Create ensgOrient.pl

# program to recover orientation of ensg genes in tracking files


unless(open(FGP,"sample2_genes.fpkm_tracking.txt")) {
        print "Unable to open sample2_genes.fpkm_tracking.txt file\n";
        exit;
}

unless(open(FTP,"sample2_transcriptSet.txt")) {
        print "Unable to open sample2_transcriptSet.txt file\n";
        exit;
}

unless(open(FP,">ensgOrient.out.txt")) {
        print "Unable to open ensgOrient.out.txt file\n";
        exit;
}

# sample2_genes.fpkm_tracking.txt
# ENSG00000223972       -       -       ENSG00000223972 DDX11L1 TSS165962,TSS165964,TSS26614,TSS72060   1:11868-14412   -       -       0.125893        0.0067484       0.245037
        OK


# sample2_transcriptSet.txt
# 1     Cufflinks       transcript      11869   14409   37      +       .       gene_id "ENSG00000223972"; transcript_id "ENST00000456328"; FPKM "0.0025026832"; frac "0.000231"; conf_lo "0.000000"; conf_hi "0.036544"; cov "0.016297";


# sample2_transcriptSet.txt
# 1     Cufflinks       transcript      11869   14409   37      +       .       gene_id "ENSG00000223972"; transcript_id "ENST00000456328"; FPKM "0.0025026832"; frac "0.000231"; conf_lo "0.000000"; conf_hi "0.036544"; cov "0.016297";