# HG changeset patch # User iuc # Date 1609685938 0 # Node ID c4ac24510b55dcfbeb9b1027de0b0cb28fbe18c0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/aegean commit e6c01517075cab35e620fe1bbdb5fd68e4d1359f" diff -r 000000000000 -r c4ac24510b55 locuspocus.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/locuspocus.xml Sun Jan 03 14:58:58 2021 +0000 @@ -0,0 +1,236 @@ + + calculate locus coordinates for the given gene annotation + + macros.xml + + + + + locuspocus --version + + + + + +

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+ + + + + + output_options['outputfiles'] and "ilens" in output_options['outputfiles'] + + + output_options['outputfiles'] and "genemap" in output_options['outputfiles'] + + + output_options['outputfiles'] and "transmap" in output_options['outputfiles'] + + + + + + + + + +

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+ + + + + + + + + + + diff -r 000000000000 -r c4ac24510b55 macros.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/macros.xml Sun Jan 03 14:58:58 2021 +0000 @@ -0,0 +1,36 @@ + + + + topic_3511 + + + operation_0362 + + + + + gaeval + + + + + aegean + + + + + + @misc{githubAEGeAn, + author = {Standage, Daniel S.}, + year = {2015}, + title = {AEGeAn}, + publisher = {GitHub}, + journal = {GitHub repository}, + url = {https://github.com/BrendelGroup/AEGeAn}, + } + + + + 0.16.0 + + diff -r 000000000000 -r c4ac24510b55 test-data/TAIR10_GFF3_alignment.gff --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/TAIR10_GFF3_alignment.gff Sun Jan 03 14:58:58 2021 +0000 @@ -0,0 +1,100 @@ +##gff-version 3 +##sequence-region 4 4174 18579887 +##sequence-region Pt 11940 153877 +##sequence-region 3 9604 23458280 +##sequence-region Mt 11727 332944 +##sequence-region 2 1089 19696461 +##sequence-region 1 3915 30423724 +##sequence-region 5 1227 26970443 +Pt . BED_feature 11940 12653 0 + . Name=region_0 +Pt . BED_feature 21863 22652 0 + . Name=region_1 +Pt . BED_feature 47925 48082 0 + . Name=region_2 +Pt . BED_feature 70139 70652 0 + . Name=region_3 +Pt . BED_feature 70946 71811 0 + . Name=region_4 +Pt . BED_feature 74848 75650 0 + . Name=region_5 +Pt . BED_feature 76490 77197 0 + . Name=region_6 +Pt . BED_feature 81589 82643 0 + . Name=region_7 +Pt . BED_feature 84773 85453 0 + . Name=region_8 +Pt . BED_feature 95704 96387 0 + . Name=region_9 +Pt . BED_feature 98026 98561 0 + . Name=region_10 +Pt . BED_feature 102404 136227 0 + . Name=region_11 +Pt . BED_feature 104306 105441 0 + . Name=region_12 +Pt . BED_feature 106980 131646 0 + . Name=region_13 +Pt . BED_feature 107004 131670 0 + . Name=region_14 +Pt . BED_feature 120378 121456 0 + . Name=region_15 +Pt . BED_feature 133209 134344 0 + . Name=region_16 +Pt . BED_feature 140089 140624 0 + . Name=region_17 +Pt . BED_feature 142263 142946 0 + . Name=region_18 +Pt . BED_feature 153197 153877 0 + . Name=region_19 +Mt . BED_feature 11727 188840 0 + . Name=region_20 +Mt . BED_feature 20719 21691 0 + . Name=region_21 +Mt . BED_feature 80134 81112 0 + . Name=region_22 +Mt . BED_feature 108929 108982 0 + . Name=region_23 +Mt . BED_feature 132215 133176 0 + . Name=region_24 +Mt . BED_feature 136074 137891 0 + . Name=region_25 +Mt . BED_feature 141941 142768 0 + . Name=region_26 +Mt . BED_feature 143479 146989 0 + . Name=region_27 +Mt . BED_feature 162155 163624 0 + . Name=region_28 +Mt . BED_feature 239003 260663 0 + . Name=region_29 +Mt . BED_feature 242068 260713 0 + . Name=region_30 +Mt . BED_feature 288110 289002 0 + . Name=region_31 +Mt . BED_feature 328080 329734 0 + . Name=region_32 +Mt . BED_feature 330308 332944 0 + . Name=region_33 +4 . BED_feature 4174 4264 0 + . Name=region_34 +4 . BED_feature 4440 4544 0 + . Name=region_35 +4 . BED_feature 4751 4838 0 + . Name=region_36 +4 . BED_feature 4903 4976 0 + . Name=region_37 +4 . BED_feature 5121 5405 0 + . Name=region_38 +4 . BED_feature 5590 5656 0 + . Name=region_39 +4 . BED_feature 5857 6604 0 + . Name=region_40 +4 . BED_feature 6678 6759 0 + . Name=region_41 +4 . BED_feature 6873 6974 0 + . Name=region_42 +4 . BED_feature 7058 7143 0 + . Name=region_43 +4 . BED_feature 7196 7293 0 + . Name=region_44 +4 . BED_feature 7640 7711 0 + . Name=region_45 +4 . BED_feature 7836 8000 0 + . Name=region_46 +4 . BED_feature 8157 8243 0 + . Name=region_47 +4 . BED_feature 8370 8462 0 + . Name=region_48 +4 . BED_feature 9439 9685 0 + . Name=region_49 +4 . BED_feature 9849 9981 0 + . Name=region_50 +4 . BED_feature 10127 10210 0 + . Name=region_51 +4 . BED_feature 11794 11896 0 + . Name=region_52 +4 . BED_feature 12018 12130 0 + . Name=region_53 +4 . BED_feature 12181 12261 0 + . Name=region_54 +4 . BED_feature 12442 12572 0 + . Name=region_55 +4 . BED_feature 12708 12790 0 + . Name=region_56 +4 . BED_feature 12811 12923 0 + . Name=region_57 +4 . BED_feature 12961 13171 0 + . Name=region_58 +4 . BED_feature 14030 14113 0 + . Name=region_59 +4 . BED_feature 14181 14257 0 + . Name=region_60 +4 . BED_feature 14835 14920 0 + . Name=region_61 +4 . BED_feature 17956 18029 0 + . Name=region_62 +4 . BED_feature 18515 18599 0 + . Name=region_63 +4 . BED_feature 18694 18804 0 + . Name=region_64 +4 . BED_feature 18872 19295 0 + . Name=region_65 +4 . BED_feature 18872 19323 0 + . Name=region_66 +4 . BED_feature 19675 19761 0 + . Name=region_67 +4 . BED_feature 22299 22686 0 + . Name=region_68 +4 . BED_feature 23201 23273 0 + . Name=region_69 +4 . BED_feature 23386 23457 0 + . Name=region_70 +4 . BED_feature 23386 23461 0 + . Name=region_71 +4 . BED_feature 23386 23470 0 + . Name=region_72 +4 . BED_feature 25220 25293 0 + . Name=region_73 +4 . BED_feature 25412 25558 0 + . Name=region_74 +4 . BED_feature 25681 25817 0 + . Name=region_75 +4 . BED_feature 25743 25817 0 + . Name=region_76 +4 . BED_feature 25882 26338 0 + . Name=region_77 +4 . BED_feature 26412 26500 0 + . Name=region_78 +4 . BED_feature 26754 26868 0 + . Name=region_79 +4 . BED_feature 26754 26883 0 + . Name=region_80 +4 . BED_feature 27005 27218 0 + . Name=region_81 +4 . BED_feature 27005 27245 0 + . Name=region_82 +4 . BED_feature 27010 27218 0 + . Name=region_83 +4 . BED_feature 27280 27382 0 + . Name=region_84 +4 . BED_feature 27425 27521 0 + . Name=region_85 +4 . BED_feature 27601 27687 0 + . Name=region_86 +4 . BED_feature 27774 27867 0 + . Name=region_87 +4 . BED_feature 28021 28155 0 + . Name=region_88 +4 . BED_feature 28078 28155 0 + . Name=region_89 +4 . BED_feature 28283 28372 0 + . Name=region_90 +4 . BED_feature 28283 28398 0 + . Name=region_91 diff -r 000000000000 -r c4ac24510b55 test-data/TAIR10_GFF3_genes.gff --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/TAIR10_GFF3_genes.gff Sun Jan 03 14:58:58 2021 +0000 @@ -0,0 +1,100 @@ +Chr1 TAIR10 chromosome 1 30427671 . . . ID=Chr1;Name=Chr1 +Chr1 TAIR10 gene 3631 5899 . + . ID=AT1G01010;Note=protein_coding_gene;Name=AT1G01010 +Chr1 TAIR10 mRNA 3631 5899 . + . ID=AT1G01010.1;Parent=AT1G01010;Name=AT1G01010.1;Index=1 +Chr1 TAIR10 protein 3760 5630 . + . ID=AT1G01010.1-Protein;Name=AT1G01010.1;Derives_from=AT1G01010.1 +Chr1 TAIR10 exon 3631 3913 . + . Parent=AT1G01010.1 +Chr1 TAIR10 five_prime_UTR 3631 3759 . + . Parent=AT1G01010.1 +Chr1 TAIR10 CDS 3760 3913 . + 0 Parent=AT1G01010.1,AT1G01010.1-Protein; +Chr1 TAIR10 exon 3996 4276 . + . Parent=AT1G01010.1 +Chr1 TAIR10 CDS 3996 4276 . + 2 Parent=AT1G01010.1,AT1G01010.1-Protein; +Chr1 TAIR10 exon 4486 4605 . + . Parent=AT1G01010.1 +Chr1 TAIR10 CDS 4486 4605 . + 0 Parent=AT1G01010.1,AT1G01010.1-Protein; +Chr1 TAIR10 exon 4706 5095 . + . Parent=AT1G01010.1 +Chr1 TAIR10 CDS 4706 5095 . + 0 Parent=AT1G01010.1,AT1G01010.1-Protein; +Chr1 TAIR10 exon 5174 5326 . + . Parent=AT1G01010.1 +Chr1 TAIR10 CDS 5174 5326 . + 0 Parent=AT1G01010.1,AT1G01010.1-Protein; +Chr1 TAIR10 exon 5439 5899 . + . Parent=AT1G01010.1 +Chr1 TAIR10 CDS 5439 5630 . + 0 Parent=AT1G01010.1,AT1G01010.1-Protein; +Chr1 TAIR10 three_prime_UTR 5631 5899 . + . Parent=AT1G01010.1 +Chr1 TAIR10 gene 5928 8737 . - . ID=AT1G01020;Note=protein_coding_gene;Name=AT1G01020 +Chr1 TAIR10 mRNA 5928 8737 . - . ID=AT1G01020.1;Parent=AT1G01020;Name=AT1G01020.1;Index=1 +Chr1 TAIR10 protein 6915 8666 . - . ID=AT1G01020.1-Protein;Name=AT1G01020.1;Derives_from=AT1G01020.1 +Chr1 TAIR10 five_prime_UTR 8667 8737 . - . Parent=AT1G01020.1 +Chr1 TAIR10 CDS 8571 8666 . - 0 Parent=AT1G01020.1,AT1G01020.1-Protein; +Chr1 TAIR10 exon 8571 8737 . - . Parent=AT1G01020.1 +Chr1 TAIR10 CDS 8417 8464 . - 0 Parent=AT1G01020.1,AT1G01020.1-Protein; +Chr1 TAIR10 exon 8417 8464 . - . Parent=AT1G01020.1 +Chr1 TAIR10 CDS 8236 8325 . - 0 Parent=AT1G01020.1,AT1G01020.1-Protein; +Chr1 TAIR10 exon 8236 8325 . - . Parent=AT1G01020.1 +Chr1 TAIR10 CDS 7942 7987 . - 0 Parent=AT1G01020.1,AT1G01020.1-Protein; +Chr1 TAIR10 exon 7942 7987 . - . Parent=AT1G01020.1 +Chr1 TAIR10 CDS 7762 7835 . - 2 Parent=AT1G01020.1,AT1G01020.1-Protein; +Chr1 TAIR10 exon 7762 7835 . - . Parent=AT1G01020.1 +Chr1 TAIR10 CDS 7564 7649 . - 0 Parent=AT1G01020.1,AT1G01020.1-Protein; +Chr1 TAIR10 exon 7564 7649 . - . Parent=AT1G01020.1 +Chr1 TAIR10 CDS 7384 7450 . - 1 Parent=AT1G01020.1,AT1G01020.1-Protein; +Chr1 TAIR10 exon 7384 7450 . - . Parent=AT1G01020.1 +Chr1 TAIR10 CDS 7157 7232 . - 0 Parent=AT1G01020.1,AT1G01020.1-Protein; +Chr1 TAIR10 exon 7157 7232 . - . Parent=AT1G01020.1 +Chr1 TAIR10 CDS 6915 7069 . - 2 Parent=AT1G01020.1,AT1G01020.1-Protein; +Chr1 TAIR10 three_prime_UTR 6437 6914 . - . Parent=AT1G01020.1 +Chr1 TAIR10 exon 6437 7069 . - . Parent=AT1G01020.1 +Chr1 TAIR10 three_prime_UTR 5928 6263 . - . Parent=AT1G01020.1 +Chr1 TAIR10 exon 5928 6263 . - . Parent=AT1G01020.1 +Chr1 TAIR10 mRNA 6790 8737 . - . ID=AT1G01020.2;Parent=AT1G01020;Name=AT1G01020.2;Index=1 +Chr1 TAIR10 protein 7315 8666 . - . ID=AT1G01020.2-Protein;Name=AT1G01020.2;Derives_from=AT1G01020.2 +Chr1 TAIR10 five_prime_UTR 8667 8737 . - . Parent=AT1G01020.2 +Chr1 TAIR10 CDS 8571 8666 . - 0 Parent=AT1G01020.2,AT1G01020.2-Protein; +Chr1 TAIR10 exon 8571 8737 . - . Parent=AT1G01020.2 +Chr1 TAIR10 CDS 8417 8464 . - 0 Parent=AT1G01020.2,AT1G01020.2-Protein; +Chr1 TAIR10 exon 8417 8464 . - . Parent=AT1G01020.2 +Chr1 TAIR10 CDS 8236 8325 . - 0 Parent=AT1G01020.2,AT1G01020.2-Protein; +Chr1 TAIR10 exon 8236 8325 . - . Parent=AT1G01020.2 +Chr1 TAIR10 CDS 7942 7987 . - 0 Parent=AT1G01020.2,AT1G01020.2-Protein; +Chr1 TAIR10 exon 7942 7987 . - . Parent=AT1G01020.2 +Chr1 TAIR10 CDS 7762 7835 . - 2 Parent=AT1G01020.2,AT1G01020.2-Protein; +Chr1 TAIR10 exon 7762 7835 . - . Parent=AT1G01020.2 +Chr1 TAIR10 CDS 7564 7649 . - 0 Parent=AT1G01020.2,AT1G01020.2-Protein; +Chr1 TAIR10 exon 7564 7649 . - . Parent=AT1G01020.2 +Chr1 TAIR10 CDS 7315 7450 . - 1 Parent=AT1G01020.2,AT1G01020.2-Protein; +Chr1 TAIR10 three_prime_UTR 7157 7314 . - . Parent=AT1G01020.2 +Chr1 TAIR10 exon 7157 7450 . - . Parent=AT1G01020.2 +Chr1 TAIR10 three_prime_UTR 6790 7069 . - . Parent=AT1G01020.2 +Chr1 TAIR10 exon 6790 7069 . - . Parent=AT1G01020.2 +Chr1 TAIR10 gene 11649 13714 . - . ID=AT1G01030;Note=protein_coding_gene;Name=AT1G01030 +Chr1 TAIR10 mRNA 11649 13714 . - . ID=AT1G01030.1;Parent=AT1G01030;Name=AT1G01030.1;Index=1 +Chr1 TAIR10 protein 11864 12940 . - . ID=AT1G01030.1-Protein;Name=AT1G01030.1;Derives_from=AT1G01030.1 +Chr1 TAIR10 five_prime_UTR 13335 13714 . - . Parent=AT1G01030.1 +Chr1 TAIR10 exon 13335 13714 . - . Parent=AT1G01030.1 +Chr1 TAIR10 five_prime_UTR 12941 13173 . - . Parent=AT1G01030.1 +Chr1 TAIR10 CDS 11864 12940 . - 0 Parent=AT1G01030.1,AT1G01030.1-Protein; +Chr1 TAIR10 three_prime_UTR 11649 11863 . - . Parent=AT1G01030.1 +Chr1 TAIR10 exon 11649 13173 . - . Parent=AT1G01030.1 +Chr1 TAIR10 gene 23146 31227 . + . ID=AT1G01040;Note=protein_coding_gene;Name=AT1G01040 +Chr1 TAIR10 mRNA 23146 31227 . + . ID=AT1G01040.1;Parent=AT1G01040;Name=AT1G01040.1;Index=1 +Chr1 TAIR10 protein 23519 31079 . + . ID=AT1G01040.1-Protein;Name=AT1G01040.1;Derives_from=AT1G01040.1 +Chr1 TAIR10 exon 23146 24451 . + . Parent=AT1G01040.1 +Chr1 TAIR10 five_prime_UTR 23146 23518 . + . Parent=AT1G01040.1 +Chr1 TAIR10 CDS 23519 24451 . + 0 Parent=AT1G01040.1,AT1G01040.1-Protein; +Chr1 TAIR10 exon 24542 24655 . + . Parent=AT1G01040.1 +Chr1 TAIR10 CDS 24542 24655 . + 0 Parent=AT1G01040.1,AT1G01040.1-Protein; +Chr1 TAIR10 exon 24752 24962 . + . Parent=AT1G01040.1 +Chr1 TAIR10 CDS 24752 24962 . + 0 Parent=AT1G01040.1,AT1G01040.1-Protein; +Chr1 TAIR10 exon 25041 25435 . + . Parent=AT1G01040.1 +Chr1 TAIR10 CDS 25041 25435 . + 2 Parent=AT1G01040.1,AT1G01040.1-Protein; +Chr1 TAIR10 exon 25524 25743 . + . Parent=AT1G01040.1 +Chr1 TAIR10 CDS 25524 25743 . + 0 Parent=AT1G01040.1,AT1G01040.1-Protein; +Chr1 TAIR10 exon 25825 25997 . + . Parent=AT1G01040.1 +Chr1 TAIR10 CDS 25825 25997 . + 2 Parent=AT1G01040.1,AT1G01040.1-Protein; +Chr1 TAIR10 exon 26081 26203 . + . Parent=AT1G01040.1 +Chr1 TAIR10 CDS 26081 26203 . + 0 Parent=AT1G01040.1,AT1G01040.1-Protein; +Chr1 TAIR10 exon 26292 26452 . + . Parent=AT1G01040.1 +Chr1 TAIR10 CDS 26292 26452 . + 0 Parent=AT1G01040.1,AT1G01040.1-Protein; +Chr1 TAIR10 exon 26543 26776 . + . Parent=AT1G01040.1 +Chr1 TAIR10 CDS 26543 26776 . + 1 Parent=AT1G01040.1,AT1G01040.1-Protein; +Chr1 TAIR10 exon 26862 27012 . + . Parent=AT1G01040.1 +Chr1 TAIR10 CDS 26862 27012 . + 1 Parent=AT1G01040.1,AT1G01040.1-Protein; +Chr1 TAIR10 exon 27099 27281 . + . Parent=AT1G01040.1 +Chr1 TAIR10 CDS 27099 27281 . + 0 Parent=AT1G01040.1,AT1G01040.1-Protein; +Chr1 TAIR10 exon 27372 27533 . + . Parent=AT1G01040.1 +Chr1 TAIR10 CDS 27372 27533 . + 0 Parent=AT1G01040.1,AT1G01040.1-Protein; diff -r 000000000000 -r c4ac24510b55 test-data/TAIR9_GFF3_genes.gff --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/TAIR9_GFF3_genes.gff Sun Jan 03 14:58:58 2021 +0000 @@ -0,0 +1,100 @@ +Chr1 TAIR9 chromosome 1 30427671 . . . ID=Chr1;Name=Chr1 +Chr1 TAIR9 gene 3631 5899 . + . ID=AT1G01010;Note=protein_coding_gene;Name=AT1G01010 +Chr1 TAIR9 mRNA 3631 5899 . + . ID=AT1G01010.1;Parent=AT1G01010;Name=AT1G01010.1;Index=1 +Chr1 TAIR9 protein 3760 5630 . + . ID=AT1G01010.1-Protein;Name=AT1G01010.1;Derives_from=AT1G01010.1 +Chr1 TAIR9 exon 3631 3913 . + . Parent=AT1G01010.1 +Chr1 TAIR9 five_prime_UTR 3631 3759 . + . Parent=AT1G01010.1 +Chr1 TAIR9 CDS 3760 3913 . + 0 Parent=AT1G01010.1,AT1G01010.1-Protein; +Chr1 TAIR9 exon 3996 4276 . + . Parent=AT1G01010.1 +Chr1 TAIR9 CDS 3996 4276 . + 2 Parent=AT1G01010.1,AT1G01010.1-Protein; +Chr1 TAIR9 exon 4486 4605 . + . Parent=AT1G01010.1 +Chr1 TAIR9 CDS 4486 4605 . + 0 Parent=AT1G01010.1,AT1G01010.1-Protein; +Chr1 TAIR9 exon 4706 5095 . + . Parent=AT1G01010.1 +Chr1 TAIR9 CDS 4706 5095 . + 0 Parent=AT1G01010.1,AT1G01010.1-Protein; +Chr1 TAIR9 exon 5174 5326 . + . Parent=AT1G01010.1 +Chr1 TAIR9 CDS 5174 5326 . + 0 Parent=AT1G01010.1,AT1G01010.1-Protein; +Chr1 TAIR9 exon 5439 5899 . + . Parent=AT1G01010.1 +Chr1 TAIR9 CDS 5439 5630 . + 0 Parent=AT1G01010.1,AT1G01010.1-Protein; +Chr1 TAIR9 three_prime_UTR 5631 5899 . + . Parent=AT1G01010.1 +Chr1 TAIR9 gene 5928 8737 . - . ID=AT1G01020;Note=protein_coding_gene;Name=AT1G01020 +Chr1 TAIR9 mRNA 5928 8737 . - . ID=AT1G01020.1;Parent=AT1G01020;Name=AT1G01020.1;Index=1 +Chr1 TAIR9 protein 6915 8666 . - . ID=AT1G01020.1-Protein;Name=AT1G01020.1;Derives_from=AT1G01020.1 +Chr1 TAIR9 five_prime_UTR 8667 8737 . - . Parent=AT1G01020.1 +Chr1 TAIR9 CDS 8571 8666 . - 0 Parent=AT1G01020.1,AT1G01020.1-Protein; +Chr1 TAIR9 exon 8571 8737 . - . Parent=AT1G01020.1 +Chr1 TAIR9 CDS 8417 8464 . - 0 Parent=AT1G01020.1,AT1G01020.1-Protein; +Chr1 TAIR9 exon 8417 8464 . - . Parent=AT1G01020.1 +Chr1 TAIR9 CDS 8236 8325 . - 0 Parent=AT1G01020.1,AT1G01020.1-Protein; +Chr1 TAIR9 exon 8236 8325 . - . Parent=AT1G01020.1 +Chr1 TAIR9 CDS 7942 7987 . - 0 Parent=AT1G01020.1,AT1G01020.1-Protein; +Chr1 TAIR9 exon 7942 7987 . - . Parent=AT1G01020.1 +Chr1 TAIR9 CDS 7762 7835 . - 2 Parent=AT1G01020.1,AT1G01020.1-Protein; +Chr1 TAIR9 exon 7762 7835 . - . Parent=AT1G01020.1 +Chr1 TAIR9 CDS 7564 7649 . - 0 Parent=AT1G01020.1,AT1G01020.1-Protein; +Chr1 TAIR9 