Mercurial > repos > hyungrolee > mgescan
view mgescan.sh @ 15:1234e527defa draft default tip
Uploaded
author | hyungrolee |
---|---|
date | Tue, 16 Feb 2016 16:05:53 -0500 |
parents | 1a143426370c |
children |
line wrap: on
line source
#!/bin/bash # 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 $repeatmasker if [ "" == "$MGESCAN_SRC" ] then echo "\$MGESCAN_SRC is not defined." exit fi script_program=`which python` script=$MGESCAN_SRC/mgescan/cmd.py input_file=$1 #input_file_name=$2 input_file_name=`basename $input_file` hmmsearch_version=$3 output_file=$4 program=$5 # N is nonLTR, L is LTR and B is both # Optional output parameters for nonLTR clade=$6 en=$7 rt=$8 ltr_gff3=$9 nonltr_gff3=${10} both_gff3=${11} #### for ltr between $11 and $20 if [ "$program" == "L" ] then sw_rm=${12} scaffold=${13} min_dist=${14} max_dist=${15} min_len_ltr=${16} max_len_ltr=${17} ltr_sim_condition=${18} cluster_sim_condition=${19} len_condition=${20} repeatmasker=${21} fi #elif [ "$program" == "B" ] if [ $# -eq 12 ] then nmpi=${12} if [ ! -z $nmpi ] && [ $nmpi -ge 1 ] then mpi_enabled="--mpi=$nmpi" fi fi # /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 #set path for transeq #export PATH=$user_dir/mgescan/EMBOSS/bin:/usr/bin:$PATH if [ "" == "`which transeq`" ] then echo "EMBOSS is not available." exit fi #move to the working directory work_dir=`dirname $script` cd $work_dir #create directory for input and output mkdir -p input t_dir=`mktemp -p input -d` #relative path input_dir="$work_dir/$t_dir/seq" # full path output_dir="$work_dir/$t_dir/data" mkdir -p $input_dir mkdir -p $output_dir #make a copy of input #/bin/cp $input_file $input_dir/$input_file_name # Check tar.gz tar tf $input_file &> /dev/null ISGZ=$? if [ 0 -eq $ISGZ ] then # It seems pre_process.pl creates ./data/genome directory and makes a copy of a genome file. # Due to this reason, extracts compressed inputs to output directory. tar xzf $input_file -C $input_dir 2> /dev/null if [ $? -ne 0 ] then tar xf $input_file -C $input_dir 2> /dev/null fi else /bin/ln -s $input_file $input_dir/$input_file_name fi VERSION2=`hmmsearch -h|grep "HMMER 2" 2> /dev/null` VERSION3=`hmmsearch -h|grep "HMMER 3" 2> /dev/null` if [ "2" == "$hmmsearch_version" ] && [ "" != "$VERSION2" ] then echo $VERSION2 selected. elif [ "3" == "$hmmsearch_version" ] && [ "" != "$VERSION3" ] then echo $VERSION3 selected. else echo HMMER is not available. exit fi if [ "$program" == "L" ] then program_name="ltr" elif [ "$program" == "N" ] then program_name="nonltr" else program_name="both" fi #run $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} #/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} #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=$program > /dev/null"` #make a copy of output if [ "$program" != "N" ] then /bin/cp $output_dir/ltr/ltr.out $output_file if [ "$ltr_gff3" != "None" ] then /bin/cp $output_dir/ltr/ltr.gff3 $ltr_gff3 fi if [ "$repeatmasker" != "None" ] && [ "$repeatmasker" != "" ] then # chr2L.fa.cat.gz chr2L.fa.masked chr2L.fa.out chr2L.fa.out.pos chr2L.fa.tbl /bin/cp $output_dir/repeatmasker/${input_file_name}.out $repeatmasker fi fi if [ "$program" != "L" ] then tmp=`mktemp` RANDOM=`basename $tmp` compressed_file=$output_dir/$RANDOM.tar.gz /bin/tar czfP $compressed_file $output_dir/info #/bin/cp $compressed_file $output_file #RES=`/bin/cp $output_dir/info/full/*/* $clade 2> /dev/null` RES=`/bin/cp $compressed_file $clade 2> /dev/null` RES=`/bin/cp $output_dir/info/validation/en $en 2> /dev/null` RES=`/bin/cp $output_dir/info/validation/rt $rt 2> /dev/null` if [ "$nonltr_gff3" != "None" ] then /bin/cp $output_dir/info/nonltr.gff3 $nonltr_gff3 # nonltr.gff3 ##gff-version 3 #chr2L.fa MGEScan_nonLTR mobile_genetic_element 19670384 19676921 . . . ID=chr2L.fa_19670384 #chr2L.fa MGEScan_nonLTR mobile_genetic_element 17689430 17695994 . . . ID=chr2L.fa_17689430 #chr2L.fa MGEScan_nonLTR mobile_genetic_element 11897186 11903717 . . . ID=chr2L.fa_11897186 #chr2L.fa MGEScan_nonLTR mobile_genetic_element 49574 56174 . . . ID=chr2L.fa_49574 fi #else # Both LTR, nonLTR executed #compressed_file=$output_dir/$RANDOM.tar.gz #/bin/tar czfP $compressed_file $output_dir #/bin/cp $compressed_file $output_file fi if [ "$program" == "B" ] then #echo "track name=LTR description=\"MGEScan-LTR\" color=0,0,255," > $both_gff3 /bin/cat $output_dir/ltr/ltr.gff3 >> $both_gff3 #echo "track name=nonLTR description=\"MGEScan-nonLTR\" color=255,0,0" >> $both_gff3 /bin/cat $output_dir/info/nonltr.gff3 >> $both_gff3 fi # delete temp directory if [ $? -eq 0 ] then rm -rf $work_dir/$t_dir #echo else #echo cp -pr $work_dir/$t_dir $work_dir/error-cases/ cp -pr $work_dir/$t_dir $work_dir/error-cases/ fi