# original gtf
Mh:0000:MhA1_Contig0    Freeze3 CDS     1425    1586    .       +       0       transcript_id "MhA1_Contig0.frz3.gene1";
Mh:0000:MhA1_Contig0    Freeze3 CDS     1637    1930    .       +       0       transcript_id "MhA1_Contig0.frz3.gene1";
Mh:0000:MhA1_Contig0    Freeze3 CDS     2143    2275    .       +       0       transcript_id "MhA1_Contig0.frz3.gene1";
Mh:0000:MhA1_Contig0    Freeze3 CDS     2333    2437    .       +       2       transcript_id "MhA1_Contig0.frz3.gene1";
Mh:0000:MhA1_Contig0    Freeze3 CDS     2652    2890    .       +       2       transcript_id "MhA1_Contig0.frz3.gene1";
Mh:0000:MhA1_Contig0    Freeze3 CDS     4027    4090    15.97   +       0       transcript_id "MhA1_Contig0.frz3.fgene1";
Mh:0000:MhA1_Contig0    Freeze3 CDS     4141    4251    7.12    +       1       transcript_id "MhA1_Contig0.frz3.fgene1";
Mh:0000:MhA1_Contig0    Freeze3 CDS     4311    4390    9.54    +       1       transcript_id "MhA1_Contig0.frz3.fgene1";
Mh:0000:MhA1_Contig0    Freeze3 CDS     4471    4576    11.80   +       0       transcript_id "MhA1_Contig0.frz3.fgene1";
Mh:0000:MhA1_Contig0    Freeze3 CDS     4635    4678    -4.98   +       1       transcript_id "MhA1_Contig0.frz3.fgene1";
Mh:0000:MhA1_Contig0    Freeze3 CDS     4760    4959    14.82   +       0       transcript_id "MhA1_Contig0.frz3.fgene1";
Mh:0000:MhA1_Contig0    Freeze3 CDS     5070    5193    4.65    +       2       transcript_id "MhA1_Contig0.frz3.fgene1";
Mh:0000:MhA1_Contig0    Freeze3 CDS     5243    5274    -3.08   +       0       transcript_id "MhA1_Contig0.frz3.fgene1";

#dexseq_prepare_annotation.py
exons = HTSeq.GenomicArrayOfSets( "auto", stranded=True )
for f in HTSeq.GFF_Reader( gtf_file ):
   if f.type != "CDS":
      continue
   f.attr['transcript_id'] = f.attr['transcript_id'].replace( ":", "_" )
   exons[f.iv] += ( f.attr['transcript_id'], f.attr['transcript_id'] )

#output gtf
Mh:0000:MhA1_Contig0    Mh.gtf  aggregate_gene  1425    2890    .       +       .       gene_id "MhA1_Contig0.frz3.gene1"
Mh:0000:MhA1_Contig0    Mh.gtf  exonic_part     1425    1586    .       +       .       transcripts "MhA1_Contig0.frz3.gene1"; exonic_part_number "001"; gene_id "MhA1_Contig0.frz3.gene1"
Mh:0000:MhA1_Contig0    Mh.gtf  exonic_part     1637    1930    .       +       .       transcripts "MhA1_Contig0.frz3.gene1"; exonic_part_number "002"; gene_id "MhA1_Contig0.frz3.gene1"
Mh:0000:MhA1_Contig0    Mh.gtf  exonic_part     2143    2275    .       +       .       transcripts "MhA1_Contig0.frz3.gene1"; exonic_part_number "003"; gene_id "MhA1_Contig0.frz3.gene1"
Mh:0000:MhA1_Contig0    Mh.gtf  exonic_part     2333    2437    .       +       .       transcripts "MhA1_Contig0.frz3.gene1"; exonic_part_number "004"; gene_id "MhA1_Contig0.frz3.gene1"
Mh:0000:MhA1_Contig0    Mh.gtf  exonic_part     2652    2890    .       +       .       transcripts "MhA1_Contig0.frz3.gene1"; exonic_part_number "005"; gene_id "MhA1_Contig0.frz3.gene1"
Mh:0000:MhA1_Contig0    Mh.gtf  aggregate_gene  4027    5970    .       +       .       gene_id "MhA1_Contig0.frz3.fgene1"
Mh:0000:MhA1_Contig0    Mh.gtf  exonic_part     4027    4090    .       +       .       transcripts "MhA1_Contig0.frz3.fgene1"; exonic_part_number "001"; gene_id "MhA1_Contig0.frz3.fgene1"
Mh:0000:MhA1_Contig0    Mh.gtf  exonic_part     4141    4251    .       +       .       transcripts "MhA1_Contig0.frz3.fgene1"; exonic_part_number "002"; gene_id "MhA1_Contig0.frz3.fgene1"