exon 7564 7649 . - . Parent=AT1G01020.1 +Chr1 TAIR9 CDS 7384 7450 . - 1 Parent=AT1G01020.1,AT1G01020.1-Protein; +Chr1 TAIR9 exon 7384 7450 . - . Parent=AT1G01020.1 +Chr1 TAIR9 CDS 7157 7232 . - 0 Parent=AT1G01020.1,AT1G01020.1-Protein; +Chr1 TAIR9 exon 7157 7232 . - . Parent=AT1G01020.1 +Chr1 TAIR9 CDS 6915 7069 . - 2 Parent=AT1G01020.1,AT1G01020.1-Protein; +Chr1 TAIR9 three_prime_UTR 6437 6914 . - . Parent=AT1G01020.1 +Chr1 TAIR9 exon 6437 7069 . - . Parent=AT1G01020.1 +Chr1 TAIR9 three_prime_UTR 5928 6263 . - . Parent=AT1G01020.1 +Chr1 TAIR9 exon 5928 6263 . - . Parent=AT1G01020.1 +Chr1 TAIR9 mRNA 6790 8737 . - . ID=AT1G01020.2;Parent=AT1G01020;Name=AT1G01020.2;Index=1 +Chr1 TAIR9 protein 7315 8666 . - . ID=AT1G01020.2-Protein;Name=AT1G01020.2;Derives_from=AT1G01020.2 +Chr1 TAIR9 five_prime_UTR 8667 8737 . - . Parent=AT1G01020.2 +Chr1 TAIR9 CDS 8571 8666 . - 0 Parent=AT1G01020.2,AT1G01020.2-Protein; +Chr1 TAIR9 exon 8571 8737 . - . Parent=AT1G01020.2 +Chr1 TAIR9 CDS 8417 8464 . - 0 Parent=AT1G01020.2,AT1G01020.2-Protein; +Chr1 TAIR9 exon 8417 8464 . - . Parent=AT1G01020.2 +Chr1 TAIR9 CDS 8236 8325 . - 0 Parent=AT1G01020.2,AT1G01020.2-Protein; +Chr1 TAIR9 exon 8236 8325 . - . Parent=AT1G01020.2 +Chr1 TAIR9 CDS 7942 7987 . - 0 Parent=AT1G01020.2,AT1G01020.2-Protein; +Chr1 TAIR9 exon 7942 7987 . - . Parent=AT1G01020.2 +Chr1 TAIR9 CDS 7762 7835 . - 2 Parent=AT1G01020.2,AT1G01020.2-Protein; +Chr1 TAIR9 exon 7762 7835 . - . Parent=AT1G01020.2 +Chr1 TAIR9 CDS 7564 7649 . - 0 Parent=AT1G01020.2,AT1G01020.2-Protein; +Chr1 TAIR9 exon 7564 7649 . - . Parent=AT1G01020.2 +Chr1 TAIR9 CDS 7315 7450 . - 1 Parent=AT1G01020.2,AT1G01020.2-Protein; +Chr1 TAIR9 three_prime_UTR 7157 7314 . - . Parent=AT1G01020.2 +Chr1 TAIR9 exon 7157 7450 . - . Parent=AT1G01020.2 +Chr1 TAIR9 three_prime_UTR 6790 7069 . - . Parent=AT1G01020.2 +Chr1 TAIR9 exon 6790 7069 . - . Parent=AT1G01020.2 +Chr1 TAIR9 gene 11649 13714 . - . ID=AT1G01030;Note=protein_coding_gene;Name=AT1G01030 +Chr1 TAIR9 mRNA 11649 13714 . - . ID=AT1G01030.1;Parent=AT1G01030;Name=AT1G01030.1;Index=1 +Chr1 TAIR9 protein 11864 12940 . - . ID=AT1G01030.1-Protein;Name=AT1G01030.1;Derives_from=AT1G01030.1 +Chr1 TAIR9 five_prime_UTR 13335 13714 . - . Parent=AT1G01030.1 +Chr1 TAIR9 exon 13335 13714 . - . Parent=AT1G01030.1 +Chr1 TAIR9 five_prime_UTR 12941 13173 . - . Parent=AT1G01030.1 +Chr1 TAIR9 CDS 11864 12940 . - 0 Parent=AT1G01030.1,AT1G01030.1-Protein; +Chr1 TAIR9 three_prime_UTR 11649 11863 . - . Parent=AT1G01030.1 +Chr1 TAIR9 exon 11649 13173 . - . Parent=AT1G01030.1 +Chr1 TAIR9 gene 23146 31227 . + . ID=AT1G01040;Note=protein_coding_gene;Name=AT1G01040 +Chr1 TAIR9 mRNA 23146 31227 . + . ID=AT1G01040.1;Parent=AT1G01040;Name=AT1G01040.1;Index=1 +Chr1 TAIR9 protein 23519 31079 . + . ID=AT1G01040.1-Protein;Name=AT1G01040.1;Derives_from=AT1G01040.1 +Chr1 TAIR9 exon 23146 24451 . + . Parent=AT1G01040.1 +Chr1 TAIR9 five_prime_UTR 23146 23518 . + . Parent=AT1G01040.1 +Chr1 TAIR9 CDS 23519 24451 . + 0 Parent=AT1G01040.1,AT1G01040.1-Protein; +Chr1 TAIR9 exon 24542 24655 . + . Parent=AT1G01040.1 +Chr1 TAIR9 CDS 24542 24655 . + 0 Parent=AT1G01040.1,AT1G01040.1-Protein; +Chr1 TAIR9 exon 24752 24962 . + . Parent=AT1G01040.1 +Chr1 TAIR9 CDS 24752 24962 . + 0 Parent=AT1G01040.1,AT1G01040.1-Protein; +Chr1 TAIR9 exon 25041 25435 . + . Parent=AT1G01040.1 +Chr1 TAIR9 CDS 25041 25435 . + 2 Parent=AT1G01040.1,AT1G01040.1-Protein; +Chr1 TAIR9 exon 25524 25743 . + . Parent=AT1G01040.1 +Chr1 TAIR9 CDS 25524 25743 . + 0 Parent=AT1G01040.1,AT1G01040.1-Protein; +Chr1 TAIR9 exon 25825 25997 . + . Parent=AT1G01040.1 +Chr1 TAIR9 CDS 25825 25997 . + 2 Parent=AT1G01040.1,AT1G01040.1-Protein; +Chr1 TAIR9 exon 26081 26203 . + . Parent=AT1G01040.1 +Chr1 TAIR9 CDS 26081 26203 . + 0 Parent=AT1G01040.1,AT1G01040.1-Protein; +Chr1 TAIR9 exon 26292 26452 . + . Parent=AT1G01040.1 +Chr1 TAIR9 CDS 26292 26452 . + 0 Parent=AT1G01040.1,AT1G01040.1-Protein; +Chr1 TAIR9 exon 26543 26776 . + . Parent=AT1G01040.1 +Chr1 TAIR9 CDS 26543 26776 . + 1 Parent=AT1G01040.1,AT1G01040.1-Protein; +Chr1 TAIR9 exon 26862 27012 . + . Parent=AT1G01040.1 +Chr1 TAIR9 CDS 26862 27012 . + 1 Parent=AT1G01040.1,AT1G01040.1-Protein; +Chr1 TAIR9 exon 27099 27281 . + . Parent=AT1G01040.1 +Chr1 TAIR9 CDS 27099 27281 . + 0 Parent=AT1G01040.1,AT1G01040.1-Protein; +Chr1 TAIR9 exon 27372 27533 . + . Parent=AT1G01040.1 +Chr1 TAIR9 CDS 27372 27533 . + 0 Parent=AT1G01040.1,AT1G01040.1-Protein; diff -r 000000000000 -r c4ac24510b55 test-data/canon-output_test1.gff3 --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/canon-output_test1.gff3 Sun Jan 03 14:58:58 2021 +0000 @@ -0,0 +1,136 @@ +##gff-version 3 +##sequence-region Chr1 1 30427671 +Chr1 TAIR10 gene 3631 5899 . + . ID=AT1G01010;Note=protein_coding_gene;Name=AT1G01010 +Chr1 TAIR10 mRNA 3631 5899 . + . ID=AT1G01010.1;Parent=AT1G01010;Name=AT1G01010.1;index=1 +Chr1 TAIR10 five_prime_UTR 3631 3759 . + . Parent=AT1G01010.1 +Chr1 TAIR10 exon 3631 3913 . + . Parent=AT1G01010.1 +Chr1 . start_codon 3760 3762 . + . Parent=AT1G01010.1 +Chr1 TAIR10 CDS 3760 3913 . + 0 ID=CDS0;Parent=AT1G01010.1 +Chr1 . intron 3914 3995 . + . Parent=AT1G01010.1 +Chr1 TAIR10 exon 3996 4276 . + . Parent=AT1G01010.1 +Chr1 TAIR10 CDS 3996 4276 . + 2 ID=CDS0;Parent=AT1G01010.1 +Chr1 . intron 4277 4485 . + . Parent=AT1G01010.1 +Chr1 TAIR10 exon 4486 4605 . + . Parent=AT1G01010.1 +Chr1 TAIR10 CDS 4486 4605 . + 0 ID=CDS0;Parent=AT1G01010.1 +Chr1 . intron 4606 4705 . + . Parent=AT1G01010.1 +Chr1 TAIR10 exon 4706 5095 . + . Parent=AT1G01010.1 +Chr1 TAIR10 CDS 4706 5095 . + 0 ID=CDS0;Parent=AT1G01010.1 +Chr1 . intron 5096 5173 . + . Parent=AT1G01010.1 +Chr1 TAIR10 exon 5174 5326 . + . Parent=AT1G01010.1 +Chr1 TAIR10 CDS 5174 5326 . + 0 ID=CDS0;Parent=AT1G01010.1 +Chr1 . intron 5327 5438 . + . Parent=AT1G01010.1 +Chr1 TAIR10 CDS 5439 5630 . + 0 ID=CDS0;Parent=AT1G01010.1 +Chr1 TAIR10 exon 5439 5899 . + . Parent=AT1G01010.1 +Chr1 . stop_codon 5628 5630 . + . Parent=AT1G01010.1 +Chr1 TAIR10 three_prime_UTR 5631 5899 . + . Parent=AT1G01010.1 +### +Chr1 TAIR10 gene 5928 8737 . - . ID=AT1G01020;Note=protein_coding_gene;Name=AT1G01020 +Chr1 TAIR10 mRNA 5928 8737 . - . ID=AT1G01020.1;Parent=AT1G01020;Name=AT1G01020.1;index=1 +Chr1 TAIR10 three_prime_UTR 5928 6263 . - . Parent=AT1G01020.1 +Chr1 TAIR10 exon 5928 6263 . - . Parent=AT1G01020.1 +Chr1 . intron 6264 6436 . - . Parent=AT1G01020.1 +Chr1 TAIR10 three_prime_UTR 6437 6914 . - . Parent=AT1G01020.1 +Chr1 TAIR10 exon 6437 7069 . - . Parent=AT1G01020.1 +Chr1 . stop_codon 6915 6917 . - . Parent=AT1G01020.1 +Chr1 TAIR10 CDS 6915 7069 . - 2 ID=CDS1;Parent=AT1G01020.1 +Chr1 TAIR10 CDS 7157 7232 . - 0 ID=CDS1;Parent=AT1G01020.1 +Chr1 TAIR10 exon 7157 7232 . - . Parent=AT1G01020.1 +Chr1 . intron 7233 7383 . - . Parent=AT1G01020.1 +Chr1 TAIR10 CDS 7384 7450 . - 1 ID=CDS1;Parent=AT1G01020.1 +Chr1 TAIR10 exon 7384 7450 . - . Parent=AT1G01020.1 +Chr1 TAIR10 CDS 7564 7649 . - 0 ID=CDS1;Parent=AT1G01020.1 +Chr1 TAIR10 exon 7564 7649 . - . Parent=AT1G01020.1 +Chr1 TAIR10 CDS 7762 7835 . - 2 ID=CDS1;Parent=AT1G01020.1 +Chr1 TAIR10 exon 7762 7835 . - . Parent=AT1G01020.1 +Chr1 TAIR10 CDS 7942 7987 . - 0 ID=CDS1;Parent=AT1G01020.1 +Chr1 TAIR10 exon 7942 7987 . - . Parent=AT1G01020.1 +Chr1 TAIR10 CDS 8236 8325 . - 0 ID=CDS1;Parent=AT1G01020.1 +Chr1 TAIR10 exon 8236 8325 . - . Parent=AT1G01020.1 +Chr1 TAIR10 CDS 8417 8464 . - 0 ID=CDS1;Parent=AT1G01020.1 +Chr1 TAIR10 exon 8417 8464 . - . Parent=AT1G01020.1 +Chr1 TAIR10 CDS 8571 8666 . - 0 ID=CDS1;Parent=AT1G01020.1 +Chr1 TAIR10 exon 8571 8737 . - . Parent=AT1G01020.1 +Chr1 . start_codon 8664 8666 . - . Parent=AT1G01020.1 +Chr1 TAIR10 five_prime_UTR 8667 8737 . - . Parent=AT1G01020.1 +Chr1 TAIR10 mRNA 6790 8737 . - . ID=AT1G01020.2;Parent=AT1G01020;Name=AT1G01020.2;index=1 +Chr1 TAIR10 three_prime_UTR 6790 7069 . - . Parent=AT1G01020.2 +Chr1 TAIR10 exon 6790 7069 . - . Parent=AT1G01020.2 +Chr1 . intron 7070 7156 . - . Parent=AT1G01020.1,AT1G01020.2 +Chr1 TAIR10 three_prime_UTR 7157 7314 . - . Parent=AT1G01020.2 +Chr1 TAIR10 exon 7157 7450 . - . Parent=AT1G01020.2 +Chr1 . stop_codon 7315 7317 . - . Parent=AT1G01020.2 +Chr1 TAIR10 CDS 7315 7450 . - 1 ID=CDS2;Parent=AT1G01020.2 +Chr1 . intron 7451 7563 . - . Parent=AT1G01020.1,AT1G01020.2 +Chr1 TAIR10 CDS 7564 7649 . - 0 ID=CDS2;Parent=AT1G01020.2 +Chr1 TAIR10 exon 7564 7649 . - . Parent=AT1G01020.2 +Chr1 . intron 7650 7761 . - . Parent=AT1G01020.1,AT1G01020.2 +Chr1 TAIR10 CDS 7762 7835 . - 2 ID=CDS2;Parent=AT1G01020.2 +Chr1 TAIR10 exon 7762 7835 . - . Parent=AT1G01020.2 +Chr1 . intron 7836 7941 . - . Parent=AT1G01020.1,AT1G01020.2 +Chr1 TAIR10 CDS 7942 7987 . - 0 ID=CDS2;Parent=AT1G01020.2 +Chr1 TAIR10 exon 7942 7987 . - . Parent=AT1G01020.2 +Chr1 . intron 7988 8235 . - . Parent=AT1G01020.1,AT1G01020.2 +Chr1 TAIR10 CDS 8236 8325 . - 0 ID=CDS2;Parent=AT1G01020.2 +Chr1 TAIR10 exon 8236 8325 . - . Parent=AT1G01020.2 +Chr1 . intron 8326 8416 . - . Parent=AT1G01020.1,AT1G01020.2 +Chr1 TAIR10 CDS 8417 8464 . - 0 ID=CDS2;Parent=AT1G01020.2 +Chr1 TAIR10 exon 8417 8464 . - . Parent=AT1G01020.2 +Chr1 . intron 8465 8570 . - . Parent=AT1G01020.1,AT1G01020.2 +Chr1 TAIR10 CDS 8571 8666 . - 0 ID=CDS2;Parent=AT1G01020.2 +Chr1 TAIR10 exon 8571 8737 . - . Parent=AT1G01020.2 +Chr1 . start_codon 8664 8666 . - . Parent=AT1G01020.2 +Chr1 TAIR10 five_prime_UTR 8667 8737 . - . Parent=AT1G01020.2 +### +Chr1 TAIR10 gene 11649 13714 . - . ID=AT1G01030;Note=protein_coding_gene;Name=AT1G01030 +Chr1 TAIR10 mRNA 11649 13714 . - . ID=AT1G01030.1;Parent=AT1G01030;Name=AT1G01030.1;index=1 +Chr1 TAIR10 three_prime_UTR 11649 11863 . - . Parent=AT1G01030.1 +Chr1 TAIR10 exon 11649 13173 . - . Parent=AT1G01030.1 +Chr1 . stop_codon 11864 11866 . - . Parent=AT1G01030.1 +Chr1 TAIR10 CDS 11864 12940 . - 0 Parent=AT1G01030.1 +Chr1 . start_codon 12938 12940 . - . Parent=AT1G01030.1 +Chr1 TAIR10 five_prime_UTR 12941 13173 . - . Parent=AT1G01030.1 +Chr1 . intron 13174 13334 . - . Parent=AT1G01030.1 +Chr1 TAIR10 five_prime_UTR 13335 13714 . - . Parent=AT1G01030.1 +Chr1 TAIR10 exon 13335 13714 . - . Parent=AT1G01030.1 +### +Chr1 TAIR10 gene 23146 31227 . + . ID=AT1G01040;Note=protein_coding_gene;Name=AT1G01040 +Chr1 TAIR10 mRNA 23146 31227 . + . ID=AT1G01040.1;Parent=AT1G01040;Name=AT1G01040.1;index=1 +Chr1 TAIR10 five_prime_UTR 23146 23518 . + . Parent=AT1G01040.1 +Chr1 TAIR10 exon 23146 24451 . + . Parent=AT1G01040.1 +Chr1 . start_codon 23519 23521 . + . Parent=AT1G01040.1 +Chr1 TAIR10 CDS 23519 24451 . + 0 ID=CDS3;Parent=AT1G01040.1 +Chr1 . intron 24452 24541 . + . Parent=AT1G01040.1 +Chr1 TAIR10 exon 24542 24655 . + . Parent=AT1G01040.1 +Chr1 TAIR10 CDS 24542 24655 . + 0 ID=CDS3;Parent=AT1G01040.1 +Chr1 . intron 24656 24751 . + . Parent=AT1G01040.1 +Chr1 TAIR10 exon 24752 24962 . + . Parent=AT1G01040.1 +Chr1 TAIR10 CDS 24752 24962 . + 0 ID=CDS3;Parent=AT1G01040.1 +Chr1 . intron 24963 25040 . + . Parent=AT1G01040.1 +Chr1 TAIR10 exon 25041 25435 . + . Parent=AT1G01040.1 +Chr1 TAIR10 CDS 25041 25435 . + 2 ID=CDS3;Parent=AT1G01040.1 +Chr1 . intron 25436 25523 . + . Parent=AT1G01040.1 +Chr1 TAIR10 exon 25524 25743 . + . Parent=AT1G01040.1 +Chr1 TAIR10 CDS 25524 25743 . + 0 ID=CDS3;Parent=AT1G01040.1 +Chr1 . intron 25744 25824 . + . Parent=AT1G01040.1 +Chr1 TAIR10 exon 25825 25997 . + . Parent=AT1G01040.1 +Chr1 TAIR10 CDS 25825 25997 . + 2 ID=CDS3;Parent=AT1G01040.1 +Chr1 . intron 25998 26080 . + . Parent=AT1G01040.1 +Chr1 TAIR10 exon 26081 26203 . + . Parent=AT1G01040.1 +Chr1 TAIR10 CDS 26081 26203 . + 0 ID=CDS3;Parent=AT1G01040.1 +Chr1 . intron 26204 26291 . + . Parent=AT1G01040.1 +Chr1 TAIR10 exon 26292 26452 . + . Parent=AT1G01040.1 +Chr1 TAIR10 CDS 26292 26452 . + 0 ID=CDS3;Parent=AT1G01040.1 +Chr1 . intron 26453 26542 . + . Parent=AT1G01040.1 +Chr1 TAIR10 exon 26543 26776 . + . Parent=AT1G01040.1 +Chr1 TAIR10 CDS 26543 26776 . + 1 ID=CDS3;Parent=AT1G01040.1 +Chr1 . intron 26777 26861 . + . Parent=AT1G01040.1 +Chr1 TAIR10 exon 26862 27012 . + . Parent=AT1G01040.1 +Chr1 TAIR10 CDS 26862 27012 . + 1 ID=CDS3;Parent=AT1G01040.1 +Chr1 . intron 27013 27098 . + . Parent=AT1G01040.1 +Chr1 TAIR10 exon 27099 27281 . + . Parent=AT1G01040.1 +Chr1 TAIR10 CDS 27099 27281 . + 0 ID=CDS3;Parent=AT1G01040.1 +Chr1 . intron 27282 27371 . + . Parent=AT1G01040.1 +Chr1 TAIR10 exon 27372 27533 . + . Parent=AT1G01040.1 +Chr1 TAIR10 CDS 27372 27533 . + 0 ID=CDS3;Parent=AT1G01040.1 +Chr1 . stop_codon 27531 27533 . + . Parent=AT1G01040.1 +### diff -r 000000000000 -r c4ac24510b55 test-data/canon-output_test2.gff3 --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/canon-output_test2.gff3 Sun Jan 03 14:58:58 2021 +0000 @@ -0,0 +1,136 @@ +##gff-version 3 +##sequence-region Chr1 1 30427671 +Chr1 test_source gene 3631 5899 . + . ID=AT1G01010;Note=protein_coding_gene;Name=AT1G01010 +Chr1 test_source mRNA 3631 5899 . + . ID=AT1G01010.1;Parent=AT1G01010;Name=AT1G01010.1;index=1 +Chr1 test_source five_prime_UTR 3631 3759 . + . Parent=AT1G01010.1 +Chr1 test_source exon 3631 3913 . + . Parent=AT1G01010.1 +Chr1 test_source start_codon 3760 3762 . + . Parent=AT1G01010.1 +Chr1 test_source CDS 3760 3913 . + 0 ID=CDS0;Parent=AT1G01010.1 +Chr1 test_source intron 3914 3995 . + . Parent=AT1G01010.1 +Chr1 test_source exon 3996 4276 . + . Parent=AT1G01010.1 +Chr1 test_source CDS 3996 4276 . + 2 ID=CDS0;Parent=AT1G01010.1 +Chr1 test_source intron 4277 4485 . + . Parent=AT1G01010.1 +Chr1 test_source exon 4486 4605 . + . Parent=AT1G01010.1 +Chr1 test_source CDS 4486 4605 . + 0 ID=CDS0;Parent=AT1G01010.1 +Chr1 test_source intron 4606 4705 . + . Parent=AT1G01010.1 +Chr1 test_source exon 4706 5095 . + . Parent=AT1G01010.1 +Chr1 test_source CDS 4706 5095 . + 0 ID=CDS0;Parent=AT1G01010.1 +Chr1 test_source intron 5096 5173 . + . Parent=AT1G01010.1 +Chr1 test_source exon 5174 5326 . + . Parent=AT1G01010.1 +Chr1 test_source CDS 5174 5326 . + 0 ID=CDS0;Parent=AT1G01010.1 +Chr1 test_source intron 5327 5438 . + . Parent=AT1G01010.1 +Chr1 test_source CDS 5439 5630 . + 0 ID=CDS0;Parent=AT1G01010.1 +Chr1 test_source exon 5439 5899 . + . Parent=AT1G01010.1 +Chr1 test_source stop_codon 5628 5630 . + . Parent=AT1G01010.1 +Chr1 test_source three_prime_UTR 5631 5899 . + . Parent=AT1G01010.1 +### +Chr1 test_source gene 5928 8737 . - . ID=AT1G01020;Note=protein_coding_gene;Name=AT1G01020 +Chr1 test_source mRNA 5928 8737 . - . ID=AT1G01020.1;Parent=AT1G01020;Name=AT1G01020.1;index=1 +Chr1 test_source three_prime_UTR 5928 6263 . - . Parent=AT1G01020.1 +Chr1 test_source exon 5928 6263 . - . Parent=AT1G01020.1 +Chr1 test_source intron 6264 6436 . - . Parent=AT1G01020.1 +Chr1 test_source three_prime_UTR 6437 6914 . - . Parent=AT1G01020.1 +Chr1 test_source exon 6437 7069 . - . Parent=AT1G01020.1 +Chr1 test_source stop_codon 6915 6917 . - . Parent=AT1G01020.1 +Chr1 test_source CDS 6915 7069 . - 2 ID=CDS1;Parent=AT1G01020.1 +Chr1 test_source CDS 7157 7232 . - 0 ID=CDS1;Parent=AT1G01020.1 +Chr1 test_source exon 7157 7232 . - . Parent=AT1G01020.1 +Chr1 test_source intron 7233 7383 . - . Parent=AT1G01020.1 +Chr1 test_source CDS 7384 7450 . - 1 ID=CDS1;Parent=AT1G01020.1 +Chr1 test_source exon 7384 7450 . - . Parent=AT1G01020.1 +Chr1 test_source CDS 7564 7649 . - 0 ID=CDS1;Parent=AT1G01020.1 +Chr1 test_source exon 7564 7649 . - . Parent=AT1G01020.1 +Chr1 test_source CDS 7762 7835 . - 2 ID=CDS1;Parent=AT1G01020.1 +Chr1 test_source exon 7762 7835 . - . Parent=AT1G01020.1 +Chr1 test_source CDS 7942 7987 . - 0 ID=CDS1;Parent=AT1G01020.1 +Chr1 test_source exon 7942 7987 . - . Parent=AT1G01020.1 +Chr1 test_source CDS 8236 8325 . - 0 ID=CDS1;Parent=AT1G01020.1 +Chr1 test_source exon 8236 8325 . - . Parent=AT1G01020.1 +Chr1 test_source CDS 8417 8464 . - 0 ID=CDS1;Parent=AT1G01020.1 +Chr1 test_source exon 8417 8464 . - . Parent=AT1G01020.1 +Chr1 test_source CDS 8571 8666 . - 0 ID=CDS1;Parent=AT1G01020.1 +Chr1 test_source exon 8571 8737 . - . Parent=AT1G01020.1 +Chr1 test_source start_codon 8664 8666 . - . Parent=AT1G01020.1 +Chr1 test_source five_prime_UTR 8667 8737 . - . Parent=AT1G01020.1 +Chr1 test_source mRNA 6790 8737 . - . ID=AT1G01020.2;Parent=AT1G01020;Name=AT1G01020.2;index=1 +Chr1 test_source three_prime_UTR 6790 7069 . - . Parent=AT1G01020.2 +Chr1 test_source exon 6790 7069 . - . Parent=AT1G01020.2 +Chr1 test_source intron 7070 7156 . - . Parent=AT1G01020.1,AT1G01020.2 +Chr1 test_source three_prime_UTR 7157 7314 . - . Parent=AT1G01020.2 +Chr1 test_source exon 7157 7450 . - . Parent=AT1G01020.2 +Chr1 test_source stop_codon 7315 7317 . - . Parent=AT1G01020.2 +Chr1 test_source CDS 7315 7450 . - 1 ID=CDS2;Parent=AT1G01020.2 +Chr1 test_source intron 7451 7563 . - . Parent=AT1G01020.1,AT1G01020.2 +Chr1 test_source CDS 7564 7649 . - 0 ID=CDS2;Parent=AT1G01020.2 +Chr1 test_source exon 7564 7649 . - . Parent=AT1G01020.2 +Chr1 test_source intron 7650 7761 . - . Parent=AT1G01020.1,AT1G01020.2 +Chr1 test_source CDS 7762 7835 . - 2 ID=CDS2;Parent=AT1G01020.2 +Chr1 test_source exon 7762 7835 . - . Parent=AT1G01020.2 +Chr1 test_source intron 7836 7941 . - . Parent=AT1G01020.1,AT1G01020.2 +Chr1 test_source CDS 7942 7987 . - 0 ID=CDS2;Parent=AT1G01020.2 +Chr1 test_source exon 7942 7987 . - . Parent=AT1G01020.2 +Chr1 test_source intron 7988 8235 . - . Parent=AT1G01020.1,AT1G01020.2 +Chr1 test_source CDS 8236 8325 . - 0 ID=CDS2;Parent=AT1G01020.2 +Chr1 test_source exon 8236 8325 . - . Parent=AT1G01020.2 +Chr1 test_source intron 8326 8416 . - . Parent=AT1G01020.1,AT1G01020.2 +Chr1 test_source CDS 8417 8464 . - 0 ID=CDS2;Parent=AT1G01020.2 +Chr1 test_source exon 8417 8464 . - . Parent=AT1G01020.2 +Chr1 test_source intron 8465 8570 . - . Parent=AT1G01020.1,AT1G01020.2 +Chr1 test_source CDS 8571 8666 . - 0 ID=CDS2;Parent=AT1G01020.2 +Chr1 test_source exon 8571 8737 . - . Parent=AT1G01020.2 +Chr1 test_source start_codon 8664 8666 . - . Parent=AT1G01020.2 +Chr1 test_source five_prime_UTR 8667 8737 . - . Parent=AT1G01020.2 +### +Chr1 test_source gene 11649 13714 . - . ID=AT1G01030;Note=protein_coding_gene;Name=AT1G01030 +Chr1 test_source mRNA 11649 13714 . - . ID=AT1G01030.1;Parent=AT1G01030;Name=AT1G01030.1;index=1 +Chr1 test_source three_prime_UTR 11649 11863 . - . Parent=AT1G01030.1 +Chr1 test_source exon 11649 13173 . - . Parent=AT1G01030.1 +Chr1 test_source stop_codon 11864 11866 . - . Parent=AT1G01030.1 +Chr1 test_source CDS 11864 12940 . - 0 Parent=AT1G01030.1 +Chr1 test_source start_codon 12938 12940 . - . Parent=AT1G01030.1 +Chr1 test_source five_prime_UTR 12941 13173 . - . Parent=AT1G01030.1 +Chr1 test_source intron 13174 13334 . - . Parent=AT1G01030.1 +Chr1 test_source five_prime_UTR 13335 13714 . - . Parent=AT1G01030.1 +Chr1 test_source exon 13335 13714 . - . Parent=AT1G01030.1 +### +Chr1 test_source gene 23146 31227 . + . ID=AT1G01040;Note=protein_coding_gene;Name=AT1G01040 +Chr1 test_source mRNA 23146 31227 . + . ID=AT1G01040.1;Parent=AT1G01040;Name=AT1G01040.1;index=1 +Chr1 test_source five_prime_UTR 23146 23518 . + . Parent=AT1G01040.1 +Chr1 test_source exon 23146 24451 . + . Parent=AT1G01040.1 +Chr1 test_source start_codon 23519 23521 . + . Parent=AT1G01040.1 +Chr1 test_source CDS 23519 24451 . + 0 ID=CDS3;Parent=AT1G01040.1 +Chr1 test_source intron 24452 24541 . + . Parent=AT1G01040.1 +Chr1 test_source exon 24542 24655 . + . Parent=AT1G01040.1 +Chr1 test_source CDS 24542 24655 . + 0 ID=CDS3;Parent=AT1G01040.1 +Chr1 test_source intron 24656 24751 . + . Parent=AT1G01040.1 +Chr1 test_source exon 24752 24962 . + . Parent=AT1G01040.1 +Chr1 test_source CDS 24752 24962 . + 0 ID=CDS3;Parent=AT1G01040.1 +Chr1 test_source intron 24963 25040 . + . Parent=AT1G01040.1 +Chr1 test_source exon 25041 25435 . + . Parent=AT1G01040.1 +Chr1 test_source CDS 25041 25435 . + 2 ID=CDS3;Parent=AT1G01040.1 +Chr1 test_source intron 25436 25523 . + . Parent=AT1G01040.1 +Chr1 test_source exon 25524 25743 . + . Parent=AT1G01040.1 +Chr1 test_source CDS 25524 25743 . + 0 ID=CDS3;Parent=AT1G01040.1 +Chr1 test_source intron 25744 25824 . + . Parent=AT1G01040.1 +Chr1 test_source exon 25825 25997 . + . Parent=AT1G01040.1 +Chr1 test_source CDS 25825 25997 . + 2 ID=CDS3;Parent=AT1G01040.1 +Chr1 test_source intron 25998 26080 . + . Parent=AT1G01040.1 +Chr1 test_source exon 26081 26203 . + . Parent=AT1G01040.1 +Chr1 test_source CDS 26081 26203 . + 0 ID=CDS3;Parent=AT1G01040.1 +Chr1 test_source intron 26204 26291 . + . Parent=AT1G01040.1 +Chr1 test_source exon 26292 26452 . + . Parent=AT1G01040.1 +Chr1 test_source CDS 26292 26452 . + 0 ID=CDS3;Parent=AT1G01040.1 +Chr1 test_source intron 26453 26542 . + . Parent=AT1G01040.1 +Chr1 test_source exon 26543 26776 . + . Parent=AT1G01040.1 +Chr1 test_source CDS 26543 26776 . + 1 ID=CDS3;Parent=AT1G01040.1 +Chr1 test_source intron 26777 26861 . + . Parent=AT1G01040.1 +Chr1 test_source exon 26862 27012 . + . Parent=AT1G01040.1 +Chr1 test_source CDS 26862 27012 . + 1 ID=CDS3;Parent=AT1G01040.1 +Chr1 test_source intron 27013 27098 . + . Parent=AT1G01040.1 +Chr1 test_source exon 27099 27281 . + . Parent=AT1G01040.1 +Chr1 test_source CDS 27099 27281 . + 0 ID=CDS3;Parent=AT1G01040.1 +Chr1 test_source intron 27282 27371 . + . Parent=AT1G01040.1 +Chr1 test_source exon 27372 27533 . + . Parent=AT1G01040.1 +Chr1 test_source CDS 27372 27533 . + 0 ID=CDS3;Parent=AT1G01040.1 +Chr1 test_source stop_codon 27531 27533 . + . Parent=AT1G01040.1 +### diff -r 000000000000 -r c4ac24510b55 test-data/canon-output_test3.gff3 --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/canon-output_test3.gff3 Sun Jan 03 14:58:58 2021 +0000 @@ -0,0 +1,136 @@ +##gff-version 3 +##sequence-region Chr1 1 30427671 +Chr1 TAIR10 gene 3631 5899 . + . ID=gene1;Note=protein_coding_gene;Name=AT1G01010 +Chr1 TAIR10 mRNA 3631 5899 . + . ID=mRNA1;Parent=gene1;Name=AT1G01010.1;index=1 +Chr1 TAIR10 five_prime_UTR 3631 3759 . + . Parent=mRNA1 +Chr1 TAIR10 exon 3631 3913 . + . Parent=mRNA1 +Chr1 . start_codon 3760 3762 . + . Parent=mRNA1 +Chr1 TAIR10 CDS 3760 3913 . + 0 ID=CDS1;Parent=mRNA1 +Chr1 . intron 3914 3995 . + . Parent=mRNA1 +Chr1 TAIR10 exon 3996 4276 . + . Parent=mRNA1 +Chr1 TAIR10 CDS 3996 4276 . + 2 ID=CDS1;Parent=mRNA1 +Chr1 . intron 4277 4485 . + . Parent=mRNA1 +Chr1 TAIR10 exon 4486 4605 . + . Parent=mRNA1 +Chr1 TAIR10 CDS 4486 4605 . + 0 ID=CDS1;Parent=mRNA1 +Chr1 . intron 4606 4705 . + . Parent=mRNA1 +Chr1 TAIR10 exon 4706 5095 . + . Parent=mRNA1 +Chr1 TAIR10 CDS 4706 5095 . + 0 ID=CDS1;Parent=mRNA1 +Chr1 . intron 5096 5173 . + . Parent=mRNA1 +Chr1 TAIR10 exon 5174 5326 . + . Parent=mRNA1 +Chr1 TAIR10 CDS 5174 5326 . + 0 ID=CDS1;Parent=mRNA1 +Chr1 . intron 5327 5438 . + . Parent=mRNA1 +Chr1 TAIR10 CDS 5439 5630 . + 0 ID=CDS1;Parent=mRNA1 +Chr1 TAIR10 exon 5439 5899 . + . Parent=mRNA1 +Chr1 . stop_codon 5628 5630 . + . Parent=mRNA1 +Chr1 TAIR10 three_prime_UTR 5631 5899 . + . Parent=mRNA1 +### +Chr1 TAIR10 gene 5928 8737 . - . ID=gene2;Note=protein_coding_gene;Name=AT1G01020 +Chr1 TAIR10 mRNA 5928 8737 . - . ID=mRNA2;Parent=gene2;Name=AT1G01020.1;index=1 +Chr1 TAIR10 three_prime_UTR 5928 6263 . - . Parent=mRNA2 +Chr1 TAIR10 exon 5928 6263 . - . Parent=mRNA2 +Chr1 . intron 6264 6436 . - . Parent=mRNA2 +Chr1 TAIR10 three_prime_UTR 6437 6914 . - . Parent=mRNA2 +Chr1 TAIR10 exon 6437 7069 . - . Parent=mRNA2 +Chr1 . stop_codon 6915 6917 . - . Parent=mRNA2 +Chr1 TAIR10 CDS 6915 7069 . - 2 ID=CDS2;Parent=mRNA2 +Chr1 TAIR10 CDS 7157 7232 . - 0 ID=CDS2;Parent=mRNA2 +Chr1 TAIR10 exon 7157 7232 . - . Parent=mRNA2 +Chr1 . intron 7233 7383 . - . Parent=mRNA2 +Chr1 TAIR10 CDS 7384 7450 . - 1 ID=CDS2;Parent=mRNA2 +Chr1 TAIR10 exon 7384 7450 . - . Parent=mRNA2 +Chr1 TAIR10 CDS 7564 7649 . - 0 ID=CDS2;Parent=mRNA2 +Chr1 TAIR10 exon 7564 7649 . - . Parent=mRNA2 +Chr1 TAIR10 CDS 7762 7835 . - 2 ID=CDS2;Parent=mRNA2 +Chr1 TAIR10 exon 7762 7835 . - . Parent=mRNA2 +Chr1 TAIR10 CDS 7942 7987 . - 0 ID=CDS2;Parent=mRNA2 +Chr1 TAIR10 exon 7942 7987 . - . Parent=mRNA2 +Chr1 TAIR10 CDS 8236 8325 . - 0 ID=CDS2;Parent=mRNA2 +Chr1 TAIR10 exon 8236 8325 . - . Parent=mRNA2 +Chr1 TAIR10 CDS 8417 8464 . - 0 ID=CDS2;Parent=mRNA2 +Chr1 TAIR10 exon 8417 8464 . - . Parent=mRNA2 +Chr1 TAIR10 CDS 8571 8666 . - 0 ID=CDS2;Parent=mRNA2 +Chr1 TAIR10 exon 8571 8737 . - . Parent=mRNA2 +Chr1 . start_codon 8664 8666 . - . Parent=mRNA2 +Chr1 TAIR10 five_prime_UTR 8667 8737 . - . Parent=mRNA2 +Chr1 TAIR10 mRNA 6790 8737 . - . ID=mRNA3;Parent=gene2;Name=AT1G01020.2;index=1 +Chr1 TAIR10 three_prime_UTR 6790 7069 . - . Parent=mRNA3 +Chr1 TAIR10 exon 6790 7069 . - . Parent=mRNA3 +Chr1 . intron 7070 7156 . - . Parent=mRNA2,mRNA3 +Chr1 TAIR10 three_prime_UTR 7157 7314 . - . Parent=mRNA3 +Chr1 TAIR10 exon 7157 7450 . - . Parent=mRNA3 +Chr1 . stop_codon 7315 7317 . - . Parent=mRNA3 +Chr1 TAIR10 CDS 7315 7450 . - 1 ID=CDS3;Parent=mRNA3 +Chr1 . intron 7451 7563 . - . Parent=mRNA2,mRNA3 +Chr1 TAIR10 CDS 7564 7649 . - 0 ID=CDS3;Parent=mRNA3 +Chr1 TAIR10 exon 7564 7649 . - . Parent=mRNA3 +Chr1 . intron 7650 7761 . - . Parent=mRNA2,mRNA3 +Chr1 TAIR10 CDS 7762 7835 . - 2 ID=CDS3;Parent=mRNA3 +Chr1 TAIR10 exon 7762 7835 . - . Parent=mRNA3 +Chr1 . intron 7836 7941 . - . Parent=mRNA2,mRNA3 +Chr1 TAIR10 CDS 7942 7987 . - 0 ID=CDS3;Parent=mRNA3 +Chr1 TAIR10 exon 7942 7987 . - . Parent=mRNA3 +Chr1 . intron 7988 8235 . - . Parent=mRNA2,mRNA3 +Chr1 TAIR10 CDS 8236 8325 . - 0 ID=CDS3;Parent=mRNA3 +Chr1 TAIR10 exon 8236 8325 . - . Parent=mRNA3 +Chr1 . intron 8326 8416 . - . Parent=mRNA2,mRNA3 +Chr1 TAIR10 CDS 8417 8464 . - 0 ID=CDS3;Parent=mRNA3 +Chr1 TAIR10 exon 8417 8464 . - . Parent=mRNA3 +Chr1 . intron 8465 8570 . - . Parent=mRNA2,mRNA3 +Chr1 TAIR10 CDS 8571 8666 . - 0 ID=CDS3;Parent=mRNA3 +Chr1 TAIR10 exon 8571 8737 . - . Parent=mRNA3 +Chr1 . start_codon 8664 8666 . - . Parent=mRNA3 +Chr1 TAIR10 five_prime_UTR 8667 8737 . - . Parent=mRNA3 +### +Chr1 TAIR10 gene 11649 13714 . - . ID=gene3;Note=protein_coding_gene;Name=AT1G01030 +Chr1 TAIR10 mRNA 11649 13714 . - . ID=mRNA4;Parent=gene3;Name=AT1G01030.1;index=1 +Chr1 TAIR10 three_prime_UTR 11649 11863 . - . Parent=mRNA4 +Chr1 TAIR10 exon 11649 13173 . - . Parent=mRNA4 +Chr1 . stop_codon 11864 11866 . - . Parent=mRNA4 +Chr1 TAIR10 CDS 11864 12940 . - 0 Parent=mRNA4 +Chr1 . start_codon 12938 12940 . - . Parent=mRNA4 +Chr1 TAIR10 five_prime_UTR 12941 13173 . - . Parent=mRNA4 +Chr1 . intron 13174 13334 . - . Parent=mRNA4 +Chr1 TAIR10 five_prime_UTR 13335 13714 . - . Parent=mRNA4 +Chr1 TAIR10 exon 13335 13714 . - . Parent=mRNA4 +### +Chr1 TAIR10 gene 23146 31227 . + . ID=gene4;Note=protein_coding_gene;Name=AT1G01040 +Chr1 TAIR10 mRNA 23146 31227 . + . ID=mRNA5;Parent=gene4;Name=AT1G01040.1;index=1 +Chr1 TAIR10 five_prime_UTR 23146 23518 . + . Parent=mRNA5 +Chr1 TAIR10 exon 23146 24451 . + . Parent=mRNA5 +Chr1 . start_codon 23519 23521 . + . Parent=mRNA5 +Chr1 TAIR10 CDS 23519 24451 . + 0 ID=CDS4;Parent=mRNA5 +Chr1 . intron 24452 24541 . + . Parent=mRNA5 +Chr1 TAIR10 exon 24542 24655 . + . Parent=mRNA5 +Chr1 TAIR10 CDS 24542 24655 . + 0 ID=CDS4;Parent=mRNA5 +Chr1 . intron 24656 24751 . + . Parent=mRNA5 +Chr1 TAIR10 exon 24752 24962 . + . Parent=mRNA5 +Chr1 TAIR10 CDS 24752 24962 . + 0 ID=CDS4;Parent=mRNA5 +Chr1 . intron 24963 25040 . + . Parent=mRNA5 +Chr1 TAIR10 exon 25041 25435 . + . Parent=mRNA5 +Chr1 TAIR10 CDS 25041 25435 . + 2 ID=CDS4;Parent=mRNA5 +Chr1 . intron 25436 25523 . + . Parent=mRNA5 +Chr1 TAIR10 exon 25524 25743 . + . Parent=mRNA5 +Chr1 TAIR10 CDS 25524 25743 . + 0 ID=CDS4;Parent=mRNA5 +Chr1 . intron 25744 25824 . + . Parent=mRNA5 +Chr1 TAIR10 exon 25825 25997 . + . Parent=mRNA5 +Chr1 TAIR10 CDS 25825 25997 . + 2 ID=CDS4;Parent=mRNA5 +Chr1 . intron 25998 26080 . + . Parent=mRNA5 +Chr1 TAIR10 exon 26081 26203 . + . Parent=mRNA5 +Chr1 TAIR10 CDS 26081 26203 . + 0 ID=CDS4;Parent=mRNA5 +Chr1 . intron 26204 26291 . + . Parent=mRNA5 +Chr1 TAIR10 exon 26292 26452 . + . Parent=mRNA5 +Chr1 TAIR10 CDS 26292 26452 . + 0 ID=CDS4;Parent=mRNA5 +Chr1 . intron 26453 26542 . + . Parent=mRNA5 +Chr1 TAIR10 exon 26543 26776 . + . Parent=mRNA5 +Chr1 TAIR10 CDS 26543 26776 . + 1 ID=CDS4;Parent=mRNA5 +Chr1 . intron 26777 26861 . + . Parent=mRNA5 +Chr1 TAIR10 exon 26862 27012 . + . Parent=mRNA5 +Chr1 TAIR10 CDS 26862 27012 . + 1 ID=CDS4;Parent=mRNA5 +Chr1 . intron 27013 27098 . + . Parent=mRNA5 +Chr1 TAIR10 exon 27099 27281 . + . Parent=mRNA5 +Chr1 TAIR10 CDS 27099 27281 . + 0 ID=CDS4;Parent=mRNA5 +Chr1 . intron 27282 27371 . + . Parent=mRNA5 +Chr1 TAIR10 exon 27372 27533 . + . Parent=mRNA5 +Chr1 TAIR10 CDS 27372 27533 . + 0 ID=CDS4;Parent=mRNA5 +Chr1 . stop_codon 27531 27533 . + . Parent=mRNA5 +### diff -r 000000000000 -r c4ac24510b55 test-data/gaeval_output_test1.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/gaeval_output_test1.txt Sun Jan 03 14:58:58 2021 +0000 @@ -0,0 +1,143 @@ +##gff-version 3 +##sequence-region Chr1 1 30427671 +Chr1 TAIR10 chromosome 1 30427671 . . . ID=Chr1;Name=Chr1 +### +Chr1 TAIR10 gene 3631 5899 . + . ID=AT1G01010;Note=protein_coding_gene;Name=AT1G01010 +Chr1 TAIR10 mRNA 3631 5899 . + . ID=AT1G01010.1;Parent=AT1G01010;Name=AT1G01010.1;index=1;gaeval_coverage=0.000;gaeval_integrity=0.082 +Chr1 TAIR10 five_prime_UTR 3631 3759 . + . Parent=AT1G01010.1 +Chr1 TAIR10 exon 3631 3913 . + . Parent=AT1G01010.1 +Chr1 AEGeAn::GAEVAL start_codon 3760 3762 . + . Parent=AT1G01010.1 +Chr1 AEGeAn::GAEVAL intron 3914 3995 . + . Parent=AT1G01010.1 +Chr1 TAIR10 exon 3996 4276 . + . Parent=AT1G01010.1 +Chr1 AEGeAn::GAEVAL intron 4277 4485 . + . Parent=AT1G01010.1 +Chr1 TAIR10 exon 4486 4605 . + . Parent=AT1G01010.1 +Chr1 AEGeAn::GAEVAL intron 4606 4705 . + . Parent=AT1G01010.1 +Chr1 TAIR10 exon 4706 5095 . + . Parent=AT1G01010.1 +Chr1 AEGeAn::GAEVAL intron 5096 5173 . + . Parent=AT1G01010.1 +Chr1 TAIR10 exon 5174 5326 . + . Parent=AT1G01010.1 +Chr1 AEGeAn::GAEVAL intron 5327 5438 . + . Parent=AT1G01010.1 +Chr1 TAIR10 exon 5439 5899 . + . Parent=AT1G01010.1 +Chr1 AEGeAn::GAEVAL stop_codon 5628 5630 . + . Parent=AT1G01010.1 +Chr1 TAIR10 three_prime_UTR 5631 5899 . + . Parent=AT1G01010.1 +Chr1 TAIR10 protein 3760 5630 . + . ID=AT1G01010.1-Protein;Name=AT1G01010.1;Derives_from=AT1G01010.1 +Chr1 TAIR10 CDS 3760 3913 . + 0 ID=CDS0;Parent=AT1G01010.1,AT1G01010.1-Protein +Chr1 TAIR10 CDS 3996 4276 . + 2 ID=CDS0;Parent=AT1G01010.1,AT1G01010.1-Protein +Chr1 TAIR10 CDS 4486 4605 . + 0 ID=CDS0;Parent=AT1G01010.1,AT1G01010.1-Protein +Chr1 TAIR10 CDS 4706 5095 . + 0 ID=CDS0;Parent=AT1G01010.1,AT1G01010.1-Protein +Chr1 TAIR10 CDS 5174 5326 . + 0 ID=CDS0;Parent=AT1G01010.1,AT1G01010.1-Protein +Chr1 TAIR10 CDS 5439 5630 . + 0 ID=CDS0;Parent=AT1G01010.1,AT1G01010.1-Protein +### +Chr1 TAIR10 gene 5928 8737 . - . ID=AT1G01020;Note=protein_coding_gene;Name=AT1G01020 +Chr1 TAIR10 mRNA 5928 8737 . - . ID=AT1G01020.1;Parent=AT1G01020;Name=AT1G01020.1;index=1;gaeval_coverage=0.000;gaeval_integrity=0.068 +Chr1 TAIR10 three_prime_UTR 5928 6263 . - . Parent=AT1G01020.1 +Chr1 TAIR10 exon 5928 6263 . - . Parent=AT1G01020.1 +Chr1 AEGeAn::GAEVAL intron 6264 6436 . - . Parent=AT1G01020.1 +Chr1 TAIR10 three_prime_UTR 6437 6914 . - . Parent=AT1G01020.1 +Chr1 TAIR10 exon 6437 7069 . - . Parent=AT1G01020.1 +Chr1 AEGeAn::GAEVAL stop_codon 6915 6917 . - . Parent=AT1G01020.1 +Chr1 TAIR10 exon 7157 7232 . - . Parent=AT1G01020.1 +Chr1 AEGeAn::GAEVAL intron 7233 7383 . - . Parent=AT1G01020.1 +Chr1 TAIR10 exon 7384 7450 . - . Parent=AT1G01020.1 +Chr1 TAIR10 exon 7564 7649 . - . Parent=AT1G01020.1 +Chr1 TAIR10 exon 7762 7835 . - . Parent=AT1G01020.1 +Chr1 TAIR10 exon 7942 7987 . - . Parent=AT1G01020.1 +Chr1 TAIR10 exon 8236 8325 . - . Parent=AT1G01020.1 +Chr1 TAIR10 exon 8417 8464 . - . Parent=AT1G01020.1 +Chr1 TAIR10 exon 8571 8737 . - . Parent=AT1G01020.1 +Chr1 AEGeAn::GAEVAL start_codon 8664 8666 . - . Parent=AT1G01020.1 +Chr1 TAIR10 five_prime_UTR 8667 8737 . - . Parent=AT1G01020.1 +Chr1 TAIR10 mRNA 6790 8737 . - . ID=AT1G01020.2;Parent=AT1G01020;Name=AT1G01020.2;index=1;gaeval_coverage=0.000;gaeval_integrity=0.068 +Chr1 TAIR10 three_prime_UTR 6790 7069 . - . Parent=AT1G01020.2 +Chr1 TAIR10 exon 6790 7069 . - . Parent=AT1G01020.2 +Chr1 AEGeAn::GAEVAL intron 7070 7156 . - . Parent=AT1G01020.1,AT1G01020.2 +Chr1 TAIR10 three_prime_UTR 7157 7314 . - . Parent=AT1G01020.2 +Chr1 TAIR10 exon 7157 7450 . - . Parent=AT1G01020.2 +Chr1 AEGeAn::GAEVAL stop_codon 7315 7317 . - . Parent=AT1G01020.2 +Chr1 AEGeAn::GAEVAL intron 7451 7563 . - . Parent=AT1G01020.1,AT1G01020.2 +Chr1 TAIR10 exon 7564 7649 . - . Parent=AT1G01020.2 +Chr1 AEGeAn::GAEVAL intron 7650 7761 . - . Parent=AT1G01020.1,AT1G01020.2 +Chr1 TAIR10 exon 7762 7835 . - . Parent=AT1G01020.2 +Chr1 AEGeAn::GAEVAL intron 7836 7941 . - . Parent=AT1G01020.1,AT1G01020.2 +Chr1 TAIR10 exon 7942 7987 . - . Parent=AT1G01020.2 +Chr1 AEGeAn::GAEVAL intron 7988 8235 . - . Parent=AT1G01020.1,AT1G01020.2 +Chr1 TAIR10 exon 8236 8325 . - . Parent=AT1G01020.2 +Chr1 AEGeAn::GAEVAL intron 8326 8416 . - . Parent=AT1G01020.1,AT1G01020.2 +Chr1 TAIR10 exon 8417 8464 . - . Parent=AT1G01020.2 +Chr1 AEGeAn::GAEVAL intron 8465 8570 . - . Parent=AT1G01020.1,AT1G01020.2 +Chr1 TAIR10 exon 8571 8737 . - . Parent=AT1G01020.2 +Chr1 AEGeAn::GAEVAL start_codon 8664 8666 . - . Parent=AT1G01020.2 +Chr1 TAIR10 five_prime_UTR 8667 8737 . - . Parent=AT1G01020.2 +Chr1 TAIR10 protein 6915 8666 . - . ID=AT1G01020.1-Protein;Name=AT1G01020.1;Derives_from=AT1G01020.1 +Chr1 TAIR10 CDS 6915 7069 . - 2 ID=CDS1;Parent=AT1G01020.1,AT1G01020.1-Protein +Chr1 TAIR10 CDS 7157 7232 . - 0 ID=CDS1;Parent=AT1G01020.1,AT1G01020.1-Protein +Chr1 TAIR10 CDS 7384 7450 . - 1 ID=CDS1;Parent=AT1G01020.1,AT1G01020.1-Protein +Chr1 TAIR10 CDS 7564 7649 . - 0 ID=CDS1;Parent=AT1G01020.1,AT1G01020.1-Protein +Chr1 TAIR10 CDS 7762 7835 . - 2 ID=CDS1;Parent=AT1G01020.1,AT1G01020.1-Protein +Chr1 TAIR10 CDS 7942 7987 . - 0 ID=CDS1;Parent=AT1G01020.1,AT1G01020.1-Protein +Chr1 TAIR10 CDS 8236 8325 . - 0 ID=CDS1;Parent=AT1G01020.1,AT1G01020.1-Protein +Chr1 TAIR10 CDS 8417 8464 . - 0 ID=CDS1;Parent=AT1G01020.1,AT1G01020.1-Protein +Chr1 TAIR10 CDS 8571 8666 . - 0 ID=CDS1;Parent=AT1G01020.1,AT1G01020.1-Protein +Chr1 TAIR10 protein 7315 8666 . - . ID=AT1G01020.2-Protein;Name=AT1G01020.2;Derives_from=AT1G01020.2 +Chr1 TAIR10 CDS 7315 7450 . - 1 ID=CDS2;Parent=AT1G01020.2,AT1G01020.2-Protein +Chr1 TAIR10 CDS 7564 7649 . - 0 ID=CDS2;Parent=AT1G01020.2,AT1G01020.2-Protein +Chr1 TAIR10 CDS 7762 7835 . - 2 ID=CDS2;Parent=AT1G01020.2,AT1G01020.2-Protein +Chr1 TAIR10 CDS 7942 7987 . - 0 ID=CDS2;Parent=AT1G01020.2,AT1G01020.2-Protein +Chr1 TAIR10 CDS 8236 8325 . - 0 ID=CDS2;Parent=AT1G01020.2,AT1G01020.2-Protein +Chr1 TAIR10 CDS 8417 8464 . - 0 ID=CDS2;Parent=AT1G01020.2,AT1G01020.2-Protein +Chr1 TAIR10 CDS 8571 8666 . - 0 ID=CDS2;Parent=AT1G01020.2,AT1G01020.2-Protein +### +Chr1 TAIR10 gene 11649 13714 . - . ID=AT1G01030;Note=protein_coding_gene;Name=AT1G01030 +Chr1 TAIR10 mRNA 11649 13714 . - . ID=AT1G01030.1;Parent=AT1G01030;Name=AT1G01030.1;index=1;gaeval_coverage=0.000;gaeval_integrity=0.100 +Chr1 TAIR10 three_prime_UTR 11649 11863 . - . Parent=AT1G01030.1 +Chr1 TAIR10 exon 11649 13173 . - . Parent=AT1G01030.1 +Chr1 AEGeAn::GAEVAL stop_codon 11864 11866 . - . Parent=AT1G01030.1 +Chr1 AEGeAn::GAEVAL start_codon 12938 12940 . - . Parent=AT1G01030.1 +Chr1 TAIR10 five_prime_UTR 12941 13173 . - . Parent=AT1G01030.1 +Chr1 AEGeAn::GAEVAL intron 13174 13334 . - . Parent=AT1G01030.1 +Chr1 TAIR10 five_prime_UTR 13335 13714 . - . Parent=AT1G01030.1 +Chr1 TAIR10 exon 13335 13714 . - . Parent=AT1G01030.1 +Chr1 TAIR10 protein 11864 12940 . - . ID=AT1G01030.1-Protein;Name=AT1G01030.1;Derives_from=AT1G01030.1 +Chr1 TAIR10 CDS 11864 12940 . - 0 Parent=AT1G01030.1,AT1G01030.1-Protein +### +Chr1 TAIR10 gene 23146 31227 . + . ID=AT1G01040;Note=protein_coding_gene;Name=AT1G01040 +Chr1 TAIR10 mRNA 23146 31227 . + . ID=AT1G01040.1;Parent=AT1G01040;Name=AT1G01040.1;index=1;gaeval_coverage=0.000;gaeval_integrity=0.050 +Chr1 TAIR10 five_prime_UTR 23146 23518 . + . Parent=AT1G01040.1 +Chr1 TAIR10 exon 23146 24451 . + . Parent=AT1G01040.1 +Chr1 AEGeAn::GAEVAL start_codon 23519 23521 . + . Parent=AT1G01040.1 +Chr1 AEGeAn::GAEVAL intron 24452 24541 . + . Parent=AT1G01040.1 +Chr1 TAIR10 exon 24542 24655 . + . Parent=AT1G01040.1 +Chr1 AEGeAn::GAEVAL intron 24656 24751 . + . Parent=AT1G01040.1 +Chr1 TAIR10 exon 24752 24962 . + . Parent=AT1G01040.1 +Chr1 AEGeAn::GAEVAL intron 24963 25040 . + . Parent=AT1G01040.1 +Chr1 TAIR10 exon 25041 25435 . + . Parent=AT1G01040.1 +Chr1 AEGeAn::GAEVAL intron 25436 25523 . + . Parent=AT1G01040.1 +Chr1 TAIR10 exon 25524 25743 . + . Parent=AT1G01040.1 +Chr1 AEGeAn::GAEVAL intron 25744 25824 . + . Parent=AT1G01040.1 +Chr1 TAIR10 exon 25825 25997 . + . Parent=AT1G01040.1 +Chr1 AEGeAn::GAEVAL intron 25998 26080 . + . Parent=AT1G01040.1 +Chr1 TAIR10 exon 26081 26203 . + . Parent=AT1G01040.1 +Chr1 AEGeAn::GAEVAL intron 26204 26291 . + . Parent=AT1G01040.1 +Chr1 TAIR10 exon 26292 26452 . + . Parent=AT1G01040.1 +Chr1 AEGeAn::GAEVAL intron 26453 26542 . + . Parent=AT1G01040.1 +Chr1 TAIR10 exon 26543 26776 . + . Parent=AT1G01040.1 +Chr1 AEGeAn::GAEVAL intron 26777 26861 . + . Parent=AT1G01040.1 +Chr1 TAIR10 exon 26862 27012 . + . Parent=AT1G01040.1 +Chr1 AEGeAn::GAEVAL intron 27013 27098 . + . Parent=AT1G01040.1 +Chr1 TAIR10 exon 27099 27281 . + . Parent=AT1G01040.1 +Chr1 AEGeAn::GAEVAL intron 27282 27371 . + . Parent=AT1G01040.1 +Chr1 TAIR10 exon 27372 27533 . + . Parent=AT1G01040.1 +Chr1 AEGeAn::GAEVAL stop_codon 27531 27533 . + . Parent=AT1G01040.1 +Chr1 TAIR10 protein 23519 31079 . + . ID=AT1G01040.1-Protein;Name=AT1G01040.1;Derives_from=AT1G01040.1 +Chr1 TAIR10 CDS 23519 24451 . + 0 ID=CDS3;Parent=AT1G01040.1,AT1G01040.1-Protein +Chr1 TAIR10 CDS 24542 24655 . + 0 ID=CDS3;Parent=AT1G01040.1,AT1G01040.1-Protein +Chr1 TAIR10 CDS 24752 24962 . + 0 ID=CDS3;Parent=AT1G01040.1,AT1G01040.1-Protein +Chr1 TAIR10 CDS 25041 25435 . + 2 ID=CDS3;Parent=AT1G01040.1,AT1G01040.1-Protein +Chr1 TAIR10 CDS 25524 25743 . + 0 ID=CDS3;Parent=AT1G01040.1,AT1G01040.1-Protein +Chr1 TAIR10 CDS 25825 25997 . + 2 ID=CDS3;Parent=AT1G01040.1,AT1G01040.1-Protein +Chr1 TAIR10 CDS 26081 26203 . + 0 ID=CDS3;Parent=AT1G01040.1,AT1G01040.1-Protein +Chr1 TAIR10 CDS 26292 26452 . + 0 ID=CDS3;Parent=AT1G01040.1,AT1G01040.1-Protein +Chr1 TAIR10 CDS 26543 26776 . + 1 ID=CDS3;Parent=AT1G01040.1,AT1G01040.1-Protein +Chr1 TAIR10 CDS 26862 27012 . + 1 ID=CDS3;Parent=AT1G01040.1,AT1G01040.1-Protein +Chr1 TAIR10 CDS 27099 27281 . + 0 ID=CDS3;Parent=AT1G01040.1,AT1G01040.1-Protein +Chr1 TAIR10 CDS 27372 27533 . + 0 ID=CDS3;Parent=AT1G01040.1,AT1G01040.1-Protein +### diff -r 000000000000 -r c4ac24510b55 test-data/gaeval_output_test2.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/gaeval_output_test2.txt Sun Jan 03 14:58:58 2021 +0000 @@ -0,0 +1,143 @@ +##gff-version 3 +##sequence-region Chr1 1 30427671 +Chr1 TAIR10 chromosome 1 30427671 . . . ID=Chr1;Name=Chr1 +### +Chr1 TAIR10 gene 3631 5899 . + . ID=AT1G01010;Note=protein_coding_gene;Name=AT1G01010 +Chr1 TAIR10 mRNA 3631 5899 . + . ID=AT1G01010.1;Parent=AT1G01010;Name=AT1G01010.1;index=1;gaeval_coverage=0.000;gaeval_integrity=0.082 +Chr1 TAIR10 five_prime_UTR 3631 3759 . + . Parent=AT1G01010.1 +Chr1 TAIR10 exon 3631 3913 . + . Parent=AT1G01010.1 +Chr1 AEGeAn::GAEVAL start_codon 3760 3762 . + . Parent=AT1G01010.1 +Chr1 AEGeAn::GAEVAL intron 3914 3995 . + . Parent=AT1G01010.1 +Chr1 TAIR10 exon 3996 4276 . + . Parent=AT1G01010.1 +Chr1 AEGeAn::GAEVAL intron 4277 4485 . + . Parent=AT1G01010.1 +Chr1 TAIR10 exon 4486 4605 . + . Parent=AT1G01010.1 +Chr1 AEGeAn::GAEVAL intron 4606 4705 . + . Parent=AT1G01010.1 +Chr1 TAIR10 exon 4706 5095 . + . Parent=AT1G01010.1 +Chr1 AEGeAn::GAEVAL intron 5096 5173 . + . Parent=AT1G01010.1 +Chr1 TAIR10 exon 5174 5326 . + . Parent=AT1G01010.1 +Chr1 AEGeAn::GAEVAL intron 5327 5438 . + . Parent=AT1G01010.1 +Chr1 TAIR10 exon 5439 5899 . + . Parent=AT1G01010.1 +Chr1 AEGeAn::GAEVAL stop_codon 5628 5630 . + . Parent=AT1G01010.1 +Chr1 TAIR10 three_prime_UTR 5631 5899 . + . Parent=AT1G01010.1 +Chr1 TAIR10 protein 3760 5630 . + . ID=AT1G01010.1-Protein;Name=AT1G01010.1;Derives_from=AT1G01010.1 +Chr1 TAIR10 CDS 3760 3913 . + 0 ID=CDS0;Parent=AT1G01010.1,AT1G01010.1-Protein +Chr1 TAIR10 CDS 3996 4276 . + 2 ID=CDS0;Parent=AT1G01010.1,AT1G01010.1-Protein +Chr1 TAIR10 CDS 4486 4605 . + 0 ID=CDS0;Parent=AT1G01010.1,AT1G01010.1-Protein +Chr1 TAIR10 CDS 4706 5095 . + 0 ID=CDS0;Parent=AT1G01010.1,AT1G01010.1-Protein +Chr1 TAIR10 CDS 5174 5326 . + 0 ID=CDS0;Parent=AT1G01010.1,AT1G01010.1-Protein +Chr1 TAIR10 CDS 5439 5630 . + 0 ID=CDS0;Parent=AT1G01010.1,AT1G01010.1-Protein +### +Chr1 TAIR10 gene 5928 8737 . - . ID=AT1G01020;Note=protein_coding_gene;Name=AT1G01020 +Chr1 TAIR10 mRNA 5928 8737 . - . ID=AT1G01020.1;Parent=AT1G01020;Name=AT1G01020.1;index=1;gaeval_coverage=0.000;gaeval_integrity=0.068 +Chr1 TAIR10 three_prime_UTR 5928 6263 . - . Parent=AT1G01020.1 +Chr1 TAIR10 exon 5928 6263 . - . Parent=AT1G01020.1 +Chr1 AEGeAn::GAEVAL intron 6264 6436 . - . Parent=AT1G01020.1 +Chr1 TAIR10 three_prime_UTR 6437 6914 . - . Parent=AT1G01020.1 +Chr1 TAIR10 exon 6437 7069 . - . Parent=AT1G01020.1 +Chr1 AEGeAn::GAEVAL stop_codon 6915 6917 . - . Parent=AT1G01020.1 +Chr1 TAIR10 exon 7157 7232 . - . Parent=AT1G01020.1 +Chr1 AEGeAn::GAEVAL intron 7233 7383 . - . Parent=AT1G01020.1 +Chr1 TAIR10 exon 7384 7450 . - . Parent=AT1G01020.1 +Chr1 TAIR10 exon 7564 7649 . - . Parent=AT1G01020.1 +Chr1 TAIR10 exon 7762 7835 . - . Parent=AT1G01020.1 +Chr1 TAIR10 exon 7942 7987 . - . Parent=AT1G01020.1 +Chr1 TAIR10 exon 8236 8325 . - . Parent=AT1G01020.1 +Chr1 TAIR10 exon 8417 8464 . - . Parent=AT1G01020.1 +Chr1 TAIR10 exon 8571 8737 . - . Parent=AT1G01020.1 +Chr1 AEGeAn::GAEVAL start_codon 8664 8666 . - . Parent=AT1G01020.1 +Chr1 TAIR10 five_prime_UTR 8667 8737 . - . Parent=AT1G01020.1 +Chr1 TAIR10 mRNA 6790 8737 . - . ID=AT1G01020.2;Parent=AT1G01020;Name=AT1G01020.2;index=1;gaeval_coverage=0.000;gaeval_integrity=0.068 +Chr1 TAIR10 three_prime_UTR 6790 7069 . - . Parent=AT1G01020.2 +Chr1 TAIR10 exon 6790 7069 . - . Parent=AT1G01020.2 +Chr1 AEGeAn::GAEVAL intron 7070 7156 . - . Parent=AT1G01020.1,AT1G01020.2 +Chr1 TAIR10 three_prime_UTR 7157 7314 . - . Parent=AT1G01020.2 +Chr1 TAIR10 exon 7157 7450 . - . Parent=AT1G01020.2 +Chr1 AEGeAn::GAEVAL stop_codon 7315 7317 . - . Parent=AT1G01020.2 +Chr1 AEGeAn::GAEVAL intron 7451 7563 . - . Parent=AT1G01020.1,AT1G01020.2 +Chr1 TAIR10 exon 7564 7649 . - . Parent=AT1G01020.2 +Chr1 AEGeAn::GAEVAL intron 7650 7761 . - . Parent=AT1G01020.1,AT1G01020.2 +Chr1 TAIR10 exon 7762 7835 . - . Parent=AT1G01020.2 +Chr1 AEGeAn::GAEVAL intron 7836 7941 . - . Parent=AT1G01020.1,AT1G01020.2 +Chr1 TAIR10 exon 7942 7987 . - . Parent=AT1G01020.2 +Chr1 AEGeAn::GAEVAL intron 7988 8235 . - . Parent=AT1G01020.1,AT1G01020.2 +Chr1 TAIR10 exon 8236 8325 . - . Parent=AT1G01020.2 +Chr1 AEGeAn::GAEVAL intron 8326 8416 . - . Parent=AT1G01020.1,AT1G01020.2 +Chr1 TAIR10 exon 8417 8464 . - . Parent=AT1G01020.2 +Chr1 AEGeAn::GAEVAL intron 8465 8570 . - . Parent=AT1G01020.1,AT1G01020.2 +Chr1 TAIR10 exon 8571 8737 . - . Parent=AT1G01020.2 +Chr1 AEGeAn::GAEVAL start_codon 8664 8666 . - . Parent=AT1G01020.2 +Chr1 TAIR10 five_prime_UTR 8667 8737 . - . Parent=AT1G01020.2 +Chr1 TAIR10 protein 6915 8666 . - . ID=AT1G01020.1-Protein;Name=AT1G01020.1;Derives_from=AT1G01020.1 +Chr1 TAIR10 CDS 6915 7069 . - 2 ID=CDS1;Parent=AT1G01020.1,AT1G01020.1-Protein +Chr1 TAIR10 CDS 7157 7232 . - 0 ID=CDS1;Parent=AT1G01020.1,AT1G01020.1-Protein +Chr1 TAIR10 CDS 7384 7450 . - 1 ID=CDS1;Parent=AT1G01020.1,AT1G01020.1-Protein +Chr1 TAIR10 CDS 7564 7649 . - 0 ID=CDS1;Parent=AT1G01020.1,AT1G01020.1-Protein +Chr1 TAIR10 CDS 7762 7835 . - 2 ID=CDS1;Parent=AT1G01020.1,AT1G01020.1-Protein +Chr1 TAIR10 CDS 7942 7987 . - 0 ID=CDS1;Parent=AT1G01020.1,AT1G01020.1-Protein +Chr1 TAIR10 CDS 8236 8325 . - 0 ID=CDS1;Parent=AT1G01020.1,AT1G01020.1-Protein +Chr1 TAIR10 CDS 8417 8464 . - 0 ID=CDS1;Parent=AT1G01020.1,AT1G01020.1-Protein +Chr1 TAIR10 CDS 8571 8666 . - 0 ID=CDS1;Parent=AT1G01020.1,AT1G01020.1-Protein +Chr1 TAIR10 protein 7315 8666 . - . ID=AT1G01020.2-Protein;Name=AT1G01020.2;Derives_from=AT1G01020.2 +Chr1 TAIR10 CDS 7315 7450 . - 1 ID=CDS2;Parent=AT1G01020.2,AT1G01020.2-Protein +Chr1 TAIR10 CDS 7564 7649 . - 0 ID=CDS2;Parent=AT1G01020.2,AT1G01020.2-Protein +Chr1 TAIR10 CDS 7762 7835 . - 2 ID=CDS2;Parent=AT1G01020.2,AT1G01020.2-Protein +Chr1 TAIR10 CDS 7942 7987 . - 0 ID=CDS2;Parent=AT1G01020.2,AT1G01020.2-Protein +Chr1 TAIR10 CDS 8236 8325 . - 0 ID=CDS2;Parent=AT1G01020.2,AT1G01020.2-Protein +Chr1 TAIR10 CDS 8417 8464 . - 0 ID=CDS2;Parent=AT1G01020.2,AT1G01020.2-Protein +Chr1 TAIR10 CDS 8571 8666 . - 0 ID=CDS2;Parent=AT1G01020.2,AT1G01020.2-Protein +### +Chr1 TAIR10 gene 11649 13714 . - . ID=AT1G01030;Note=protein_coding_gene;Name=AT1G01030 +Chr1 TAIR10 mRNA 11649 13714 . - . ID=AT1G01030.1;Parent=AT1G01030;Name=AT1G01030.1;index=1;gaeval_coverage=0.000;gaeval_integrity=0.100 +Chr1 TAIR10 three_prime_UTR 11649 11863 . - . Parent=AT1G01030.1 +Chr1 TAIR10 exon 11649 13173 . - . Parent=AT1G01030.1 +Chr1 AEGeAn::GAEVAL stop_codon 11864 11866 . - . Parent=AT1G01030.1 +Chr1 AEGeAn::GAEVAL start_codon 12938 12940 . - . Parent=AT1G01030.1 +Chr1 TAIR10 five_prime_UTR 12941 13173 . - . Parent=AT1G01030.1 +Chr1 AEGeAn::GAEVAL intron 13174 13334 . - . Parent=AT1G01030.1 +Chr1 TAIR10 five_prime_UTR 13335 13714 . - . Parent=AT1G01030.1 +Chr1 TAIR10 exon 13335 13714 . - . Parent=AT1G01030.1 +Chr1 TAIR10 protein 11864 12940 . - . ID=AT1G01030.1-Protein;Name=AT1G01030.1;Derives_from=AT1G01030.1 +Chr1 TAIR10 CDS 11864 12940 . - 0 Parent=AT1G01030.1,AT1G01030.1-Protein +### +Chr1 TAIR10 gene 23146 31227 . + . ID=AT1G01040;Note=protein_coding_gene;Name=AT1G01040 +Chr1 TAIR10 mRNA 23146 31227 . + . ID=AT1G01040.1;Parent=AT1G01040;Name=AT1G01040.1;index=1;gaeval_coverage=0.000;gaeval_integrity=0.050 +Chr1 TAIR10 five_prime_UTR 23146 23518 . + . Parent=AT1G01040.1 +Chr1 TAIR10 exon 23146 24451 . + . Parent=AT1G01040.1 +Chr1 AEGeAn::GAEVAL start_codon 23519 23521 . + . Parent=AT1G01040.1 +Chr1 AEGeAn::GAEVAL intron 24452 24541 . + . Parent=AT1G01040.1 +Chr1 TAIR10 exon 24542 24655 . + . Parent=AT1G01040.1 +Chr1 AEGeAn::GAEVAL intron 24656 24751 . + . Parent=AT1G01040.1 +Chr1 TAIR10 exon 24752 24962 . + . Parent=AT1G01040.1 +Chr1 AEGeAn::GAEVAL intron 24963 25040 . + . Parent=AT1G01040.1 +Chr1 TAIR10 exon 25041 25435 . + . Parent=AT1G01040.1 +Chr1 AEGeAn::GAEVAL intron 25436 25523 . + . Parent=AT1G01040.1 +Chr1 TAIR10 exon 25524 25743 . + . Parent=AT1G01040.1 +Chr1 AEGeAn::GAEVAL intron 25744 25824 . + . Parent=AT1G01040.1 +Chr1 TAIR10 exon 25825 25997 . + . Parent=AT1G01040.1 +Chr1 AEGeAn::GAEVAL intron 25998 26080 . + . Parent=AT1G01040.1 +Chr1 TAIR10 exon 26081 26203 . + . Parent=AT1G01040.1 +Chr1 AEGeAn::GAEVAL intron 26204 26291 . + . Parent=AT1G01040.1 +Chr1 TAIR10 exon 26292 26452 . + . Parent=AT1G01040.1 +Chr1 AEGeAn::GAEVAL intron 26453 26542 . + . Parent=AT1G01040.1 +Chr1 TAIR10 exon 26543 26776 . + . Parent=AT1G01040.1 +Chr1 AEGeAn::GAEVAL intron 26777 26861 . + . Parent=AT1G01040.1 +Chr1 TAIR10 exon 26862 27012 . + . Parent=AT1G01040.1 +Chr1 AEGeAn::GAEVAL intron 27013 27098 . + . Parent=AT1G01040.1 +Chr1 TAIR10 exon 27099 27281 . + . Parent=AT1G01040.1 +Chr1 AEGeAn::GAEVAL intron 27282 27371 . + . Parent=AT1G01040.1 +Chr1 TAIR10 exon 27372 27533 . + . Parent=AT1G01040.1 +Chr1 AEGeAn::GAEVAL stop_codon 27531 27533 . + . Parent=AT1G01040.1 +Chr1 TAIR10 protein 23519 31079 . + . ID=AT1G01040.1-Protein;Name=AT1G01040.1;Derives_from=AT1G01040.1 +Chr1 TAIR10 CDS 23519 24451 . + 0 ID=CDS3;Parent=AT1G01040.1,AT1G01040.1-Protein +Chr1 TAIR10 CDS 24542 24655 . + 0 ID=CDS3;Parent=AT1G01040.1,AT1G01040.1-Protein +Chr1 TAIR10 CDS 24752 24962 . + 0 ID=CDS3;Parent=AT1G01040.1,AT1G01040.1-Protein +Chr1 TAIR10 CDS 25041 25435 . + 2 ID=CDS3;Parent=AT1G01040.1,AT1G01040.1-Protein +Chr1 TAIR10 CDS 25524 25743 . + 0 ID=CDS3;Parent=AT1G01040.1,AT1G01040.1-Protein +Chr1 TAIR10 CDS 25825 25997 . + 2 ID=CDS3;Parent=AT1G01040.1,AT1G01040.1-Protein +Chr1 TAIR10 CDS 26081 26203 . + 0 ID=CDS3;Parent=AT1G01040.1,AT1G01040.1-Protein +Chr1 TAIR10 CDS 26292 26452 . + 0 ID=CDS3;Parent=AT1G01040.1,AT1G01040.1-Protein +Chr1 TAIR10 CDS 26543 26776 . + 1 ID=CDS3;Parent=AT1G01040.1,AT1G01040.1-Protein +Chr1 TAIR10 CDS 26862 27012 . + 1 ID=CDS3;Parent=AT1G01040.1,AT1G01040.1-Protein +Chr1 TAIR10 CDS 27099 27281 . + 0 ID=CDS3;Parent=AT1G01040.1,AT1G01040.1-Protein +Chr1 TAIR10 CDS 27372 27533 . + 0 ID=CDS3;Parent=AT1G01040.1,AT1G01040.1-Protein +### diff -r 000000000000 -r c4ac24510b55 test-data/gaeval_output_test3.