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mgescan.sh |
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| diff -r f65687bfdc0a -r b14f55bb20be mgescan.sh --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/mgescan.sh Mon Feb 15 03:33:48 2016 -0500 |
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| @@ -0,0 +1,183 @@ +#!/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 +transeq --version 2> /dev/null +res=$? +if [ 0 -ne $res ] +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 |