Mercurial > repos > chawhwa > neuma
diff NEUMA-1.2.1/NIR2LVKM.pl @ 0:c44c43d185ef draft default tip
NEUMA-1.2.1 Uploaded
author | chawhwa |
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date | Thu, 08 Aug 2013 00:46:13 -0400 |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/NEUMA-1.2.1/NIR2LVKM.pl Thu Aug 08 00:46:13 2013 -0400 @@ -0,0 +1,64 @@ +#!/usr/bin/perl + + +# This version (v.12) has an option of datatype (Refseq vs Ensembl). + +if(@ARGV<13) { print "usage: $0 sample_name readcount_dir midrefix(samplename.midrefix.i.all.gMA) EUMA_out_dir FVKM_out_dir LVKM_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 $EUMA_out_dir = 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 $EUMA_out_dir) { `mkdir -p $EUMA_out_dir`; } +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. +#`$perlcommand $gNIR2gFVKM_script $readcount_dir/$sample.$midrefix.gNIR $EUMA_out_dir/$sample.$midrefix.gEUMA > $FVKM_out_dir/$sample.$midrefix.gFVKM`; +#`$perlcommand $iNIR2iFVKM_script $readcount_dir/$sample.$midrefix.iNIR $EUMA_out_dir/$sample.$midrefix.iEUMA > $FVKM_out_dir/$sample.$midrefix.iFVKM`; + +`$gNIR2gFVKM_script $readcount_dir/$sample.$midrefix.gNIR $EUMA_out_dir/$sample.$midrefix.gEUMA > $FVKM_out_dir/$sample.$midrefix.gFVKM`; +`$iNIR2iFVKM_script $readcount_dir/$sample.$midrefix.iNIR $EUMA_out_dir/$sample.$midrefix.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`; +} + +