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/gaeval_output_test3.txt Sun Jan 03 14:58:58 2021 +0000 @@ -0,0 +1,143 @@ +##gff-version 3 +##sequence-region Chr1 1 30427671 +Chr1 TAIR10 chromosome 1 30427671 . . . ID=Chr1;Name=Chr1 +### +Chr1 TAIR10 gene 3631 5899 . + . ID=AT1G01010;Note=protein_coding_gene;Name=AT1G01010 +Chr1 TAIR10 mRNA 3631 5899 . + . ID=AT1G01010.1;Parent=AT1G01010;Name=AT1G01010.1;index=1;gaeval_coverage=0.000;gaeval_integrity=0.093 +Chr1 TAIR10 five_prime_UTR 3631 3759 . + . Parent=AT1G01010.1 +Chr1 TAIR10 exon 3631 3913 . + . Parent=AT1G01010.1 +Chr1 AEGeAn::GAEVAL start_codon 3760 3762 . + . Parent=AT1G01010.1 +Chr1 AEGeAn::GAEVAL intron 3914 3995 . + . Parent=AT1G01010.1 +Chr1 TAIR10 exon 3996 4276 . + . Parent=AT1G01010.1 +Chr1 AEGeAn::GAEVAL intron 4277 4485 . + . Parent=AT1G01010.1 +Chr1 TAIR10 exon 4486 4605 . + . Parent=AT1G01010.1 +Chr1 AEGeAn::GAEVAL intron 4606 4705 . + . Parent=AT1G01010.1 +Chr1 TAIR10 exon 4706 5095 . + . Parent=AT1G01010.1 +Chr1 AEGeAn::GAEVAL intron 5096 5173 . + . Parent=AT1G01010.1 +Chr1 TAIR10 exon 5174 5326 . + . Parent=AT1G01010.1 +Chr1 AEGeAn::GAEVAL intron 5327 5438 . + . Parent=AT1G01010.1 +Chr1 TAIR10 exon 5439 5899 . + . Parent=AT1G01010.1 +Chr1 AEGeAn::GAEVAL stop_codon 5628 5630 . + . Parent=AT1G01010.1 +Chr1 TAIR10 three_prime_UTR 5631 5899 . + . Parent=AT1G01010.1 +Chr1 TAIR10 protein 3760 5630 . + . ID=AT1G01010.1-Protein;Name=AT1G01010.1;Derives_from=AT1G01010.1 +Chr1 TAIR10 CDS 3760 3913 . + 0 ID=CDS0;Parent=AT1G01010.1,AT1G01010.1-Protein +Chr1 TAIR10 CDS 3996 4276 . + 2 ID=CDS0;Parent=AT1G01010.1,AT1G01010.1-Protein +Chr1 TAIR10 CDS 4486 4605 . + 0 ID=CDS0;Parent=AT1G01010.1,AT1G01010.1-Protein +Chr1 TAIR10 CDS 4706 5095 . + 0 ID=CDS0;Parent=AT1G01010.1,AT1G01010.1-Protein +Chr1 TAIR10 CDS 5174 5326 . + 0 ID=CDS0;Parent=AT1G01010.1,AT1G01010.1-Protein +Chr1 TAIR10 CDS 5439 5630 . + 0 ID=CDS0;Parent=AT1G01010.1,AT1G01010.1-Protein +### +Chr1 TAIR10 gene 5928 8737 . - . ID=AT1G01020;Note=protein_coding_gene;Name=AT1G01020 +Chr1 TAIR10 mRNA 5928 8737 . - . ID=AT1G01020.1;Parent=AT1G01020;Name=AT1G01020.1;index=1;gaeval_coverage=0.000;gaeval_integrity=0.074 +Chr1 TAIR10 three_prime_UTR 5928 6263 . - . Parent=AT1G01020.1 +Chr1 TAIR10 exon 5928 6263 . - . Parent=AT1G01020.1 +Chr1 AEGeAn::GAEVAL intron 6264 6436 . - . Parent=AT1G01020.1 +Chr1 TAIR10 three_prime_UTR 6437 6914 . - . Parent=AT1G01020.1 +Chr1 TAIR10 exon 6437 7069 . - . Parent=AT1G01020.1 +Chr1 AEGeAn::GAEVAL stop_codon 6915 6917 . - . Parent=AT1G01020.1 +Chr1 TAIR10 exon 7157 7232 . - . Parent=AT1G01020.1 +Chr1 AEGeAn::GAEVAL intron 7233 7383 . - . Parent=AT1G01020.1 +Chr1 TAIR10 exon 7384 7450 . - . Parent=AT1G01020.1 +Chr1 TAIR10 exon 7564 7649 . - . Parent=AT1G01020.1 +Chr1 TAIR10 exon 7762 7835 . - . Parent=AT1G01020.1 +Chr1 TAIR10 exon 7942 7987 . - . Parent=AT1G01020.1 +Chr1 TAIR10 exon 8236 8325 . - . Parent=AT1G01020.1 +Chr1 TAIR10 exon 8417 8464 . - . Parent=AT1G01020.1 +Chr1 TAIR10 exon 8571 8737 . - . Parent=AT1G01020.1 +Chr1 AEGeAn::GAEVAL start_codon 8664 8666 . - . Parent=AT1G01020.1 +Chr1 TAIR10 five_prime_UTR 8667 8737 . - . Parent=AT1G01020.1 +Chr1 TAIR10 mRNA 6790 8737 . - . ID=AT1G01020.2;Parent=AT1G01020;Name=AT1G01020.2;index=1;gaeval_coverage=0.000;gaeval_integrity=0.074 +Chr1 TAIR10 three_prime_UTR 6790 7069 . - . Parent=AT1G01020.2 +Chr1 TAIR10 exon 6790 7069 . - . Parent=AT1G01020.2 +Chr1 AEGeAn::GAEVAL intron 7070 7156 . - . Parent=AT1G01020.1,AT1G01020.2 +Chr1 TAIR10 three_prime_UTR 7157 7314 . - . Parent=AT1G01020.2 +Chr1 TAIR10 exon 7157 7450 . - . Parent=AT1G01020.2 +Chr1 AEGeAn::GAEVAL stop_codon 7315 7317 . - . Parent=AT1G01020.2 +Chr1 AEGeAn::GAEVAL intron 7451 7563 . - . Parent=AT1G01020.1,AT1G01020.2 +Chr1 TAIR10 exon 7564 7649 . - . Parent=AT1G01020.2 +Chr1 AEGeAn::GAEVAL intron 7650 7761 . - . Parent=AT1G01020.1,AT1G01020.2 +Chr1 TAIR10 exon 7762 7835 . - . Parent=AT1G01020.2 +Chr1 AEGeAn::GAEVAL intron 7836 7941 . - . Parent=AT1G01020.1,AT1G01020.2 +Chr1 TAIR10 exon 7942 7987 . - . Parent=AT1G01020.2 +Chr1 AEGeAn::GAEVAL intron 7988 8235 . - . Parent=AT1G01020.1,AT1G01020.2 +Chr1 TAIR10 exon 8236 8325 . - . Parent=AT1G01020.2 +Chr1 AEGeAn::GAEVAL intron 8326 8416 . - . Parent=AT1G01020.1,AT1G01020.2 +Chr1 TAIR10 exon 8417 8464 . - . Parent=AT1G01020.2 +Chr1 AEGeAn::GAEVAL intron 8465 8570 . - . Parent=AT1G01020.1,AT1G01020.2 +Chr1 TAIR10 exon 8571 8737 . - . Parent=AT1G01020.2 +Chr1 AEGeAn::GAEVAL start_codon 8664 8666 . - . Parent=AT1G01020.2 +Chr1 TAIR10 five_prime_UTR 8667 8737 . - . Parent=AT1G01020.2 +Chr1 TAIR10 protein 6915 8666 . - . ID=AT1G01020.1-Protein;Name=AT1G01020.1;Derives_from=AT1G01020.1 +Chr1 TAIR10 CDS 6915 7069 . - 2 ID=CDS1;Parent=AT1G01020.1,AT1G01020.1-Protein +Chr1 TAIR10 CDS 7157 7232 . - 0 ID=CDS1;Parent=AT1G01020.1,AT1G01020.1-Protein +Chr1 TAIR10 CDS 7384 7450 . - 1 ID=CDS1;Parent=AT1G01020.1,AT1G01020.1-Protein +Chr1 TAIR10 CDS 7564 7649 . - 0 ID=CDS1;Parent=AT1G01020.1,AT1G01020.1-Protein +Chr1 TAIR10 CDS 7762 7835 . - 2 ID=CDS1;Parent=AT1G01020.1,AT1G01020.1-Protein +Chr1 TAIR10 CDS 7942 7987 . - 0 ID=CDS1;Parent=AT1G01020.1,AT1G01020.1-Protein +Chr1 TAIR10 CDS 8236 8325 . - 0 ID=CDS1;Parent=AT1G01020.1,AT1G01020.1-Protein +Chr1 TAIR10 CDS 8417 8464 . - 0 ID=CDS1;Parent=AT1G01020.1,AT1G01020.1-Protein +Chr1 TAIR10 CDS 8571 8666 . - 0 ID=CDS1;Parent=AT1G01020.1,AT1G01020.1-Protein +Chr1 TAIR10 protein 7315 8666 . - . ID=AT1G01020.2-Protein;Name=AT1G01020.2;Derives_from=AT1G01020.2 +Chr1 TAIR10 CDS 7315 7450 . - 1 ID=CDS2;Parent=AT1G01020.2,AT1G01020.2-Protein +Chr1 TAIR10 CDS 7564 7649 . - 0 ID=CDS2;Parent=AT1G01020.2,AT1G01020.2-Protein +Chr1 TAIR10 CDS 7762 7835 . - 2 ID=CDS2;Parent=AT1G01020.2,AT1G01020.2-Protein +Chr1 TAIR10 CDS 7942 7987 . - 0 ID=CDS2;Parent=AT1G01020.2,AT1G01020.2-Protein +Chr1 TAIR10 CDS 8236 8325 . - 0 ID=CDS2;Parent=AT1G01020.2,AT1G01020.2-Protein +Chr1 TAIR10 CDS 8417 8464 . - 0 ID=CDS2;Parent=AT1G01020.2,AT1G01020.2-Protein +Chr1 TAIR10 CDS 8571 8666 . - 0 ID=CDS2;Parent=AT1G01020.2,AT1G01020.2-Protein +### +Chr1 TAIR10 gene 11649 13714 . - . ID=AT1G01030;Note=protein_coding_gene;Name=AT1G01030 +Chr1 TAIR10 mRNA 11649 13714 . - . ID=AT1G01030.1;Parent=AT1G01030;Name=AT1G01030.1;index=1;gaeval_coverage=0.000;gaeval_integrity=0.100 +Chr1 TAIR10 three_prime_UTR 11649 11863 . - . Parent=AT1G01030.1 +Chr1 TAIR10 exon 11649 13173 . - . Parent=AT1G01030.1 +Chr1 AEGeAn::GAEVAL stop_codon 11864 11866 . - . Parent=AT1G01030.1 +Chr1 AEGeAn::GAEVAL start_codon 12938 12940 . - . Parent=AT1G01030.1 +Chr1 TAIR10 five_prime_UTR 12941 13173 . - . Parent=AT1G01030.1 +Chr1 AEGeAn::GAEVAL intron 13174 13334 . - . Parent=AT1G01030.1 +Chr1 TAIR10 five_prime_UTR 13335 13714 . - . Parent=AT1G01030.1 +Chr1 TAIR10 exon 13335 13714 . - . Parent=AT1G01030.1 +Chr1 TAIR10 protein 11864 12940 . - . ID=AT1G01030.1-Protein;Name=AT1G01030.1;Derives_from=AT1G01030.1 +Chr1 TAIR10 CDS 11864 12940 . - 0 Parent=AT1G01030.1,AT1G01030.1-Protein +### +Chr1 TAIR10 gene 23146 31227 . + . ID=AT1G01040;Note=protein_coding_gene;Name=AT1G01040 +Chr1 TAIR10 mRNA 23146 31227 . + . ID=AT1G01040.1;Parent=AT1G01040;Name=AT1G01040.1;index=1;gaeval_coverage=0.000;gaeval_integrity=0.050 +Chr1 TAIR10 five_prime_UTR 23146 23518 . + . Parent=AT1G01040.1 +Chr1 TAIR10 exon 23146 24451 . + . Parent=AT1G01040.1 +Chr1 AEGeAn::GAEVAL start_codon 23519 23521 . + . Parent=AT1G01040.1 +Chr1 AEGeAn::GAEVAL intron 24452 24541 . + . Parent=AT1G01040.1 +Chr1 TAIR10 exon 24542 24655 . + . Parent=AT1G01040.1 +Chr1 AEGeAn::GAEVAL intron 24656 24751 . + . Parent=AT1G01040.1 +Chr1 TAIR10 exon 24752 24962 . + . Parent=AT1G01040.1 +Chr1 AEGeAn::GAEVAL intron 24963 25040 . + . Parent=AT1G01040.1 +Chr1 TAIR10 exon 25041 25435 . + . Parent=AT1G01040.1 +Chr1 AEGeAn::GAEVAL intron 25436 25523 . + . Parent=AT1G01040.1 +Chr1 TAIR10 exon 25524 25743 . + . Parent=AT1G01040.1 +Chr1 AEGeAn::GAEVAL intron 25744 25824 . + . Parent=AT1G01040.1 +Chr1 TAIR10 exon 25825 25997 . + . Parent=AT1G01040.1 +Chr1 AEGeAn::GAEVAL intron 25998 26080 . + . Parent=AT1G01040.1 +Chr1 TAIR10 exon 26081 26203 . + . Parent=AT1G01040.1 +Chr1 AEGeAn::GAEVAL intron 26204 26291 . + . Parent=AT1G01040.1 +Chr1 TAIR10 exon 26292 26452 . + . Parent=AT1G01040.1 +Chr1 AEGeAn::GAEVAL intron 26453 26542 . + . Parent=AT1G01040.1 +Chr1 TAIR10 exon 26543 26776 . + . Parent=AT1G01040.1 +Chr1 AEGeAn::GAEVAL intron 26777 26861 . + . Parent=AT1G01040.1 +Chr1 TAIR10 exon 26862 27012 . + . Parent=AT1G01040.1 +Chr1 AEGeAn::GAEVAL intron 27013 27098 . + . Parent=AT1G01040.1 +Chr1 TAIR10 exon 27099 27281 . + . Parent=AT1G01040.1 +Chr1 AEGeAn::GAEVAL intron 27282 27371 . + . Parent=AT1G01040.1 +Chr1 TAIR10 exon 27372 27533 . + . Parent=AT1G01040.1 +Chr1 AEGeAn::GAEVAL stop_codon 27531 27533 . + . Parent=AT1G01040.1 +Chr1 TAIR10 protein 23519 31079 . + . ID=AT1G01040.1-Protein;Name=AT1G01040.1;Derives_from=AT1G01040.1 +Chr1 TAIR10 CDS 23519 24451 . + 0 ID=CDS3;Parent=AT1G01040.1,AT1G01040.1-Protein +Chr1 TAIR10 CDS 24542 24655 . + 0 ID=CDS3;Parent=AT1G01040.1,AT1G01040.1-Protein +Chr1 TAIR10 CDS 24752 24962 . + 0 ID=CDS3;Parent=AT1G01040.1,AT1G01040.1-Protein +Chr1 TAIR10 CDS 25041 25435 . + 2 ID=CDS3;Parent=AT1G01040.1,AT1G01040.1-Protein +Chr1 TAIR10 CDS 25524 25743 . + 0 ID=CDS3;Parent=AT1G01040.1,AT1G01040.1-Protein +Chr1 TAIR10 CDS 25825 25997 . + 2 ID=CDS3;Parent=AT1G01040.1,AT1G01040.1-Protein +Chr1 TAIR10 CDS 26081 26203 . + 0 ID=CDS3;Parent=AT1G01040.1,AT1G01040.1-Protein +Chr1 TAIR10 CDS 26292 26452 . + 0 ID=CDS3;Parent=AT1G01040.1,AT1G01040.1-Protein +Chr1 TAIR10 CDS 26543 26776 . + 1 ID=CDS3;Parent=AT1G01040.1,AT1G01040.1-Protein +Chr1 TAIR10 CDS 26862 27012 . + 1 ID=CDS3;Parent=AT1G01040.1,AT1G01040.1-Protein +Chr1 TAIR10 CDS 27099 27281 . + 0 ID=CDS3;Parent=AT1G01040.1,AT1G01040.1-Protein +Chr1 TAIR10 CDS 27372 27533 . + 0 ID=CDS3;Parent=AT1G01040.1,AT1G01040.1-Protein +### diff -r 000000000000 -r c4ac24510b55 test-data/locuspocus_genemap_test7.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/locuspocus_genemap_test7.txt Sun Jan 03 14:58:58 2021 +0000 @@ -0,0 +1,4 @@ +AT1G01010 testXlu +AT1G01020 testXlu +AT1G01030 testXlu +AT1G01040 testXlu diff -r 000000000000 -r c4ac24510b55 test-data/locuspocus_genemap_test8.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/locuspocus_genemap_test8.txt Sun Jan 03 14:58:58 2021 +0000 @@ -0,0 +1,4 @@ +AT1G01010 locus:Chr1_3231-6299. +AT1G01020 locus:Chr1_5528-9137. +AT1G01030 locus:Chr1_11249-14114. +AT1G01040 locus:Chr1_22746-31627. diff -r 000000000000 -r c4ac24510b55 test-data/locuspocus_lenght_test7.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/locuspocus_lenght_test7.txt Sun Jan 03 14:58:58 2021 +0000 @@ -0,0 +1,3 @@ +Chr1 0 +Chr1 1911 +Chr1 8431 diff -r 000000000000 -r c4ac24510b55 test-data/locuspocus_lenght_test8.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/locuspocus_lenght_test8.txt Sun Jan 03 14:58:58 2021 +0000 @@ -0,0 +1,3 @@ +Chr1 0 +Chr1 2111 +Chr1 8631 diff -r 000000000000 -r c4ac24510b55 test-data/locuspocus_output_test1.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/locuspocus_output_test1.txt Sun Jan 03 14:58:58 2021 +0000 @@ -0,0 +1,10 @@ +##gff-version 3 +##sequence-region Chr1 1 30427671 +Chr1 AEGeAn::LocusPocus locus 1 3130 . . . . +Chr1 AEGeAn::LocusPocus locus 3131 6399 . . . child_gene=1;child_mRNA=1;right_overlap=972;iiLocus_exception=delta-overlap-gene;riil=0 +Chr1 AEGeAn::LocusPocus locus 5428 9237 . . . left_overlap=972;liil=0;child_gene=1;child_mRNA=2;riil=1911 +Chr1 AEGeAn::LocusPocus locus 9238 11148 . . . fg_orient=RR +Chr1 AEGeAn::LocusPocus locus 11149 14214 . . . liil=1911;child_gene=1;child_mRNA=1;riil=8431 +Chr1 AEGeAn::LocusPocus locus 14215 22645 . . . fg_orient=RF +Chr1 AEGeAn::LocusPocus locus 22646 31727 . . . liil=8431;child_gene=1;child_mRNA=1 +Chr1 AEGeAn::LocusPocus locus 31728 30427671 . . . . diff -r 000000000000 -r c4ac24510b55 test-data/locuspocus_output_test2.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/locuspocus_output_test2.txt Sun Jan 03 14:58:58 2021 +0000 @@ -0,0 +1,8 @@ +##gff-version 3 +##sequence-region Chr1 1 30427671 +Chr1 AEGeAn::LocusPocus locus 3231 6299 . . . child_gene=1;child_mRNA=1;right_overlap=772;iiLocus_exception=delta-overlap-gene;riil=0 +Chr1 AEGeAn::LocusPocus locus 5528 9137 . . . left_overlap=772;liil=0;child_gene=1;child_mRNA=2;riil=2111 +Chr1 AEGeAn::LocusPocus locus 9138 11248 . . . fg_orient=RR +Chr1 AEGeAn::LocusPocus locus 11249 14114 . . . liil=2111;child_gene=1;child_mRNA=1;riil=8631 +Chr1 AEGeAn::LocusPocus locus 14115 22745 . . . fg_orient=RF +Chr1 AEGeAn::LocusPocus locus 22746 31627 . . . liil=8631;child_gene=1;child_mRNA=1 diff -r 000000000000 -r c4ac24510b55 test-data/locuspocus_output_test3.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/locuspocus_output_test3.txt Sun Jan 03 14:58:58 2021 +0000 @@ -0,0 +1,6 @@ +##gff-version 3 +##sequence-region Chr1 1 30427671 +Chr1 AEGeAn::LocusPocus locus 3131 6399 . . . child_gene=1;child_mRNA=1;right_overlap=972;iiLocus_exception=delta-overlap-gene;riil=0 +Chr1 AEGeAn::LocusPocus locus 5428 9237 . . . left_overlap=972;liil=0;child_gene=1;child_mRNA=2 +Chr1 AEGeAn::LocusPocus locus 11149 14214 . . . child_gene=1;child_mRNA=1 +Chr1 AEGeAn::LocusPocus locus 22646 31727 . . . child_gene=1;child_mRNA=1 diff -r 000000000000 -r c4ac24510b55 test-data/locuspocus_output_test4.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/locuspocus_output_test4.txt Sun Jan 03 14:58:58 2021 +0000 @@ -0,0 +1,10 @@ +##gff-version 3 +##sequence-region Chr1 1 30427671 +Chr1 AEGeAn::LocusPocus locus 1 3130 . . . . +Chr1 AEGeAn::LocusPocus locus 3131 6399 . . . child_gene=1;child_mRNA=1;right_overlap=972;iiLocus_exception=delta-overlap-gene;riil=0 +Chr1 AEGeAn::LocusPocus locus 5428 9237 . . . left_overlap=972;liil=0;child_gene=1;child_mRNA=2;riil=1911 +Chr1 AEGeAn::LocusPocus locus 9238 11148 . . . fg_orient=RR +Chr1 AEGeAn::LocusPocus locus 11149 14214 . . . liil=1911;child_gene=1;child_mRNA=1;riil=8431 +Chr1 AEGeAn::LocusPocus locus 14215 22645 . . . fg_orient=RF +Chr1 AEGeAn::LocusPocus locus 22646 31727 . . . liil=8431;child_gene=1;child_mRNA=1 +Chr1 AEGeAn::LocusPocus locus 31728 30427671 . . . . diff -r 000000000000 -r c4ac24510b55 test-data/locuspocus_output_test5.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/locuspocus_output_test5.txt Sun Jan 03 14:58:58 2021 +0000 @@ -0,0 +1,10 @@ +##gff-version 3 +##sequence-region Chr1 1 30427671 +Chr1 AEGeAn::LocusPocus locus 1 3130 . . . . +Chr1 AEGeAn::LocusPocus locus 3131 6399 . . . child_gene=1;child_mRNA=1;right_overlap=972;iiLocus_exception=delta-overlap-gene;riil=0 +Chr1 AEGeAn::LocusPocus locus 5428 9237 . . . left_overlap=972;liil=0;child_gene=1;child_mRNA=2;riil=1911 +Chr1 AEGeAn::LocusPocus locus 9238 11148 . . . fg_orient=RR +Chr1 AEGeAn::LocusPocus locus 11149 14214 . . . liil=1911;child_gene=1;child_mRNA=1;riil=8431 +Chr1 AEGeAn::LocusPocus locus 14215 22645 . . . fg_orient=RF +Chr1 AEGeAn::LocusPocus locus 22646 31727 . . . liil=8431;child_gene=1;child_mRNA=1 +Chr1 AEGeAn::LocusPocus locus 31728 30427671 . . . . diff -r 000000000000 -r c4ac24510b55 test-data/locuspocus_output_test6.