I've got another data from where hopefully will be easier you guys to calculate intron length. It's "gtf" extension. Shortly it look like this. 

I    Cufflinks    transcript    218549    219145    1000    +    .    
+gene_id "CUFF.54"; transcript_id "YAR062W"; FPKM "18.7631305676"; fra
+c "0.697479"; conf_lo "12.494853"; conf_hi "25.031408"; cov "15.86482
+9"; full_read_support "yes";

I    Cufflinks    exon    218549    219145    1000    +    .    gene_i
+d "CUFF.54"; transcript_id "YAR062W"; exon_number "1"; FPKM "18.76313
+05676"; frac "0.697479"; conf_lo "12.494853"; conf_hi "25.031408"; co
+v "15.864829";

I    Cufflinks    transcript    217157    217492    1000    -    .    
+gene_id "CUFF.55"; transcript_id "YAR060C"; FPKM "23.1145085280"; fra
+c "0.302521"; conf_lo "11.245570"; conf_hi "34.983447"; cov "19.54405
+9"; full_read_support "yes";

I    Cufflinks    exon    217157    217492    1000    -    .    gene_i
+d "CUFF.55"; transcript_id "YAR060C"; exon_number "1"; FPKM "23.11450
+85280"; frac "0.302521"; conf_lo "11.245570"; conf_hi "34.983447"; co
+v "19.544059";

II    Cufflinks    transcript    7605    7733    1000    -    .    gen
+e_id "YBL108C-A"; transcript_id "YBL108C-A"; FPKM "18.0747134240"; fr
+ac "1.000000"; conf_lo "0.000000"; conf_hi "90.373567"; cov "8.950119
+"; full_read_support "yes";

II    Cufflinks    exon    7605    7733    1000    -    .    gene_id "
+YBL108C-A"; transcript_id "YBL108C-A"; exon_number "1"; FPKM "18.0747
+134240"; frac "1.000000"; conf_lo "0.000000"; conf_hi "90.373567"; co
+v "8.950119";

II    Cufflinks    transcript    8177    8482    1    +    .    gene_i
+d "YBL108W"; transcript_id "YBL108W"; FPKM "0.0000000000"; frac "0.00
+0000"; conf_lo "0.000000"; conf_hi "0.000000"; cov "0.000000"; full_r
+ead_support "no";

II    Cufflinks    exon    8177    8482    1    +    .    gene_id "YBL
+108W"; transcript_id "YBL108W"; exon_number "1"; FPKM "0.0000000000";
+ frac "0.000000"; conf_lo "0.000000"; conf_hi "0.000000"; cov "0.0000
+00";

II    Cufflinks    transcript    9268    9372    1    +    .    gene_i
+d "YBL107W-A"; transcript_id "YBL107W-A"; FPKM "0.0000000000"; frac "
+0.000000"; conf_lo "0.000000"; conf_hi "0.000000"; cov "0.000000"; fu
+ll_read_support "no";

II    Cufflinks    exon    9268    9372    1    +    .    gene_id "YBL
+107W-A"; transcript_id "YBL107W-A"; exon_number "1"; FPKM "0.00000000
+00"; frac "0.000000"; conf_lo "0.000000"; conf_hi "0.000000"; cov "0.
+000000";

II    Cufflinks    transcript    9583    9666    1    +    .    gene_i
+d "tL(UAA)B1"; transcript_id "tL(UAA)B1"; FPKM "0.0000000000"; frac "
+0.000000"; conf_lo "0.000000"; conf_hi "0.000000"; cov "0.000000"; fu
+ll_read_support "no";

II    Cufflinks    exon    9583    9666    1    +    .    gene_id "tL(
+UAA)B1"; transcript_id "tL(UAA)B1"; exon_number "1"; FPKM "0.00000000
+00"; frac "0.000000"; conf_lo "0.000000"; conf_hi "0.000000"; cov "0.
+000000";

I    Cufflinks    transcript    227742    228953    1000    +    .    
+gene_id "CUFF.57"; transcript_id "YAR073W"; FPKM "5.8852029015"; frac
+ "0.892308"; conf_lo "3.699493"; conf_hi "8.070912"; cov "3.517134"; 
+full_read_support "yes";

I    Cufflinks    exon    227742    228953    1000    +    .    gene_i
+d "CUFF.57"; transcript_id "YAR073W"; exon_number "1"; FPKM "5.885202
+9015"; frac "0.892308"; conf_lo "3.699493"; conf_hi "8.070912"; cov "
+3.517134";

II    Cufflinks    transcript    142112    142868    1000    -    .   
+ gene_id "YBL040C"; transcript_id "YBL040C"; FPKM "246.2287249186"; f
+rac "0.288110"; conf_lo "225.158166"; conf_hi "267.299284"; cov "208.
+319539"; full_read_support "yes";

II    Cufflinks    exon    142112    142749    1000    -    .    gene_
+id "YBL040C"; transcript_id "YBL040C"; exon_number "1"; FPKM "246.228
+7249186"; frac "0.288110"; conf_lo "225.158166"; conf_hi "267.299284"
+; cov "208.319539";

II    Cufflinks    exon    142847    142868    1000    -    .    gene_
+id "YBL040C"; transcript_id "YBL040C"; exon_number "2"; FPKM "246.228
+7249186"; frac "0.288110"; conf_lo "225.158166"; conf_hi "267.299284"
+; cov "208.319539";

[download]
Each lines starts with "I", "II" and etc. Here they may seen written in several lines. After each transcript there comes exon. I need to minus total exon length from transcription length to get intron length in most cases it's equal to zero but some how a few transcripts include couple of exons between which can be found gaps, which will be intron length.

In reply to intron length by MBobur

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