
156 #chr2L.fa MGEScan_nonLTR mobile_genetic_element 11897186 11903717 . . . ID=chr2L.fa_11897186
157 #chr2L.fa MGEScan_nonLTR mobile_genetic_element 49574 56174 . . . ID=chr2L.fa_49574
158 fi
159
160 #else
161 # Both LTR, nonLTR executed
162 #compressed_file=$output_dir/$RANDOM.tar.gz
163 #/bin/tar czfP $compressed_file $output_dir
164 #/bin/cp $compressed_file $output_file
165 fi
166
167 if [ "$program" == "B" ]
168 then
169 #echo "track name=LTR description=\"MGEScan-LTR\" color=0,0,255," > $both_gff3
170 /bin/cat $output_dir/ltr/ltr.gff3 >> $both_gff3
171 #echo "track name=nonLTR description=\"MGEScan-nonLTR\" color=255,0,0" >> $both_gff3
172 /bin/cat $output_dir/info/nonltr.gff3 >> $both_gff3
173 fi
174
175 # delete temp directory
176 if [ $? -eq 0 ]
177 then
178 rm -rf $work_dir/$t_dir
179 #echo
180 else
181 #echo cp -pr $work_dir/$t_dir $work_dir/error-cases/
182 cp -pr $work_dir/$t_dir $work_dir/error-cases/
183 fi