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/locuspocus_output_test6.txt Sun Jan 03 14:58:58 2021 +0000 @@ -0,0 +1,10 @@ +##gff-version 3 +##sequence-region Chr1 1 30427671 +Chr1 AEGeAn::LocusPocus locus 1 3130 . . . . +Chr1 AEGeAn::LocusPocus locus 3131 6399 . . . child_gene=1;child_mRNA=1;right_overlap=972;iiLocus_exception=delta-overlap-gene;riil=0 +Chr1 AEGeAn::LocusPocus locus 5428 9237 . . . left_overlap=972;liil=0;child_gene=1;child_mRNA=2;riil=1911 +Chr1 AEGeAn::LocusPocus locus 9238 11148 . . . fg_orient=RR +Chr1 AEGeAn::LocusPocus locus 11149 14214 . . . liil=1911;child_gene=1;child_mRNA=1;riil=8431 +Chr1 AEGeAn::LocusPocus locus 14215 22645 . . . fg_orient=RF +Chr1 AEGeAn::LocusPocus locus 22646 31727 . . . liil=8431;child_gene=1;child_mRNA=1 +Chr1 AEGeAn::LocusPocus locus 31728 30427671 . . . . diff -r 000000000000 -r c4ac24510b55 test-data/locuspocus_output_test7.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/locuspocus_output_test7.txt Sun Jan 03 14:58:58 2021 +0000 @@ -0,0 +1,10 @@ +##gff-version 3 +##sequence-region Chr1 1 30427671 +Chr1 AEGeAn::LocusPocus locus 1 3130 . . . Name=testXlu +Chr1 AEGeAn::LocusPocus locus 3131 6399 . . . Name=testXlu;child_gene=1;child_mRNA=1;right_overlap=972;iiLocus_exception=delta-overlap-gene;riil=0 +Chr1 AEGeAn::LocusPocus locus 5428 9237 . . . left_overlap=972;liil=0;Name=testXlu;child_gene=1;child_mRNA=2;riil=1911 +Chr1 AEGeAn::LocusPocus locus 9238 11148 . . . fg_orient=RR;Name=testXlu +Chr1 AEGeAn::LocusPocus locus 11149 14214 . . . liil=1911;Name=testXlu;child_gene=1;child_mRNA=1;riil=8431 +Chr1 AEGeAn::LocusPocus locus 14215 22645 . . . fg_orient=RF;Name=testXlu +Chr1 AEGeAn::LocusPocus locus 22646 31727 . . . liil=8431;Name=testXlu;child_gene=1;child_mRNA=1 +Chr1 AEGeAn::LocusPocus locus 31728 30427671 . . . Name=testXlu diff -r 000000000000 -r c4ac24510b55 test-data/locuspocus_output_test8.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/locuspocus_output_test8.txt Sun Jan 03 14:58:58 2021 +0000 @@ -0,0 +1,8 @@ +##gff-version 3 +##sequence-region Chr1 1 30427671 +Chr1 AEGeAn::LocusPocus locus 3231 6299 . . . child_gene=1;child_mRNA=1;right_overlap=772;iiLocus_exception=delta-overlap-gene;riil=0 +Chr1 AEGeAn::LocusPocus locus 5528 9137 . . . left_overlap=772;liil=0;child_gene=1;child_mRNA=2;riil=2111 +Chr1 AEGeAn::LocusPocus locus 9138 11248 . . . fg_orient=RR +Chr1 AEGeAn::LocusPocus locus 11249 14114 . . . liil=2111;child_gene=1;child_mRNA=1;riil=8631 +Chr1 AEGeAn::LocusPocus locus 14115 22745 . . . fg_orient=RF +Chr1 AEGeAn::LocusPocus locus 22746 31627 . . . liil=8631;child_gene=1;child_mRNA=1 diff -r 000000000000 -r c4ac24510b55 test-data/locuspocus_transmap_test7.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/locuspocus_transmap_test7.txt Sun Jan 03 14:58:58 2021 +0000 @@ -0,0 +1,5 @@ +AT1G01010.1 testXlu +AT1G01020.1 testXlu +AT1G01020.2 testXlu +AT1G01030.1 testXlu +AT1G01040.1 testXlu diff -r 000000000000 -r c4ac24510b55 test-data/locuspocus_transmap_test8.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/locuspocus_transmap_test8.txt Sun Jan 03 14:58:58 2021 +0000 @@ -0,0 +1,5 @@ +AT1G01010.1 locus:Chr1_3231-6299. +AT1G01020.1 locus:Chr1_5528-9137. +AT1G01020.2 locus:Chr1_5528-9137. +AT1G01030.1 locus:Chr1_11249-14114. +AT1G01040.1 locus:Chr1_22746-31627. diff -r 000000000000 -r c4ac24510b55 test-data/parseval_output_test1.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/parseval_output_test1.txt Sun Jan 03 14:58:58 2021 +0000 @@ -0,0 +1,577 @@ +|------------------------------------------------- +|---- Locus: seqid=Chr1 range=3626-5904 +|------------------------------------------------- +| +| reference genes: +| AT1G01010 +| +| prediction genes: +| AT1G01010 +| +|---------- + | + |-------------------------- + |---- Begin comparison ---- + |-------------------------- + | + | reference transcripts: + | AT1G01010.1 + | prediction transcripts: + | AT1G01010.1 + | + | reference GFF3: +##gff-version 3 +Chr1 TAIR9 mRNA 3631 5899 . + . ID=AT1G01010.1;Name=AT1G01010.1;index=1 +Chr1 TAIR9 five_prime_UTR 3631 3759 . + . Parent=AT1G01010.1 +Chr1 TAIR9 exon 3631 3913 . + . Parent=AT1G01010.1 +Chr1 . start_codon 3760 3762 . + . Parent=AT1G01010.1 +Chr1 TAIR9 CDS 3760 3913 . + 0 ID=CDS0;Parent=AT1G01010.1 +Chr1 . intron 3914 3995 . + . Parent=AT1G01010.1 +Chr1 TAIR9 exon 3996 4276 . + . Parent=AT1G01010.1 +Chr1 TAIR9 CDS 3996 4276 . + 2 ID=CDS0;Parent=AT1G01010.1 +Chr1 . intron 4277 4485 . + . Parent=AT1G01010.1 +Chr1 TAIR9 exon 4486 4605 . + . Parent=AT1G01010.1 +Chr1 TAIR9 CDS 4486 4605 . + 0 ID=CDS0;Parent=AT1G01010.1 +Chr1 . intron 4606 4705 . + . Parent=AT1G01010.1 +Chr1 TAIR9 exon 4706 5095 . + . Parent=AT1G01010.1 +Chr1 TAIR9 CDS 4706 5095 . + 0 ID=CDS0;Parent=AT1G01010.1 +Chr1 . intron 5096 5173 . + . Parent=AT1G01010.1 +Chr1 TAIR9 exon 5174 5326 . + . Parent=AT1G01010.1 +Chr1 TAIR9 CDS 5174 5326 . + 0 ID=CDS0;Parent=AT1G01010.1 +Chr1 . intron 5327 5438 . + . Parent=AT1G01010.1 +Chr1 TAIR9 CDS 5439 5630 . + 0 ID=CDS0;Parent=AT1G01010.1 +Chr1 TAIR9 exon 5439 5899 . + . Parent=AT1G01010.1 +Chr1 . stop_codon 5628 5630 . + . Parent=AT1G01010.1 +Chr1 TAIR9 three_prime_UTR 5631 5899 . + . Parent=AT1G01010.1 +### + | prediction GFF3: +##gff-version 3 +Chr1 TAIR10 mRNA 3631 5899 . + . ID=AT1G01010.1;Name=AT1G01010.1;index=1 +Chr1 TAIR10 five_prime_UTR 3631 3759 . + . Parent=AT1G01010.1 +Chr1 TAIR10 exon 3631 3913 . + . Parent=AT1G01010.1 +Chr1 . start_codon 3760 3762 . + . Parent=AT1G01010.1 +Chr1 TAIR10 CDS 3760 3913 . + 0 ID=CDS1;Parent=AT1G01010.1 +Chr1 . intron 3914 3995 . + . Parent=AT1G01010.1 +Chr1 TAIR10 exon 3996 4276 . + . Parent=AT1G01010.1 +Chr1 TAIR10 CDS 3996 4276 . + 2 ID=CDS1;Parent=AT1G01010.1 +Chr1 . intron 4277 4485 . + . Parent=AT1G01010.1 +Chr1 TAIR10 exon 4486 4605 . + . Parent=AT1G01010.1 +Chr1 TAIR10 CDS 4486 4605 . + 0 ID=CDS1;Parent=AT1G01010.1 +Chr1 . intron 4606 4705 . + . Parent=AT1G01010.1 +Chr1 TAIR10 exon 4706 5095 . + . Parent=AT1G01010.1 +Chr1 TAIR10 CDS 4706 5095 . + 0 ID=CDS1;Parent=AT1G01010.1 +Chr1 . intron 5096 5173 . + . Parent=AT1G01010.1 +Chr1 TAIR10 exon 5174 5326 . + . Parent=AT1G01010.1 +Chr1 TAIR10 CDS 5174 5326 . + 0 ID=CDS1;Parent=AT1G01010.1 +Chr1 . intron 5327 5438 . + . Parent=AT1G01010.1 +Chr1 TAIR10 CDS 5439 5630 . + 0 ID=CDS1;Parent=AT1G01010.1 +Chr1 TAIR10 exon 5439 5899 . + . Parent=AT1G01010.1 +Chr1 . stop_codon 5628 5630 . + . Parent=AT1G01010.1 +Chr1 TAIR10 three_prime_UTR 5631 5899 . + . Parent=AT1G01010.1 +### + | + | CDS structure comparison + | 6 reference CDS segments + | 6 prediction CDS segments + | CDS structures match perfectly! + | + | Exon structure comparison + | 6 reference exons + | 6 prediction exons + | Exon structures match perfectly! + | + | UTR structure comparison + | 2 reference UTR segments + | 2 prediction UTR segments + | UTR structures match perfectly! + | + | Gene structures match perfectly! + | + | + |-------------------------- + |----- End comparison ----- + |-------------------------- + +|------------------------------------------------- +|---- Locus: seqid=Chr1 range=5923-8742 +|------------------------------------------------- +| +| reference genes: +| AT1G01020 +| +| prediction genes: +| AT1G01020 +| +|---------- + | + |-------------------------- + |---- Begin comparison ---- + |-------------------------- + | + | reference transcripts: + | AT1G01020.1 + | prediction transcripts: + | AT1G01020.1 + | + | reference GFF3: +##gff-version 3 +Chr1 TAIR9 mRNA 5928 8737 . - . ID=AT1G01020.1;Name=AT1G01020.1;index=1 +Chr1 TAIR9 three_prime_UTR 5928 6263 . - . Parent=AT1G01020.1 +Chr1 TAIR9 exon 5928 6263 . - . Parent=AT1G01020.1 +Chr1 . intron 6264 6436 . - . Parent=AT1G01020.1 +Chr1 TAIR9 three_prime_UTR 6437 6914 . - . Parent=AT1G01020.1 +Chr1 TAIR9 exon 6437 7069 . - . Parent=AT1G01020.1 +Chr1 . stop_codon 6915 6917 . - . Parent=AT1G01020.1 +Chr1 TAIR9 CDS 6915 7069 . - 2 ID=CDS2;Parent=AT1G01020.1 +Chr1 . intron 7070 7156 . - . Parent=AT1G01020.1 +Chr1 TAIR9 CDS 7157 7232 . - 0 ID=CDS2;Parent=AT1G01020.1 +Chr1 TAIR9 exon 7157 7232 . - . Parent=AT1G01020.1 +Chr1 . intron 7233 7383 . - . Parent=AT1G01020.1 +Chr1 TAIR9 CDS 7384 7450 . - 1 ID=CDS2;Parent=AT1G01020.1 +Chr1 TAIR9 exon 7384 7450 . - . Parent=AT1G01020.1 +Chr1 . intron 7451 7563 . - . Parent=AT1G01020.1 +Chr1 TAIR9 CDS 7564 7649 . - 0 ID=CDS2;Parent=AT1G01020.1 +Chr1 TAIR9 exon 7564 7649 . - . Parent=AT1G01020.1 +Chr1 . intron 7650 7761 . - . Parent=AT1G01020.1 +Chr1 TAIR9 CDS 7762 7835 . - 2 ID=CDS2;Parent=AT1G01020.1 +Chr1 TAIR9 exon 7762 7835 . - . Parent=AT1G01020.1 +Chr1 . intron 7836 7941 . - . Parent=AT1G01020.1 +Chr1 TAIR9 CDS 7942 7987 . - 0 ID=CDS2;Parent=AT1G01020.1 +Chr1 TAIR9 exon 7942 7987 . - . Parent=AT1G01020.1 +Chr1 . intron 7988 8235 . - . Parent=AT1G01020.1 +Chr1 TAIR9 CDS 8236 8325 . - 0 ID=CDS2;Parent=AT1G01020.1 +Chr1 TAIR9 exon 8236 8325 . - . Parent=AT1G01020.1 +Chr1 . intron 8326 8416 . - . Parent=AT1G01020.1 +Chr1 TAIR9 CDS 8417 8464 . - 0 ID=CDS2;Parent=AT1G01020.1 +Chr1 TAIR9 exon 8417 8464 . - . Parent=AT1G01020.1 +Chr1 . intron 8465 8570 . - . Parent=AT1G01020.1 +Chr1 TAIR9 CDS 8571 8666 . - 0 ID=CDS2;Parent=AT1G01020.1 +Chr1 TAIR9 exon 8571 8737 . - . Parent=AT1G01020.1 +Chr1 . start_codon 8664 8666 . - . Parent=AT1G01020.1 +Chr1 TAIR9 five_prime_UTR 8667 8737 . - . Parent=AT1G01020.1 +### + | prediction GFF3: +##gff-version 3 +Chr1 TAIR10 mRNA 5928 8737 . - . ID=AT1G01020.1;Name=AT1G01020.1;index=1 +Chr1 TAIR10 three_prime_UTR 5928 6263 . - . Parent=AT1G01020.1 +Chr1 TAIR10 exon 5928 6263 . - . Parent=AT1G01020.1 +Chr1 . intron 6264 6436 . - . Parent=AT1G01020.1 +Chr1 TAIR10 three_prime_UTR 6437 6914 . - . Parent=AT1G01020.1 +Chr1 TAIR10 exon 6437 7069 . - . Parent=AT1G01020.1 +Chr1 . stop_codon 6915 6917 . - . Parent=AT1G01020.1 +Chr1 TAIR10 CDS 6915 7069 . - 2 ID=CDS4;Parent=AT1G01020.1 +Chr1 . intron 7070 7156 . - . Parent=AT1G01020.1 +Chr1 TAIR10 CDS 7157 7232 . - 0 ID=CDS4;Parent=AT1G01020.1 +Chr1 TAIR10 exon 7157 7232 . - . Parent=AT1G01020.1 +Chr1 . intron 7233 7383 . - . Parent=AT1G01020.1 +Chr1 TAIR10 CDS 7384 7450 . - 1 ID=CDS4;Parent=AT1G01020.1 +Chr1 TAIR10 exon 7384 7450 . - . Parent=AT1G01020.1 +Chr1 . intron 7451 7563 . - . Parent=AT1G01020.1 +Chr1 TAIR10 CDS 7564 7649 . - 0 ID=CDS4;Parent=AT1G01020.1 +Chr1 TAIR10 exon 7564 7649 . - . Parent=AT1G01020.1 +Chr1 . intron 7650 7761 . - . Parent=AT1G01020.1 +Chr1 TAIR10 CDS 7762 7835 . - 2 ID=CDS4;Parent=AT1G01020.1 +Chr1 TAIR10 exon 7762 7835 . - . Parent=AT1G01020.1 +Chr1 . intron 7836 7941 . - . Parent=AT1G01020.1 +Chr1 TAIR10 CDS 7942 7987 . - 0 ID=CDS4;Parent=AT1G01020.1 +Chr1 TAIR10 exon 7942 7987 . - . Parent=AT1G01020.1 +Chr1 . intron 7988 8235 . - . Parent=AT1G01020.1 +Chr1 TAIR10 CDS 8236 8325 . - 0 ID=CDS4;Parent=AT1G01020.1 +Chr1 TAIR10 exon 8236 8325 . - . Parent=AT1G01020.1 +Chr1 . intron 8326 8416 . - . Parent=AT1G01020.1 +Chr1 TAIR10 CDS 8417 8464 . - 0 ID=CDS4;Parent=AT1G01020.1 +Chr1 TAIR10 exon 8417 8464 . - . Parent=AT1G01020.1 +Chr1 . intron 8465 8570 . - . Parent=AT1G01020.1 +Chr1 TAIR10 CDS 8571 8666 . - 0 ID=CDS4;Parent=AT1G01020.1 +Chr1 TAIR10 exon 8571 8737 . - . Parent=AT1G01020.1 +Chr1 . start_codon 8664 8666 . - . Parent=AT1G01020.1 +Chr1 TAIR10 five_prime_UTR 8667 8737 . - . Parent=AT1G01020.1 +### + | + | CDS structure comparison + | 9 reference CDS segments + | 9 prediction CDS segments + | CDS structures match perfectly! + | + | Exon structure comparison + | 10 reference exons + | 10 prediction exons + | Exon structures match perfectly! + | + | UTR structure comparison + | 3 reference UTR segments + | 3 prediction UTR segments + | UTR structures match perfectly! + | + | Gene structures match perfectly! + | + | + |-------------------------- + |----- End comparison ----- + |-------------------------- + | + |-------------------------- + |---- Begin comparison ---- + |-------------------------- + | + | reference transcripts: + | AT1G01020.2 + | prediction transcripts: + | AT1G01020.2 + | + | reference GFF3: +##gff-version 3 +Chr1 TAIR9 mRNA 6790 8737 . - . ID=AT1G01020.2;Name=AT1G01020.2;index=1 +Chr1 TAIR9 three_prime_UTR 6790 7069 . - . Parent=AT1G01020.2 +Chr1 TAIR9 exon 6790 7069 . - . Parent=AT1G01020.2 +Chr1 TAIR9 three_prime_UTR 7157 7314 . - . Parent=AT1G01020.2 +Chr1 TAIR9 exon 7157 7450 . - . Parent=AT1G01020.2 +Chr1 . stop_codon 7315 7317 . - . Parent=AT1G01020.2 +Chr1 TAIR9 CDS 7315 7450 . - 1 ID=CDS3;Parent=AT1G01020.2 +Chr1 TAIR9 CDS 7564 7649 . - 0 ID=CDS3;Parent=AT1G01020.2 +Chr1 TAIR9 exon 7564 7649 . - . Parent=AT1G01020.2 +Chr1 TAIR9 CDS 7762 7835 . - 2 ID=CDS3;Parent=AT1G01020.2 +Chr1 TAIR9 exon 7762 7835 . - . Parent=AT1G01020.2 +Chr1 TAIR9 CDS 7942 7987 . - 0 ID=CDS3;Parent=AT1G01020.2 +Chr1 TAIR9 exon 7942 7987 . - . Parent=AT1G01020.2 +Chr1 TAIR9 CDS 8236 8325 . - 0 ID=CDS3;Parent=AT1G01020.2 +Chr1 TAIR9 exon 8236 8325 . - . Parent=AT1G01020.2 +Chr1 TAIR9 CDS 8417 8464 . - 0 ID=CDS3;Parent=AT1G01020.2 +Chr1 TAIR9 exon 8417 8464 . - . Parent=AT1G01020.2 +Chr1 TAIR9 CDS 8571 8666 . - 0 ID=CDS3;Parent=AT1G01020.2 +Chr1 TAIR9 exon 8571 8737 . - . Parent=AT1G01020.2 +Chr1 . start_codon 8664 8666 . - . Parent=AT1G01020.2 +Chr1 TAIR9 five_prime_UTR 8667 8737 . - . Parent=AT1G01020.2 +### + | prediction GFF3: +##gff-version 3 +Chr1 TAIR10 mRNA 6790 8737 . - . ID=AT1G01020.2;Name=AT1G01020.2;index=1 +Chr1 TAIR10 three_prime_UTR 6790 7069 . - . Parent=AT1G01020.2 +Chr1 TAIR10 exon 6790 7069 . - . Parent=AT1G01020.2 +Chr1 TAIR10 three_prime_UTR 7157 7314 . - . Parent=AT1G01020.2 +Chr1 TAIR10 exon 7157 7450 . - . Parent=AT1G01020.2 +Chr1 . stop_codon 7315 7317 . - . Parent=AT1G01020.2 +Chr1 TAIR10 CDS 7315 7450 . - 1 ID=CDS5;Parent=AT1G01020.2 +Chr1 TAIR10 CDS 7564 7649 . - 0 ID=CDS5;Parent=AT1G01020.2 +Chr1 TAIR10 exon 7564 7649 . - . Parent=AT1G01020.2 +Chr1 TAIR10 CDS 7762 7835 . - 2 ID=CDS5;Parent=AT1G01020.2 +Chr1 TAIR10 exon 7762 7835 . - . Parent=AT1G01020.2 +Chr1 TAIR10 CDS 7942 7987 . - 0 ID=CDS5;Parent=AT1G01020.2 +Chr1 TAIR10 exon 7942 7987 . - . Parent=AT1G01020.2 +Chr1 TAIR10 CDS 8236 8325 . - 0 ID=CDS5;Parent=AT1G01020.2 +Chr1 TAIR10 exon 8236 8325 . - . Parent=AT1G01020.2 +Chr1 TAIR10 CDS 8417 8464 . - 0 ID=CDS5;Parent=AT1G01020.2 +Chr1 TAIR10 exon 8417 8464 . - . Parent=AT1G01020.2 +Chr1 TAIR10 CDS 8571 8666 . - 0 ID=CDS5;Parent=AT1G01020.2 +Chr1 TAIR10 exon 8571 8737 . - . Parent=AT1G01020.2 +Chr1 . start_codon 8664 8666 . - . Parent=AT1G01020.2 +Chr1 TAIR10 five_prime_UTR 8667 8737 . - . Parent=AT1G01020.2 +### + | + | CDS structure comparison + | 7 reference CDS segments + | 7 prediction CDS segments + | CDS structures match perfectly! + | + | Exon structure comparison + | 8 reference exons + | 8 prediction exons + | Exon structures match perfectly! + | + | UTR structure comparison + | 3 reference UTR segments + | 3 prediction UTR segments + | UTR structures match perfectly! + | + | Gene structures match perfectly! + | + | + |-------------------------- + |----- End comparison ----- + |-------------------------- + +|------------------------------------------------- +|---- Locus: seqid=Chr1 range=11644-13719 +|------------------------------------------------- +| +| reference genes: +| AT1G01030 +| +| prediction genes: +| AT1G01030 +| +|---------- + | + |-------------------------- + |---- Begin comparison ---- + |-------------------------- + | + | reference transcripts: + | AT1G01030.1 + | prediction transcripts: + | AT1G01030.1 + | + | reference GFF3: +##gff-version 3 +Chr1 TAIR9 mRNA 11649 13714 . - . ID=AT1G01030.1;Name=AT1G01030.1;index=1 +Chr1 TAIR9 three_prime_UTR 11649 11863 . - . Parent=AT1G01030.1 +Chr1 TAIR9 exon 11649 13173 . - . Parent=AT1G01030.1 +Chr1 . stop_codon 11864 11866 . - . Parent=AT1G01030.1 +Chr1 TAIR9 CDS 11864 12940 . - 0 Parent=AT1G01030.1 +Chr1 . start_codon 12938 12940 . - . Parent=AT1G01030.1 +Chr1 TAIR9 five_prime_UTR 12941 13173 . - . Parent=AT1G01030.1 +Chr1 . intron 13174 13334 . - . Parent=AT1G01030.1 +Chr1 TAIR9 five_prime_UTR 13335 