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