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1 #!/usr/bin/perl
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2
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3
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4 # This version (v.12) has an option of datatype (Refseq vs Ensembl).
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5
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6 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; }
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7
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8 my $sample = shift @ARGV;
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9 my $readcount_dir = shift @ARGV;
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10 my $midrefix = shift @ARGV;
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11 my $EUMA_out_dir = shift @ARGV;
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12 my $FVKM_out_dir = shift @ARGV;
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13 my $LVKM_out_dir = shift @ARGV;
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14 my $EUMA_cut = shift @ARGV;
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15 my $mapping_stat_column = shift @ARGV;
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16 my $mapping_stat_file = shift @ARGV;
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17 my $i_after_midrefix = shift @ARGV;
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18 my $final_adjustment_option = shift @ARGV;
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19 my $gene2NM_file = shift @ARGV;
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20 my $gene2symbol_file = shift @ARGV;
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21 my $datatype = shift @ARGV;
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22 my $scriptdir = shift @ARGV;
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23
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24 if(!-d $EUMA_out_dir) { `mkdir -p $EUMA_out_dir`; }
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25 if(!-d $FVKM_out_dir) { `mkdir -p $FVKM_out_dir`; }
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26 if(!-d $LVKM_out_dir) { `mkdir -p $LVKM_out_dir`;}
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27
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28 #$perlcommand = "perl -I $scriptdir";
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29 $perlcommand = "perl";
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30
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31 $gNIR2gFVKM_script = "$scriptdir/gNIR2gFVKM.pl";
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32 $iNIR2iFVKM_script = "$scriptdir/iNIR2iFVKM.pl";
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33
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34 $combine_gFVKM_iFVKM_script = "$scriptdir/combine_gFVKM_iFVKM_max.pl";
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35
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36 $normalize_gFVKM_script = "$scriptdir/normalize_gFVKM_5.pl";
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37 $normalize_iFVKM_script = "$scriptdir/normalize_iFVKM_6.pl";
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38 $NR_filter_script = "$scriptdir/filter_exclusive_NRgene_from_gene_table.pl";
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39
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40
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41 #computing gFVKM and iFVKM, from EUMA/iEUMA and gMA/iMA files.
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42 #`$perlcommand $gNIR2gFVKM_script $readcount_dir/$sample.$midrefix.gNIR $EUMA_out_dir/$sample.$midrefix.gEUMA > $FVKM_out_dir/$sample.$midrefix.gFVKM`;
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43 #`$perlcommand $iNIR2iFVKM_script $readcount_dir/$sample.$midrefix.iNIR $EUMA_out_dir/$sample.$midrefix.iEUMA > $FVKM_out_dir/$sample.$midrefix.iFVKM`;
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44
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45 `$gNIR2gFVKM_script $readcount_dir/$sample.$midrefix.gNIR $EUMA_out_dir/$sample.$midrefix.gEUMA > $FVKM_out_dir/$sample.$midrefix.gFVKM`;
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46 `$iNIR2iFVKM_script $readcount_dir/$sample.$midrefix.iNIR $EUMA_out_dir/$sample.$midrefix.iEUMA > $FVKM_out_dir/$sample.$midrefix.iFVKM`;
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47
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48 #updating gFVKM & iFVKM baed on each other
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49 `$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`;
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50
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51 #normalize and compute LGPM/LTPM
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52 #`$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`;
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53 #`$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`;
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54
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55 `$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`;
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56 `$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`;
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57
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58 #filter NR-only genes
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59 if($datatype eq 'R'){
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60 `$perlcommand $NR_filter_script $gene2NM_file $LVKM_out_dir/$sample.$midrefix.$EUMA_cut.gLVKM > $LVKM_out_dir/$sample.$midrefix.$EUMA_cut.-NR.gLVKM`;
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61 `$perlcommand $NR_filter_script $gene2NM_file $LVKM_out_dir/$sample.$midrefix.$EUMA_cut.iLVKM > $LVKM_out_dir/$sample.$midrefix.$EUMA_cut.-NR.iLVKM`;
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62 }
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63
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