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@Juke34
Juke34 committed Sep 12, 2024
1 parent ebd740d commit dece970
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250 changes: 143 additions & 107 deletions t/scripts_output/out/agat_sp_manage_introns_1.txt
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Original file line number Diff line number Diff line change
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usage: bin/agat_sp_manage_introns.pl --gff t/scripts_output/in/1.gff -o tmp.gff
usage: bin/agat_sp_manage_introns.pl --gff t/scripts_output/in/1.gff -o resuTes

--------------------------------------------------------------------------------

---------------------------------- chromosome ----------------------------------
Number of chromosome 1
Number chromosome overlapping 0
Total chromosome length (bp) 43270923
mean chromosome length (bp) 43270923
Longest chromosome (bp) 43270923
Shortest chromosome (bp) 43270923
Number of chromosome 1
Number chromosome overlapping 0
Total chromosome length (bp) 43270923
mean chromosome length (bp) 43270923
median chromosome length (bp) 43270923
90 percentile chromosome length (bp) na
Longest chromosome (bp) 43270923
Shortest chromosome (bp) 43270923

-------------------------------- repeat_region ---------------------------------
Number of repeat_region 2
Number repeat_region overlapping 0
Total repeat_region length (bp) 202
mean repeat_region length (bp) 101
Longest repeat_region (bp) 101
Shortest repeat_region (bp) 101
Number of repeat_region 2
Number repeat_region overlapping 0
Total repeat_region length (bp) 202
mean repeat_region length (bp) 101
median repeat_region length (bp) 101
90 percentile repeat_region length (bp) na
Longest repeat_region (bp) 101
Shortest repeat_region (bp) 101

------------------------------------- mrna -------------------------------------
Number of gene 52
Number of mrna 65
Number of mrnas with utr both sides 59
Number of mrnas with at least one utr 62
Number of cds 64
Number of exon 319
Number of five_prime_utr 60
Number of three_prime_utr 61
Number of exon in cds 290
Number of exon in five_prime_utr 79
Number of exon in three_prime_utr 70
Number of intron in cds 226
Number of intron in exon 254
Number of intron in five_prime_utr 19
Number of intron in three_prime_utr 9
Number gene overlapping 9
Number of single exon gene 8
Number of single exon mrna 10
mean mrnas per gene 1.2
mean cdss per mrna 1.0
mean exons per mrna 4.9
mean five_prime_utrs per mrna 0.9
mean three_prime_utrs per mrna 0.9
mean exons per cds 4.5
mean exons per five_prime_utr 1.3
mean exons per three_prime_utr 1.1
mean introns in cdss per mrna 3.5
mean introns in exons per mrna 3.9
mean introns in five_prime_utrs per mrna 0.3
mean introns in three_prime_utrs per mrna 0.1
Total gene length (bp) 158829
Total mrna length (bp) 197986
Total cds length (bp) 69687
Total exon length (bp) 108170
Total five_prime_utr length (bp) 11773
Total three_prime_utr length (bp) 25596
Total intron length per cds (bp) 77787
Total intron length per exon (bp) 89816
Total intron length per five_prime_utr (bp) 11235
Total intron length per three_prime_utr (bp) 794
mean gene length (bp) 3054
mean mrna length (bp) 3045
mean cds length (bp) 1088
mean exon length (bp) 339
mean five_prime_utr length (bp) 196
mean three_prime_utr length (bp) 419
mean cds piece length (bp) 240
mean five_prime_utr piece length (bp) 149
mean three_prime_utr piece length (bp) 365
mean intron in cds length (bp) 344
mean intron in exon length (bp) 353
mean intron in five_prime_utr length (bp) 591
mean intron in three_prime_utr length (bp) 88
Longest gene (bp) 8045
Longest mrna (bp) 8045
Longest cds (bp) 2937
Longest exon (bp) 2854
Longest five_prime_utr (bp) 2197
Longest three_prime_utr (bp) 2780
Longest cds piece (bp) 2433
Longest five_prime_utr piece (bp) 2027
Longest three_prime_utr piece (bp) 2780
Longest intron into cds part (bp) 3534
Longest intron into exon part (bp) 4350
Longest intron into five_prime_utr part (bp) 4350
Longest intron into three_prime_utr part (bp)127
Shortest gene (bp) 346
Shortest mrna (bp) 346
Shortest cds piece (bp) 2
Shortest five_prime_utr piece (bp) 1
Shortest three_prime_utr piece (bp) 16
Shortest intron into cds part (bp) 69
Shortest intron into exon part (bp) 39
Shortest intron into five_prime_utr part (bp)76
Shortest intron into three_prime_utr part (bp)39
Number of gene 52
Number of mrna 65
Number of mrnas with utr both sides 59
Number of mrnas with at least one utr 62
Number of cds 64
Number of exon 319
Number of five_prime_utr 60
Number of three_prime_utr 61
Number of exon in cds 290
Number of exon in five_prime_utr 79
Number of exon in three_prime_utr 70
Number of intron in cds 226
Number of intron in exon 254
Number of intron in five_prime_utr 19
Number of intron in three_prime_utr 9
Number gene overlapping 9
Number of single exon gene 8
Number of single exon mrna 10
mean mrnas per gene 1.2
mean cdss per mrna 1.0
mean exons per mrna 4.9
mean five_prime_utrs per mrna 0.9
mean three_prime_utrs per mrna 0.9
mean exons per cds 4.5
mean exons per five_prime_utr 1.3
mean exons per three_prime_utr 1.1
mean introns in cdss per mrna 3.5
mean introns in exons per mrna 3.9
mean introns in five_prime_utrs per mrna 0.3
mean introns in three_prime_utrs per mrna 0.1
Total gene length (bp) 158829
Total mrna length (bp) 197986
Total cds length (bp) 69687
Total exon length (bp) 108170
Total five_prime_utr length (bp) 11773
Total three_prime_utr length (bp) 25596
Total intron length per cds (bp) 77787
Total intron length per exon (bp) 89816
Total intron length per five_prime_utr (bp) 11235
Total intron length per three_prime_utr (bp) 794
mean gene length (bp) 3054
mean mrna length (bp) 3046
mean cds length (bp) 1089
mean exon length (bp) 339
mean five_prime_utr length (bp) 196
mean three_prime_utr length (bp) 420
mean cds piece length (bp) 240
mean five_prime_utr piece length (bp) 149
mean three_prime_utr piece length (bp) 366
mean intron in cds length (bp) 344
mean intron in exon length (bp) 354
mean intron in five_prime_utr length (bp) 591
mean intron in three_prime_utr length (bp) 88
median gene length (bp) 2540
median mrna length (bp) 2484
median cds length (bp) 128
median exon length (bp) 165
median five_prime_utr length (bp) 78
median three_prime_utr length (bp) 245
median cds piece length (bp) 128
median five_prime_utr piece length (bp) 78
median three_prime_utr piece length (bp) 245
median intron in cds length (bp) 133
median intron in exon length (bp) 129
median intron in five_prime_utr length (bp) 123
median intron in three_prime_utr length (bp) 79
90 percentile gene length (bp) 5514
90 percentile mrna length (bp) 5514
90 percentile cds length (bp) 521
90 percentile exon length (bp) 818
90 percentile five_prime_utr length (bp) 379
90 percentile three_prime_utr length (bp) 691
90 percentile cds piece length (bp) 521
90 percentile five_prime_utr piece length (bp) 379
90 percentile three_prime_utr piece length (bp) 691
90 percentile intron in cds length (bp) 791
90 percentile intron in exon length (bp) 770
90 percentile intron in five_prime_utr length (bp) 3593
90 percentile intron in three_prime_utr length (bp) na
Longest gene (bp) 8045
Longest mrna (bp) 8045
Longest cds (bp) 2937
Longest exon (bp) 2854
Longest five_prime_utr (bp) 2197
Longest three_prime_utr (bp) 2780
Longest cds piece (bp) 2433
Longest five_prime_utr piece (bp) 2027
Longest three_prime_utr piece (bp) 2780
Longest intron into cds part (bp) 3534
Longest intron into exon part (bp) 4350
Longest intron into five_prime_utr part (bp) 4350
Longest intron into three_prime_utr part (bp) 127
Shortest gene (bp) 346
Shortest mrna (bp) 346
Shortest cds piece (bp) 2
Shortest five_prime_utr piece (bp) 1
Shortest three_prime_utr piece (bp) 16
Shortest intron into cds part (bp) 69
Shortest intron into exon part (bp) 39
Shortest intron into five_prime_utr part (bp) 76
Shortest intron into three_prime_utr part (bp) 39