# original gtf
Mt:3452:Mt3.5.1Chr1     E       exon    150051  150327  .       -       .       transcript_id "Medtr1g005000.1"; gene_id "Medtr1g005000";
Mt:3452:Mt3.5.1Chr1     E       exon    150871  154771  .       -       .       transcript_id "Medtr1g005000.1"; gene_id "Medtr1g005000";
Mt:3452:Mt3.5.1Chr1     E       CDS     150051  150327  .       -       1       transcript_id "Medtr1g005000.1"; gene_id "Medtr1g005000";
Mt:3452:Mt3.5.1Chr1     E       CDS     150871  150875  .       -       0       transcript_id "Medtr1g005000.1"; gene_id "Medtr1g005000";
Mt:3452:Mt3.5.1Chr1     E       exon    154859  155160  .       +       .       transcript_id "Medtr1g005010.1"; gene_id "Medtr1g005010";
Mt:3452:Mt3.5.1Chr1     E       CDS     154903  155139  .       +       0       transcript_id "Medtr1g005010.1"; gene_id "Medtr1g005010";
Mt:3452:Mt3.5.1Chr1     E       exon    155201  161330  .       +       .       transcript_id "Medtr1g005020.1"; gene_id "Medtr1g005020";
Mt:3452:Mt3.5.1Chr1     E       exon    161501  161880  .       +       .       transcript_id "Medtr1g005020.1"; gene_id "Medtr1g005020";
Mt:3452:Mt3.5.1Chr1     E       exon    162000  162267  .       +       .       transcript_id "Medtr1g005020.1"; gene_id "Medtr1g005020";

#dexseq_prepare_annotation.py
exons = HTSeq.GenomicArrayOfSets( "auto", stranded=True )
for f in HTSeq.GFF_Reader( gtf_file ):
   if f.type != "exon":
      continue
   f.attr['transcript_id'] = f.attr['transcript_id'].replace( ":", "_" )
   exons[f.iv] += ( f.attr['transcript_id'], f.attr['transcript_id'] )

#output gtf
Mt:3452:Mt3.5.1Chr1     Mt.gtf  aggregate_gene  150051  154771  .       -       .       gene_id "Medtr1g005000.1"
Mt:3452:Mt3.5.1Chr1     Mt.gtf  exonic_part     150051  150327  .       -       .       transcripts "Medtr1g005000.1"; exonic_part_number "001"; gene_id "Medtr1g005000.1"
Mt:3452:Mt3.5.1Chr1     Mt.gtf  exonic_part     150871  154771  .       -       .       transcripts "Medtr1g005000.1"; exonic_part_number "002"; gene_id "Medtr1g005000.1"
Mt:3452:Mt3.5.1Chr1     Mt.gtf  aggregate_gene  154859  155160  .       +       .       gene_id "Medtr1g005010.1"
Mt:3452:Mt3.5.1Chr1     Mt.gtf  exonic_part     154859  155160  .       +       .       transcripts "Medtr1g005010.1"; exonic_part_number "001"; gene_id "Medtr1g005010.1"
Mt:3452:Mt3.5.1Chr1     Mt.gtf  aggregate_gene  155201  162479  .       +       .       gene_id "Medtr1g005020.1"