13714 . - . Parent=AT1G01030.1 +Chr1 TAIR9 exon 13335 13714 . - . Parent=AT1G01030.1 +### + | prediction GFF3: +##gff-version 3 +Chr1 TAIR10 mRNA 11649 13714 . - . ID=AT1G01030.1;Name=AT1G01030.1;index=1 +Chr1 TAIR10 three_prime_UTR 11649 11863 . - . Parent=AT1G01030.1 +Chr1 TAIR10 exon 11649 13173 . - . Parent=AT1G01030.1 +Chr1 . stop_codon 11864 11866 . - . Parent=AT1G01030.1 +Chr1 TAIR10 CDS 11864 12940 . - 0 Parent=AT1G01030.1 +Chr1 . start_codon 12938 12940 . - . Parent=AT1G01030.1 +Chr1 TAIR10 five_prime_UTR 12941 13173 . - . Parent=AT1G01030.1 +Chr1 . intron 13174 13334 . - . Parent=AT1G01030.1 +Chr1 TAIR10 five_prime_UTR 13335 13714 . - . Parent=AT1G01030.1 +Chr1 TAIR10 exon 13335 13714 . - . Parent=AT1G01030.1 +### + | + | CDS structure comparison + | 1 reference CDS segments + | 1 prediction CDS segments + | CDS structures match perfectly! + | + | Exon structure comparison + | 2 reference exons + | 2 prediction exons + | Exon structures match perfectly! + | + | UTR structure comparison + | 3 reference UTR segments + | 3 prediction UTR segments + | UTR structures match perfectly! + | + | Gene structures match perfectly! + | + | + |-------------------------- + |----- End comparison ----- + |-------------------------- + +|------------------------------------------------- +|---- Locus: seqid=Chr1 range=23141-31232 +|------------------------------------------------- +| +| reference genes: +| AT1G01040 +| +| prediction genes: +| AT1G01040 +| +|---------- + | + |-------------------------- + |---- Begin comparison ---- + |-------------------------- + | + | reference transcripts: + | AT1G01040.1 + | prediction transcripts: + | AT1G01040.1 + | + | reference GFF3: +##gff-version 3 +Chr1 TAIR9 mRNA 23146 31227 . + . ID=AT1G01040.1;Name=AT1G01040.1;index=1 +Chr1 TAIR9 five_prime_UTR 23146 23518 . + . Parent=AT1G01040.1 +Chr1 TAIR9 exon 23146 24451 . + . Parent=AT1G01040.1 +Chr1 . start_codon 23519 23521 . + . Parent=AT1G01040.1 +Chr1 TAIR9 CDS 23519 24451 . + 0 ID=CDS6;Parent=AT1G01040.1 +Chr1 . intron 24452 24541 . + . Parent=AT1G01040.1 +Chr1 TAIR9 exon 24542 24655 . + . Parent=AT1G01040.1 +Chr1 TAIR9 CDS 24542 24655 . + 0 ID=CDS6;Parent=AT1G01040.1 +Chr1 . intron 24656 24751 . + . Parent=AT1G01040.1 +Chr1 TAIR9 exon 24752 24962 . + . Parent=AT1G01040.1 +Chr1 TAIR9 CDS 24752 24962 . + 0 ID=CDS6;Parent=AT1G01040.1 +Chr1 . intron 24963 25040 . + . Parent=AT1G01040.1 +Chr1 TAIR9 exon 25041 25435 . + . Parent=AT1G01040.1 +Chr1 TAIR9 CDS 25041 25435 . + 2 ID=CDS6;Parent=AT1G01040.1 +Chr1 . intron 25436 25523 . + . Parent=AT1G01040.1 +Chr1 TAIR9 exon 25524 25743 . + . Parent=AT1G01040.1 +Chr1 TAIR9 CDS 25524 25743 . + 0 ID=CDS6;Parent=AT1G01040.1 +Chr1 . intron 25744 25824 . + . Parent=AT1G01040.1 +Chr1 TAIR9 exon 25825 25997 . + . Parent=AT1G01040.1 +Chr1 TAIR9 CDS 25825 25997 . + 2 ID=CDS6;Parent=AT1G01040.1 +Chr1 . intron 25998 26080 . + . Parent=AT1G01040.1 +Chr1 TAIR9 exon 26081 26203 . + . Parent=AT1G01040.1 +Chr1 TAIR9 CDS 26081 26203 . + 0 ID=CDS6;Parent=AT1G01040.1 +Chr1 . intron 26204 26291 . + . Parent=AT1G01040.1 +Chr1 TAIR9 exon 26292 26452 . + . Parent=AT1G01040.1 +Chr1 TAIR9 CDS 26292 26452 . + 0 ID=CDS6;Parent=AT1G01040.1 +Chr1 . intron 26453 26542 . + . Parent=AT1G01040.1 +Chr1 TAIR9 exon 26543 26776 . + . Parent=AT1G01040.1 +Chr1 TAIR9 CDS 26543 26776 . + 1 ID=CDS6;Parent=AT1G01040.1 +Chr1 . intron 26777 26861 . + . Parent=AT1G01040.1 +Chr1 TAIR9 exon 26862 27012 . + . Parent=AT1G01040.1 +Chr1 TAIR9 CDS 26862 27012 . + 1 ID=CDS6;Parent=AT1G01040.1 +Chr1 . intron 27013 27098 . + . Parent=AT1G01040.1 +Chr1 TAIR9 exon 27099 27281 . + . Parent=AT1G01040.1 +Chr1 TAIR9 CDS 27099 27281 . + 0 ID=CDS6;Parent=AT1G01040.1 +Chr1 . intron 27282 27371 . + . Parent=AT1G01040.1 +Chr1 TAIR9 exon 27372 27533 . + . Parent=AT1G01040.1 +Chr1 TAIR9 CDS 27372 27533 . + 0 ID=CDS6;Parent=AT1G01040.1 +Chr1 . stop_codon 27531 27533 . + . Parent=AT1G01040.1 +### + | prediction GFF3: +##gff-version 3 +Chr1 TAIR10 mRNA 23146 31227 . + . ID=AT1G01040.1;Name=AT1G01040.1;index=1 +Chr1 TAIR10 five_prime_UTR 23146 23518 . + . Parent=AT1G01040.1 +Chr1 TAIR10 exon 23146 24451 . + . Parent=AT1G01040.1 +Chr1 . start_codon 23519 23521 . + . Parent=AT1G01040.1 +Chr1 TAIR10 CDS 23519 24451 . + 0 ID=CDS7;Parent=AT1G01040.1 +Chr1 . intron 24452 24541 . + . Parent=AT1G01040.1 +Chr1 TAIR10 exon 24542 24655 . + . Parent=AT1G01040.1 +Chr1 TAIR10 CDS 24542 24655 . + 0 ID=CDS7;Parent=AT1G01040.1 +Chr1 . intron 24656 24751 . + . Parent=AT1G01040.1 +Chr1 TAIR10 exon 24752 24962 . + . Parent=AT1G01040.1 +Chr1 TAIR10 CDS 24752 24962 . + 0 ID=CDS7;Parent=AT1G01040.1 +Chr1 . intron 24963 25040 . + . Parent=AT1G01040.1 +Chr1 TAIR10 exon 25041 25435 . + . Parent=AT1G01040.1 +Chr1 TAIR10 CDS 25041 25435 . + 2 ID=CDS7;Parent=AT1G01040.1 +Chr1 . intron 25436 25523 . + . Parent=AT1G01040.1 +Chr1 TAIR10 exon 25524 25743 . + . Parent=AT1G01040.1 +Chr1 TAIR10 CDS 25524 25743 . + 0 ID=CDS7;Parent=AT1G01040.1 +Chr1 . intron 25744 25824 . + . Parent=AT1G01040.1 +Chr1 TAIR10 exon 25825 25997 . + . Parent=AT1G01040.1 +Chr1 TAIR10 CDS 25825 25997 . + 2 ID=CDS7;Parent=AT1G01040.1 +Chr1 . intron 25998 26080 . + . Parent=AT1G01040.1 +Chr1 TAIR10 exon 26081 26203 . + . Parent=AT1G01040.1 +Chr1 TAIR10 CDS 26081 26203 . + 0 ID=CDS7;Parent=AT1G01040.1 +Chr1 . intron 26204 26291 . + . Parent=AT1G01040.1 +Chr1 TAIR10 exon 26292 26452 . + . Parent=AT1G01040.1 +Chr1 TAIR10 CDS 26292 26452 . + 0 ID=CDS7;Parent=AT1G01040.1 +Chr1 . intron 26453 26542 . + . Parent=AT1G01040.1 +Chr1 TAIR10 exon 26543 26776 . + . Parent=AT1G01040.1 +Chr1 TAIR10 CDS 26543 26776 . + 1 ID=CDS7;Parent=AT1G01040.1 +Chr1 . intron 26777 26861 . + . Parent=AT1G01040.1 +Chr1 TAIR10 exon 26862 27012 . + . Parent=AT1G01040.1 +Chr1 TAIR10 CDS 26862 27012 . + 1 ID=CDS7;Parent=AT1G01040.1 +Chr1 . intron 27013 27098 . + . Parent=AT1G01040.1 +Chr1 TAIR10 exon 27099 27281 . + . Parent=AT1G01040.1 +Chr1 TAIR10 CDS 27099 27281 . + 0 ID=CDS7;Parent=AT1G01040.1 +Chr1 . intron 27282 27371 . + . Parent=AT1G01040.1 +Chr1 TAIR10 exon 27372 27533 . + . Parent=AT1G01040.1 +Chr1 TAIR10 CDS 27372 27533 . + 0 ID=CDS7;Parent=AT1G01040.1 +Chr1 . stop_codon 27531 27533 . + . Parent=AT1G01040.1 +### + | + | CDS structure comparison + | 12 reference CDS segments + | 12 prediction CDS segments + | CDS structures match perfectly! + | + | Exon structure comparison + | 12 reference exons + | 12 prediction exons + | Exon structures match perfectly! + | + | UTR structure comparison + | 1 reference UTR segments + | 1 prediction UTR segments + | UTR structures match perfectly! + | + | Gene structures match perfectly! + | + | + |-------------------------- + |----- End comparison ----- + |-------------------------- + +============================================================ +========== ParsEval Summary +============================================================ + +Started: 31 Dec 2020, 08:38PM +Reference annotations: /tmp/tmpuaspc0eb/files/5/1/b/dataset_51bd183d-470e-4a87-a230-5a73a406179d.dat +Prediction annotations: /tmp/tmpuaspc0eb/files/6/f/b/dataset_6fba7592-2a44-4ea7-ae0a-ba0c87badb42.dat +Executing command: parseval -l 5 -t 20 -w -f text -o /tmp/tmpuaspc0eb/files/9/2/0/dataset_92006ba5-932e-40f8-a785-2a9b2932d88a.dat /tmp/tmpuaspc0eb/files/5/1/b/dataset_51bd183d-470e-4a87-a230-5a73a406179d.dat /tmp/tmpuaspc0eb/files/6/f/b/dataset_6fba7592-2a44-4ea7-ae0a-ba0c87badb42.dat + + Sequences compared + Chr1 + + Gene loci................................4 + shared.................................4 + unique to reference....................0 + unique to prediction...................0 + + Reference annotations + genes..................................4 + average per locus....................1.000 + transcripts............................5 + average per locus....................1.250 + average per gene.....................1.250 + + Prediction annotations + genes..................................4 + average per locus....................1.000 + transcripts............................5 + average per locus....................1.250 + average per gene.....................1.250 + + Total comparisons........................5 + perfect matches........................5 (100.0%) + avg. length..........................3617.40 bp + avg. # refr exons....................7.60 + avg. # pred exons....................7.60 + avg. refr CDS length.................449.40 aa + avg. pred CDS length.................449.40 aa + perfect matches with mislabeled UTRs...0 (0.0%) + CDS structure matches..................0 (0.0%) + exon structure matches.................0 (0.0%) + UTR structure matches..................0 (0.0%) + non-matches............................0 (0.0%) + + CDS structure comparison + reference CDS segments.................35 + match prediction.....................35 (100.0%) + don't match prediction...............0 (0.0%) + prediction CDS segments................35 + match reference......................35 (100.0%) + don't match reference................0 (0.0%) + Sensitivity............................1.000 + Specificity............................1.000 + F1 Score...............................1.000 + Annotation edit distance...............0.000 + + Exon structure comparison + reference exons........................38 + match prediction.....................38 (100.0%) + don't match prediction...............0 (0.0%) + prediction exons.......................38 + match reference......................38 (100.0%) + don't match reference................0 (0.0%) + Sensitivity............................1.000 + Specificity............................1.000 + F1 Score...............................1.000 + Annotation edit distance...............0.000 + + UTR structure comparison + reference UTR segments.................12 + match prediction.....................12 (100.0%) + don't match prediction...............0 (0.0%) + prediction UTR segments................12 + match reference......................12 (100.0%) + don't match reference................0 (0.0%) + Sensitivity............................1.000 + Specificity............................1.000 + F1 Score...............................1.000 + Annotation edit distance...............0.000 + + Nucleotide-level comparison CDS UTRs Overall + Matching coefficient: 1.000 1.000 1.000 + Correlation coefficient: 1.000 1.000 -- + Sensitivity: 1.000 1.000 -- + Specificity: 1.000 1.000 -- + F1 Score: 1.000 1.000 -- + Annotation edit distance: 0.000 0.000 -- diff -r 000000000000 -r c4ac24510b55 test-data/parseval_output_test2.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/parseval_output_test2.txt Sun Jan 03 14:58:58 2021 +0000 @@ -0,0 +1,577 @@ +|------------------------------------------------- +|---- Locus: seqid=Chr1 range=3631-5899 +|------------------------------------------------- +| +| reference genes: +| AT1G01010 +| +| prediction genes: +| AT1G01010 +| +|---------- + | + |-------------------------- + |---- Begin comparison ---- + |-------------------------- + | + | reference transcripts: + | AT1G01010.1 + | prediction transcripts: + | AT1G01010.1 + | + | reference GFF3: +##gff-version 3 +Chr1 TAIR9 mRNA 3631 5899 . + . ID=AT1G01010.1;Name=AT1G01010.1;index=1 +Chr1 TAIR9 five_prime_UTR 3631 3759 . + . Parent=AT1G01010.1 +Chr1 TAIR9 exon 3631 3913 . + . Parent=AT1G01010.1 +Chr1 . start_codon 3760 3762 . + . Parent=AT1G01010.1 +Chr1 TAIR9 CDS 3760 3913 . + 0 ID=CDS0;Parent=AT1G01010.1 +Chr1 . intron 3914 3995 . + . Parent=AT1G01010.1 +Chr1 TAIR9 exon 3996 4276 . + . Parent=AT1G01010.1 +Chr1 TAIR9 CDS 3996 4276 . + 2 ID=CDS0;Parent=AT1G01010.1 +Chr1 . intron 4277 4485 . + . Parent=AT1G01010.1 +Chr1 TAIR9 exon 4486 4605 . + . Parent=AT1G01010.1 +Chr1 TAIR9 CDS 4486 4605 . + 0 ID=CDS0;Parent=AT1G01010.1 +Chr1 . intron 4606 4705 . + . Parent=AT1G01010.1 +Chr1 TAIR9 exon 4706 5095 . + . Parent=AT1G01010.1 +Chr1 TAIR9 CDS 4706 5095 . + 0 ID=CDS0;Parent=AT1G01010.1 +Chr1 . intron 5096 5173 . + . Parent=AT1G01010.1 +Chr1 TAIR9 exon 5174 5326 . + . Parent=AT1G01010.1 +Chr1 TAIR9 CDS 5174 5326 . + 0 ID=CDS0;Parent=AT1G01010.1 +Chr1 . intron 5327 5438 . + . Parent=AT1G01010.1 +Chr1 TAIR9 CDS 5439 5630 . + 0 ID=CDS0;Parent=AT1G01010.1 +Chr1 TAIR9 exon 5439 5899 . + . Parent=AT1G01010.1 +Chr1 . stop_codon 5628 5630 . + . Parent=AT1G01010.1 +Chr1 TAIR9 three_prime_UTR 5631 5899 . + . Parent=AT1G01010.1 +### + | prediction GFF3: +##gff-version 3 +Chr1 TAIR10 mRNA 3631 5899 . + . ID=AT1G01010.1;Name=AT1G01010.1;index=1 +Chr1 TAIR10 five_prime_UTR 3631 3759 . + . Parent=AT1G01010.1 +Chr1 TAIR10 exon 3631 3913 . + . Parent=AT1G01010.1 +Chr1 . start_codon 3760 3762 . + . Parent=AT1G01010.1 +Chr1 TAIR10 CDS 3760 3913 . + 0 ID=CDS1;Parent=AT1G01010.1 +Chr1 . intron 3914 3995 . + . Parent=AT1G01010.1 +Chr1 TAIR10 exon 3996 4276 . + . Parent=AT1G01010.1 +Chr1 TAIR10 CDS 3996 4276 . + 2 ID=CDS1;Parent=AT1G01010.1 +Chr1 . intron 4277 4485 . + . Parent=AT1G01010.1 +Chr1 TAIR10 exon 4486 4605 . + . Parent=AT1G01010.1 +Chr1 TAIR10 CDS 4486 4605 . + 0 ID=CDS1;Parent=AT1G01010.1 +Chr1 . intron 4606 4705 . + . Parent=AT1G01010.1 +Chr1 TAIR10 exon 4706 5095 . + . Parent=AT1G01010.1 +Chr1 TAIR10 CDS 4706 5095 . + 0 ID=CDS1;Parent=AT1G01010.1 +Chr1 . intron 5096 5173 . + . Parent=AT1G01010.1 +Chr1 TAIR10 exon 5174 5326 . + . Parent=AT1G01010.1 +Chr1 TAIR10 CDS 5174 5326 . + 0 ID=CDS1;Parent=AT1G01010.1 +Chr1 . intron 5327 5438 . + . Parent=AT1G01010.1 +Chr1 TAIR10 CDS 5439 5630 . + 0 ID=CDS1;Parent=AT1G01010.1 +Chr1 TAIR10 exon 5439 5899 . + . Parent=AT1G01010.1 +Chr1 . stop_codon 5628 5630 . + . Parent=AT1G01010.1 +Chr1 TAIR10 three_prime_UTR 5631 5899 . + . Parent=AT1G01010.1 +### + | + | CDS structure comparison + | 6 reference CDS segments + | 6 prediction CDS segments + | CDS structures match perfectly! + | + | Exon structure comparison + | 6 reference exons + | 6 prediction exons + | Exon structures match perfectly! + | + | UTR structure comparison + | 2 reference UTR segments + | 2 prediction UTR segments + | UTR structures match perfectly! + | + | Gene structures match perfectly! + | + | + |-------------------------- + |----- End comparison ----- + |-------------------------- + +|------------------------------------------------- +|---- Locus: seqid=Chr1 range=5928-8737 +|------------------------------------------------- +| +| reference genes: +| AT1G01020 +| +| prediction genes: +| AT1G01020 +| +|---------- + | + |-------------------------- + |---- Begin comparison ---- + |-------------------------- + | + | reference transcripts: + | AT1G01020.1 + | prediction transcripts: + | AT1G01020.1 + | + | reference GFF3: +##gff-version 3 +Chr1 TAIR9 mRNA 5928 8737 . - . ID=AT1G01020.1;Name=AT1G01020.1;index=1 +Chr1 TAIR9 three_prime_UTR 5928 6263 . - . Parent=AT1G01020.1 +Chr1 TAIR9 exon 5928 6263 . - . Parent=AT1G01020.1 +Chr1 . intron 6264 6436 . - . Parent=AT1G01020.1 +Chr1 TAIR9 three_prime_UTR 6437 6914 . - . Parent=AT1G01020.1 +Chr1 TAIR9 exon 6437 7069 . - . Parent=AT1G01020.1 +Chr1 . stop_codon 6915 6917 . - . Parent=AT1G01020.1 +Chr1 TAIR9 CDS 6915 7069 . - 2 ID=CDS2;Parent=AT1G01020.1 +Chr1 . intron 7070 7156 . - . Parent=AT1G01020.1 +Chr1 TAIR9 CDS 7157 7232 . - 0 ID=CDS2;Parent=AT1G01020.1 +Chr1 TAIR9 exon 7157 7232 . - . Parent=AT1G01020.1 +Chr1 . intron 7233 7383 . - . Parent=AT1G01020.1 +Chr1 TAIR9 CDS 7384 7450 . - 1 ID=CDS2;Parent=AT1G01020.1 +Chr1 TAIR9 exon 7384 7450 . - . Parent=AT1G01020.1 +Chr1 . intron 7451 7563 . - . Parent=AT1G01020.1 +Chr1 TAIR9 CDS 7564 7649 . - 0 ID=CDS2;Parent=AT1G01020.1 +Chr1 TAIR9 exon 7564 7649 . - . Parent=AT1G01020.1 +Chr1 . intron 7650 7761 . - . Parent=AT1G01020.1 +Chr1 TAIR9 CDS 7762 7835 . - 2 ID=CDS2;Parent=AT1G01020.1 +Chr1 TAIR9 exon 7762 7835 . - . Parent=AT1G01020.1 +Chr1 . intron 7836 7941 . - . Parent=AT1G01020.1 +Chr1 TAIR9 CDS 7942 7987 . - 0 ID=CDS2;Parent=AT1G01020.1 +Chr1 TAIR9 exon 7942 7987 . - . Parent=AT1G01020.1 +Chr1 . intron 7988 