------------------------------------- trna -------------------------------------
Number of ncrna_gene 1
Number of trna 1
Number of exon 1
Number ncrna_gene overlapping 0
Number of single exon ncrna_gene 1
Number of single exon trna 1
mean trnas per ncrna_gene 1.0
mean exons per trna 1.0
Total ncrna_gene length (bp) 81
Total trna length (bp) 81
Total exon length (bp) 81
mean ncrna_gene length (bp) 81
mean trna length (bp) 81
mean exon length (bp) 81
Longest ncrna_gene (bp) 81
Longest trna (bp) 81
Longest exon (bp) 81
Shortest ncrna_gene (bp) 81
Shortest trna (bp) 81
Number of ncrna_gene 1
Number of trna 1
Number of exon 1
Number ncrna_gene overlapping 0
Number of single exon ncrna_gene 1
Number of single exon trna 1
mean trnas per ncrna_gene 1.0
mean exons per trna 1.0
Total ncrna_gene length (bp) 81
Total trna length (bp) 81
Total exon length (bp) 81
mean ncrna_gene length (bp) 81
mean trna length (bp) 81
mean exon length (bp) 81
median ncrna_gene length (bp) 81
median trna length (bp) 81
median exon length (bp) 81
90 percentile ncrna_gene length (bp) na
90 percentile trna length (bp) na
90 percentile exon length (bp) na
Longest ncrna_gene (bp) 81
Longest trna (bp) 81
Longest exon (bp) 81
Shortest ncrna_gene (bp) 81
Shortest trna (bp) 81

Introns in feature cds: Removing 1 percent of the highest values (2 values) gives you 3196 bp as the longest intron in cds.
Introns in feature exon: Removing 1 percent of the highest values (2 values) gives you 3535 bp as the longest intron in exon.
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