--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/NEUMA-1.2.1/NIR2LVKM_SE.pl	Thu Aug 08 00:46:13 2013 -0400
@@ -0,0 +1,60 @@
+#!/usr/bin/perl
+
+if(@ARGV<13) { print "usage: $0 sample_name readcount_dir midrefix(samplename.midrefix.i.all.gMA) EUMAprefix(before .gEUMA or .iEUMA) gFVKM_out_dir LGPM_out_dir EUMA_cut mapping_stat_column mapping_stat_file presence_of_i_at_end_of_midrefix[1/0] final_adjustment_option[1:average & rescaling/2:max & no rescaling] gene2NM_file gene2symbol_file datatype(R(Refseq)_or_E(Ensembl)) scriptdir\n"; exit; }
+
+my $sample = shift @ARGV;
+my $readcount_dir = shift @ARGV;
+my $midrefix = shift @ARGV;
+my $EUMAprefix = shift @ARGV;
+my $FVKM_out_dir = shift @ARGV;
+my $LVKM_out_dir = shift @ARGV;
+my $EUMA_cut = shift @ARGV;
+my $mapping_stat_column = shift @ARGV;
+my $mapping_stat_file = shift @ARGV;
+my $i_after_midrefix = shift @ARGV;
+my $final_adjustment_option = shift @ARGV;
+my $gene2NM_file = shift @ARGV;
+my $gene2symbol_file = shift @ARGV;
+my $datatype = shift @ARGV;
+my $scriptdir = shift @ARGV;
+
+if(!-d $FVKM_out_dir) { `mkdir -p $FVKM_out_dir`; }
+if(!-d $LVKM_out_dir) { `mkdir -p $LVKM_out_dir`;}
+
+#$perlcommand= "perl -I $scriptdir";
+$perlcommand= "perl";
+
+$gNIR2gFVKM_script = "$scriptdir/gNIR2gFVKM.pl";
+$iNIR2iFVKM_script = "$scriptdir/iNIR2iFVKM.pl";
+$combine_gFVKM_iFVKM_script = "$scriptdir/combine_gFVKM_iFVKM_max.pl";
+$normalize_gFVKM_script = "$scriptdir/normalize_gFVKM_5.pl";
+$normalize_iFVKM_script = "$scriptdir/normalize_iFVKM_6.pl";
+$NR_filter_script = "$scriptdir/filter_exclusive_NRgene_from_gene_table.pl";
+
+
+#computing gFVKM and iFVKM, from EUMA/iEUMA and gMA/iMA files.
+if($i_after_midrefix eq '1'){ $MA_midrefix = "$midrefix.i";}
+else { $MA_midrefix = $midrefix; }
+#`$perlcommand $gNIR2gFVKM_script $readcount_dir/$sample.$midrefix.gNIR $EUMAprefix.gEUMA > $FVKM_out_dir/$sample.$midrefix.gFVKM`;
+#`$perlcommand $iNIR2iFVKM_script $readcount_dir/$sample.$midrefix.iNIR $EUMAprefix.iEUMA > $FVKM_out_dir/$sample.$midrefix.iFVKM`;
+
+`$gNIR2gFVKM_script $readcount_dir/$sample.$midrefix.gNIR $EUMAprefix.gEUMA > $FVKM_out_dir/$sample.$midrefix.gFVKM`;
+`$iNIR2iFVKM_script $readcount_dir/$sample.$midrefix.iNIR $EUMAprefix.iEUMA > $FVKM_out_dir/$sample.$midrefix.iFVKM`;
+
+#updating gFVKM & iFVKM baed on each other
+`$perlcommand $combine_gFVKM_iFVKM_script $FVKM_out_dir/$sample.$midrefix.gFVKM $FVKM_out_dir/$sample.$midrefix.iFVKM $gene2NM_file $EUMA_cut $FVKM_out_dir/$sample.$midrefix.$EUMA_cut.final.gFVKM $FVKM_out_dir/$sample.$midrefix.$EUMA_cut.final.iFVKM`;
+
+#normalize and compute LGPM/LTPM
+#`$perlcommand $normalize_gFVKM_script $FVKM_out_dir/$sample.$midrefix.$EUMA_cut.final.gFVKM $mapping_stat_file $gene2symbol_file $mapping_stat_column $sample $LVKM_out_dir/$sample.$midrefix.$EUMA_cut.gLVKM`;
+#`$perlcommand $normalize_iFVKM_script $FVKM_out_dir/$sample.$midrefix.$EUMA_cut.final.iFVKM $mapping_stat_file $gene2symbol_file $mapping_stat_column $sample $LVKM_out_dir/$sample.$midrefix.$EUMA_cut.iLVKM`;
+
+`$normalize_gFVKM_script $FVKM_out_dir/$sample.$midrefix.$EUMA_cut.final.gFVKM $mapping_stat_file $gene2symbol_file $mapping_stat_column $sample $LVKM_out_dir/$sample.$midrefix.$EUMA_cut.gLVKM`;
+`$normalize_iFVKM_script $FVKM_out_dir/$sample.$midrefix.$EUMA_cut.final.iFVKM $mapping_stat_file $gene2symbol_file $mapping_stat_column $sample $LVKM_out_dir/$sample.$midrefix.$EUMA_cut.iLVKM`;
+
+#filter NR-only genes
+if($datatype eq 'R'){
+ `$perlcommand $NR_filter_script $gene2NM_file $LVKM_out_dir/$sample.$midrefix.$EUMA_cut.gLVKM > $LVKM_out_dir/$sample.$midrefix.$EUMA_cut.-NR.gLVKM`;
+ `$perlcommand $NR_filter_script $gene2NM_file $LVKM_out_dir/$sample.$midrefix.$EUMA_cut.iLVKM > $LVKM_out_dir/$sample.$midrefix.$EUMA_cut.-NR.iLVKM`;
+}
+
+