| Previous changeset 0:c9fe27da991c (2014-06-14) Next changeset 2:2fd354a78c56 (2014-06-14) |
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mgescan.sh |
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| diff -r c9fe27da991c -r b7ea9a0e2714 mgescan.sh --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/mgescan.sh Sat Jun 14 19:06:49 2014 -0400 |
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| @@ -0,0 +1,126 @@ +#!/bin/bash +# 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 $repeatmasker +user_dir=/u/lee212 +#script=$user_dir/retrotminer/wazim/MGEScan1.1/run_MGEScan.pl +#script=$user_dir/retrotminer/wazim/MGEScan1.3.1/run_MGEScan2.pl +source $user_dir/virtualenv/retrotminer/bin/activate +script_program=`which python` +script=$user_dir/github/retrotminer/retrotminer/retrotminer.py +input_file=$1 +input_file_name=$2 +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} +#### for ltr between $11 and $20 +sw_rm=${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} +repeatmasker=${20} + +# /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 + +#load env? +source $user_dir/.bashrc +source $user_dir/.bash_profile + +#set path for transeq +export PATH=$user_dir/retrotminer/EMBOSS/bin:/usr/bin:$PATH + +#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 + +if [ "2" == "$hmmsearch_version" ] +then + export PATH=$user_dir/retrotminer/HMMER2.0/bin:$PATH +else + export PATH=/usr/bin:$PATH +fi + +if [ "$program" == "L" ] +then + program_name="ltr" +else + programname="nonltr" +fi + +#run +$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} +#/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" ] + 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 + + #compressed_file=$output_dir/$RANDOM.tar.gz + #/bin/tar cvzfP $compressed_file $output_dir/info + #/bin/cp $compressed_file $output_file + /bin/cp $output_dir/info/full/*/* $clade + /bin/cp $output_dir/info/validation/en $en + /bin/cp $output_dir/info/validation/rt $rt + if [ "$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 cvzfP $compressed_file $output_dir + #/bin/cp $compressed_file $output_file +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 |