8235 . - . Parent=AT1G01020.1 +Chr1 TAIR9 CDS 8236 8325 . - 0 ID=CDS2;Parent=AT1G01020.1 +Chr1 TAIR9 exon 8236 8325 . - . Parent=AT1G01020.1 +Chr1 . intron 8326 8416 . - . Parent=AT1G01020.1 +Chr1 TAIR9 CDS 8417 8464 . - 0 ID=CDS2;Parent=AT1G01020.1 +Chr1 TAIR9 exon 8417 8464 . - . Parent=AT1G01020.1 +Chr1 . intron 8465 8570 . - . Parent=AT1G01020.1 +Chr1 TAIR9 CDS 8571 8666 . - 0 ID=CDS2;Parent=AT1G01020.1 +Chr1 TAIR9 exon 8571 8737 . - . Parent=AT1G01020.1 +Chr1 . start_codon 8664 8666 . - . Parent=AT1G01020.1 +Chr1 TAIR9 five_prime_UTR 8667 8737 . - . Parent=AT1G01020.1 +### + | prediction GFF3: +##gff-version 3 +Chr1 TAIR10 mRNA 5928 8737 . - . ID=AT1G01020.1;Name=AT1G01020.1;index=1 +Chr1 TAIR10 three_prime_UTR 5928 6263 . - . Parent=AT1G01020.1 +Chr1 TAIR10 exon 5928 6263 . - . Parent=AT1G01020.1 +Chr1 . intron 6264 6436 . - . Parent=AT1G01020.1 +Chr1 TAIR10 three_prime_UTR 6437 6914 . - . Parent=AT1G01020.1 +Chr1 TAIR10 exon 6437 7069 . - . Parent=AT1G01020.1 +Chr1 . stop_codon 6915 6917 . - . Parent=AT1G01020.1 +Chr1 TAIR10 CDS 6915 7069 . - 2 ID=CDS4;Parent=AT1G01020.1 +Chr1 . intron 7070 7156 . - . Parent=AT1G01020.1 +Chr1 TAIR10 CDS 7157 7232 . - 0 ID=CDS4;Parent=AT1G01020.1 +Chr1 TAIR10 exon 7157 7232 . - . Parent=AT1G01020.1 +Chr1 . intron 7233 7383 . - . Parent=AT1G01020.1 +Chr1 TAIR10 CDS 7384 7450 . - 1 ID=CDS4;Parent=AT1G01020.1 +Chr1 TAIR10 exon 7384 7450 . - . Parent=AT1G01020.1 +Chr1 . intron 7451 7563 . - . Parent=AT1G01020.1 +Chr1 TAIR10 CDS 7564 7649 . - 0 ID=CDS4;Parent=AT1G01020.1 +Chr1 TAIR10 exon 7564 7649 . - . Parent=AT1G01020.1 +Chr1 . intron 7650 7761 . - . Parent=AT1G01020.1 +Chr1 TAIR10 CDS 7762 7835 . - 2 ID=CDS4;Parent=AT1G01020.1 +Chr1 TAIR10 exon 7762 7835 . - . Parent=AT1G01020.1 +Chr1 . intron 7836 7941 . - . Parent=AT1G01020.1 +Chr1 TAIR10 CDS 7942 7987 . - 0 ID=CDS4;Parent=AT1G01020.1 +Chr1 TAIR10 exon 7942 7987 . - . Parent=AT1G01020.1 +Chr1 . intron 7988 8235 . - . Parent=AT1G01020.1 +Chr1 TAIR10 CDS 8236 8325 . - 0 ID=CDS4;Parent=AT1G01020.1 +Chr1 TAIR10 exon 8236 8325 . - . Parent=AT1G01020.1 +Chr1 . intron 8326 8416 . - . Parent=AT1G01020.1 +Chr1 TAIR10 CDS 8417 8464 . - 0 ID=CDS4;Parent=AT1G01020.1 +Chr1 TAIR10 exon 8417 8464 . - . Parent=AT1G01020.1 +Chr1 . intron 8465 8570 . - . Parent=AT1G01020.1 +Chr1 TAIR10 CDS 8571 8666 . - 0 ID=CDS4;Parent=AT1G01020.1 +Chr1 TAIR10 exon 8571 8737 . - . Parent=AT1G01020.1 +Chr1 . start_codon 8664 8666 . - . Parent=AT1G01020.1 +Chr1 TAIR10 five_prime_UTR 8667 8737 . - . Parent=AT1G01020.1 +### + | + | CDS structure comparison + | 9 reference CDS segments + | 9 prediction CDS segments + | CDS structures match perfectly! + | + | Exon structure comparison + | 10 reference exons + | 10 prediction exons + | Exon structures match perfectly! + | + | UTR structure comparison + | 3 reference UTR segments + | 3 prediction UTR segments + | UTR structures match perfectly! + | + | Gene structures match perfectly! + | + | + |-------------------------- + |----- End comparison ----- + |-------------------------- + | + |-------------------------- + |---- Begin comparison ---- + |-------------------------- + | + | reference transcripts: + | AT1G01020.2 + | prediction transcripts: + | AT1G01020.2 + | + | reference GFF3: +##gff-version 3 +Chr1 TAIR9 mRNA 6790 8737 . - . ID=AT1G01020.2;Name=AT1G01020.2;index=1 +Chr1 TAIR9 three_prime_UTR 6790 7069 . - . Parent=AT1G01020.2 +Chr1 TAIR9 exon 6790 7069 . - . Parent=AT1G01020.2 +Chr1 TAIR9 three_prime_UTR 7157 7314 . - . Parent=AT1G01020.2 +Chr1 TAIR9 exon 7157 7450 . - . Parent=AT1G01020.2 +Chr1 . stop_codon 7315 7317 . - . Parent=AT1G01020.2 +Chr1 TAIR9 CDS 7315 7450 . - 1 ID=CDS3;Parent=AT1G01020.2 +Chr1 TAIR9 CDS 7564 7649 . - 0 ID=CDS3;Parent=AT1G01020.2 +Chr1 TAIR9 exon 7564 7649 . - . Parent=AT1G01020.2 +Chr1 TAIR9 CDS 7762 7835 . - 2 ID=CDS3;Parent=AT1G01020.2 +Chr1 TAIR9 exon 7762 7835 . - . Parent=AT1G01020.2 +Chr1 TAIR9 CDS 7942 7987 . - 0 ID=CDS3;Parent=AT1G01020.2 +Chr1 TAIR9 exon 7942 7987 . - . Parent=AT1G01020.2 +Chr1 TAIR9 CDS 8236 8325 . - 0 ID=CDS3;Parent=AT1G01020.2 +Chr1 TAIR9 exon 8236 8325 . - . Parent=AT1G01020.2 +Chr1 TAIR9 CDS 8417 8464 . - 0 ID=CDS3;Parent=AT1G01020.2 +Chr1 TAIR9 exon 8417 8464 . - . Parent=AT1G01020.2 +Chr1 TAIR9 CDS 8571 8666 . - 0 ID=CDS3;Parent=AT1G01020.2 +Chr1 TAIR9 exon 8571 8737 . - . Parent=AT1G01020.2 +Chr1 . start_codon 8664 8666 . - . Parent=AT1G01020.2 +Chr1 TAIR9 five_prime_UTR 8667 8737 . - . Parent=AT1G01020.2 +### + | prediction GFF3: +##gff-version 3 +Chr1 TAIR10 mRNA 6790 8737 . - . ID=AT1G01020.2;Name=AT1G01020.2;index=1 +Chr1 TAIR10 three_prime_UTR 6790 7069 . - . Parent=AT1G01020.2 +Chr1 TAIR10 exon 6790 7069 . - . Parent=AT1G01020.2 +Chr1 TAIR10 three_prime_UTR 7157 7314 . - . Parent=AT1G01020.2 +Chr1 TAIR10 exon 7157 7450 . - . Parent=AT1G01020.2 +Chr1 . stop_codon 7315 7317 . - . Parent=AT1G01020.2 +Chr1 TAIR10 CDS 7315 7450 . - 1 ID=CDS5;Parent=AT1G01020.2 +Chr1 TAIR10 CDS 7564 7649 . - 0 ID=CDS5;Parent=AT1G01020.2 +Chr1 TAIR10 exon 7564 7649 . - . Parent=AT1G01020.2 +Chr1 TAIR10 CDS 7762 7835 . - 2 ID=CDS5;Parent=AT1G01020.2 +Chr1 TAIR10 exon 7762 7835 . - . Parent=AT1G01020.2 +Chr1 TAIR10 CDS 7942 7987 . - 0 ID=CDS5;Parent=AT1G01020.2 +Chr1 TAIR10 exon 7942 7987 . - . Parent=AT1G01020.2 +Chr1 TAIR10 CDS 8236 8325 . - 0 ID=CDS5;Parent=AT1G01020.2 +Chr1 TAIR10 exon 8236 8325 . - . Parent=AT1G01020.2 +Chr1 TAIR10 CDS 8417 8464 . - 0 ID=CDS5;Parent=AT1G01020.2 +Chr1 TAIR10 exon 8417 8464 . - . Parent=AT1G01020.2 +Chr1 TAIR10 CDS 8571 8666 . - 0 ID=CDS5;Parent=AT1G01020.2 +Chr1 TAIR10 exon 8571 8737 . - . Parent=AT1G01020.2 +Chr1 . start_codon 8664 8666 . - . Parent=AT1G01020.2 +Chr1 TAIR10 five_prime_UTR 8667 8737 . - . Parent=AT1G01020.2 +### + | + | CDS structure comparison + | 7 reference CDS segments + | 7 prediction CDS segments + | CDS structures match perfectly! + | + | Exon structure comparison + | 8 reference exons + | 8 prediction exons + | Exon structures match perfectly! + | + | UTR structure comparison + | 3 reference UTR segments + | 3 prediction UTR segments + | UTR structures match perfectly! + | + | Gene structures match perfectly! + | + | + |-------------------------- + |----- End comparison ----- + |-------------------------- + +|------------------------------------------------- +|---- Locus: seqid=Chr1 range=11649-13714 +|------------------------------------------------- +| +| reference genes: +| AT1G01030 +| +| prediction genes: +| AT1G01030 +| +|---------- + | + |-------------------------- + |---- Begin comparison ---- + |-------------------------- + | + | reference transcripts: + | AT1G01030.1 + | prediction transcripts: + | AT1G01030.1 + | + | reference GFF3: +##gff-version 3 +Chr1 TAIR9 mRNA 11649 13714 . - . ID=AT1G01030.1;Name=AT1G01030.1;index=1 +Chr1 TAIR9 three_prime_UTR 11649 11863 . - . Parent=AT1G01030.1 +Chr1 TAIR9 exon 11649 13173 . - . Parent=AT1G01030.1 +Chr1 . stop_codon 11864 11866 . - . Parent=AT1G01030.1 +Chr1 TAIR9 CDS 11864 12940 . - 0 Parent=AT1G01030.1 +Chr1 . start_codon 12938 12940 . - . Parent=AT1G01030.1 +Chr1 TAIR9 five_prime_UTR 12941 13173 . - . Parent=AT1G01030.1 +Chr1 . intron 13174 13334 . - . Parent=AT1G01030.1 +Chr1 TAIR9 five_prime_UTR 13335 13714 . - . Parent=AT1G01030.1 +Chr1 TAIR9 exon 13335 13714 . - . Parent=AT1G01030.1 +### + | prediction GFF3: +##gff-version 3 +Chr1 TAIR10 mRNA 11649 13714 . - . ID=AT1G01030.1;Name=AT1G01030.1;index=1 +Chr1 TAIR10 three_prime_UTR 11649 11863 . - . Parent=AT1G01030.1 +Chr1 TAIR10 exon 11649 13173 . - . Parent=AT1G01030.1 +Chr1 . stop_codon 11864 11866 . - . Parent=AT1G01030.1 +Chr1 TAIR10 CDS 11864 12940 . - 0 Parent=AT1G01030.1 +Chr1 . start_codon 12938 12940 . - . Parent=AT1G01030.1 +Chr1 TAIR10 five_prime_UTR 12941 13173 . - . Parent=AT1G01030.1 +Chr1 . intron 13174 13334 . - . Parent=AT1G01030.1 +Chr1 TAIR10 five_prime_UTR 13335 13714 . - . Parent=AT1G01030.1 +Chr1 TAIR10 exon 13335 13714 . - . Parent=AT1G01030.1 +### + | + | CDS structure comparison + | 1 reference CDS segments + | 1 prediction CDS segments + | CDS structures match perfectly! + | + | Exon structure comparison + | 2 reference exons + | 2 prediction exons + | Exon structures match perfectly! + | + | UTR structure comparison + | 3 reference UTR segments + | 3 prediction UTR segments + | UTR structures match perfectly! + | + | Gene structures match perfectly! + | + | + |-------------------------- + |----- End comparison ----- + |-------------------------- + +|------------------------------------------------- +|---- Locus: seqid=Chr1 range=23146-31227 +|------------------------------------------------- +| +| reference genes: +| AT1G01040 +| +| prediction genes: +| AT1G01040 +| +|---------- + | + |-------------------------- + |---- Begin comparison ---- + |-------------------------- + | + | reference transcripts: + | AT1G01040.1 + | prediction transcripts: + | AT1G01040.1 + | + | reference GFF3: +##gff-version 3 +Chr1 TAIR9 mRNA 23146 31227 . + . ID=AT1G01040.1;Name=AT1G01040.1;index=1 +Chr1 TAIR9 five_prime_UTR 23146 23518 . + . Parent=AT1G01040.1 +Chr1 TAIR9 exon 23146 24451 . + . Parent=AT1G01040.1 +Chr1 . start_codon 23519 23521 . + . Parent=AT1G01040.1 +Chr1 TAIR9 CDS 23519 24451 . + 0 ID=CDS6;Parent=AT1G01040.1 +Chr1 . intron 24452 24541 . + . Parent=AT1G01040.1 +Chr1 TAIR9 exon 24542 24655 . + . Parent=AT1G01040.1 +Chr1 TAIR9 CDS 24542 24655 . + 0 ID=CDS6;Parent=AT1G01040.1 +Chr1 . intron 24656 24751 . + . Parent=AT1G01040.1 +Chr1 TAIR9 exon 24752 24962 . + . Parent=AT1G01040.1 +Chr1 TAIR9 CDS 24752 24962 . + 0 ID=CDS6;Parent=AT1G01040.1 +Chr1 . intron 24963 25040 . + . Parent=AT1G01040.1 +Chr1 TAIR9 exon 25041 25435 . + . Parent=AT1G01040.1 +Chr1 TAIR9 CDS 25041 25435 . + 2 ID=CDS6;Parent=AT1G01040.1 +Chr1 . intron 25436 25523 . + . Parent=AT1G01040.1 +Chr1 TAIR9 exon 25524 25743 . + . Parent=AT1G01040.1 +Chr1 TAIR9 CDS 25524 25743 . + 0 ID=CDS6;Parent=AT1G01040.1 +Chr1 . intron 25744 25824 . + . Parent=AT1G01040.1 +Chr1 TAIR9 exon 25825 25997 . + . Parent=AT1G01040.1 +Chr1 TAIR9 CDS 25825 25997 . + 2 ID=CDS6;Parent=AT1G01040.1 +Chr1 . intron 25998 26080 . + . Parent=AT1G01040.1 +Chr1 TAIR9 exon 26081 26203 . + . Parent=AT1G01040.1 +Chr1 TAIR9 CDS 26081 26203 . + 0 ID=CDS6;Parent=AT1G01040.1 +Chr1 . intron 26204 26291 . + . Parent=AT1G01040.1 +Chr1 TAIR9 exon 26292 26452 . + . Parent=AT1G01040.1 +Chr1 TAIR9 CDS 26292 26452 . + 0 ID=CDS6;Parent=AT1G01040.1 +Chr1 . intron 26453 26542 . + . Parent=AT1G01040.1 +Chr1 TAIR9 exon 26543 26776 . + . Parent=AT1G01040.1 +Chr1 TAIR9 CDS 26543 26776 . + 1 ID=CDS6;Parent=AT1G01040.1 +Chr1 . intron 26777 26861 . + . Parent=AT1G01040.1 +Chr1 TAIR9 exon 26862 27012 . + . Parent=AT1G01040.1 +Chr1 TAIR9 CDS 26862 27012 . + 1 ID=CDS6;Parent=AT1G01040.1 +Chr1 . intron 27013 27098 . + . Parent=AT1G01040.1 +Chr1 TAIR9 exon 27099 27281 . + . Parent=AT1G01040.1 +Chr1 TAIR9 CDS 27099 27281 . + 0 ID=CDS6;Parent=AT1G01040.1 +Chr1 . intron 27282 27371 . + . Parent=AT1G01040.1 +Chr1 TAIR9 exon 27372 27533 . + . Parent=AT1G01040.1 +Chr1 TAIR9 CDS 27372 27533 . + 0 ID=CDS6;Parent=AT1G01040.1 +Chr1 . stop_codon 27531 27533 . + . Parent=AT1G01040.1 +### + | prediction GFF3: +##gff-version 3 +Chr1 TAIR10 mRNA 23146 31227 . + . ID=AT1G01040.1;Name=AT1G01040.1;index=1 +Chr1 TAIR10 five_prime_UTR 23146 23518 . + . Parent=AT1G01040.1 +Chr1 TAIR10 exon 23146 24451 . + . Parent=AT1G01040.1 +Chr1 . start_codon 23519 23521 . + . Parent=AT1G01040.1 +Chr1 TAIR10 CDS 23519 24451 . + 0 ID=CDS7;Parent=AT1G01040.1 +Chr1 . intron 24452 24541 . + . Parent=AT1G01040.1 +Chr1 TAIR10 exon 24542 24655 . + . Parent=AT1G01040.1 +Chr1 TAIR10 CDS 24542 24655 . + 0 ID=CDS7;Parent=AT1G01040.1 +Chr1 . intron 24656 24751 . + . Parent=AT1G01040.1 +Chr1 TAIR10 exon 24752 24962 . + . Parent=AT1G01040.1 +Chr1 TAIR10 CDS 24752 24962 . + 0 ID=CDS7;Parent=AT1G01040.1 +Chr1 . intron 24963 25040 . + . Parent=AT1G01040.1 +Chr1 TAIR10 exon 25041 25435 . + . Parent=AT1G01040.1 +Chr1 TAIR10 CDS 25041 25435 . + 2 ID=CDS7;Parent=AT1G01040.1 +Chr1 . intron 25436 25523 . + . Parent=AT1G01040.1 +Chr1 TAIR10 exon 25524 25743 . + . Parent=AT1G01040.1 +Chr1 TAIR10 CDS 25524 25743 . + 0 ID=CDS7;Parent=AT1G01040.1 +Chr1 . intron 25744 25824 . + . Parent=AT1G01040.1 +Chr1 TAIR10 exon 25825 25997 . + . Parent=AT1G01040.1 +Chr1 TAIR10 CDS 25825 25997 . + 2 ID=CDS7;Parent=AT1G01040.1 +Chr1 . intron 25998 26080 . + . Parent=AT1G01040.1 +Chr1 TAIR10 exon 26081 26203 . + . Parent=AT1G01040.1 +Chr1 TAIR10 CDS 26081 26203 . + 0 ID=CDS7;Parent=AT1G01040.1 +Chr1 . intron 26204 26291 . + . Parent=AT1G01040.1 +Chr1 TAIR10 exon 26292 26452 . + . Parent=AT1G01040.1 +Chr1 TAIR10 CDS 26292 26452 . + 0 ID=CDS7;Parent=AT1G01040.1 +Chr1 . intron 26453 26542 . + . Parent=AT1G01040.1 +Chr1 TAIR10 exon 26543 26776 . + . Parent=AT1G01040.1 +Chr1 TAIR10 CDS 26543 26776 . + 1 ID=CDS7;Parent=AT1G01040.1 +Chr1 . intron 26777 26861 . + . Parent=AT1G01040.1 +Chr1 TAIR10 exon 26862 27012 . + . Parent=AT1G01040.1 +Chr1 TAIR10 CDS 26862 27012 . + 1 ID=CDS7;Parent=AT1G01040.1 +Chr1 . intron 27013 27098 . + . Parent=AT1G01040.1 +Chr1 TAIR10 exon 27099 27281 . + . Parent=AT1G01040.1 +Chr1 TAIR10 CDS 27099 27281 . + 0 ID=CDS7;Parent=AT1G01040.1 +Chr1 . intron 27282 27371 . + . Parent=AT1G01040.1 +Chr1 TAIR10 exon 27372 27533 . + . Parent=AT1G01040.1 +Chr1 TAIR10 CDS 27372 27533 . + 0 ID=CDS7;Parent=AT1G01040.1 +Chr1 . stop_codon 27531 27533 . + . Parent=AT1G01040.1 +### + | + | CDS structure comparison + | 12 reference CDS segments + | 12 prediction CDS segments + | CDS structures match perfectly! + | + | Exon structure comparison + | 12 reference exons + | 12 prediction exons + | Exon structures match perfectly! + | + | UTR structure comparison + | 1 reference UTR segments + | 1 prediction UTR segments + | UTR structures match perfectly! + | + | Gene structures match perfectly! + | + | + |-------------------------- + |----- End comparison ----- + |-------------------------- + +============================================================ +========== ParsEval Summary +============================================================ + +Started: 31 Dec 2020, 08:38PM +Reference annotations: /tmp/tmpuaspc0eb/files/0/4/3/dataset_0436aebb-5e69-4845-b8d6-cc6932c61142.dat +Prediction annotations: /tmp/tmpuaspc0eb/files/f/a/e/dataset_fae0f82b-28de-405b-9da1-0a227c4b4b92.dat +Executing command: parseval -l 0 -t 32 -w -f text -o /tmp/tmpuaspc0eb/files/3/2/7/dataset_327cf1a1-a7ea-412e-ac0f-e23f78ff553a.dat /tmp/tmpuaspc0eb/files/0/4/3/dataset_0436aebb-5e69-4845-b8d6-cc6932c61142.dat /tmp/tmpuaspc0eb/files/f/a/e/dataset_fae0f82b-28de-405b-9da1-0a227c4b4b92.dat + + Sequences compared + Chr1 + + Gene loci................................4 + shared.................................4 + unique to reference....................0 + unique to prediction...................0 + + Reference annotations + genes..................................4 + average per locus....................1.000 + transcripts............................5 + average per locus....................1.250 + average per gene.....................1.250 + + Prediction annotations + genes..................................4 + average per locus....................1.000 + transcripts............................5 + average per locus....................1.250 + average per gene.....................1.250 + + Total comparisons........................5 + perfect matches........................5 (100.0%) + avg. length..........................3607.40 bp + avg. # refr exons....................7.60 + avg. # pred exons....................7.60 + avg. refr CDS length.................449.40 aa + avg. pred CDS length.................449.40 aa + perfect matches with mislabeled UTRs...0 (0.0%) + CDS structure matches..................0 (0.0%) + exon structure matches.................0 (0.0%) + UTR structure matches..................0 (0.0%) + non-matches............................0 (0.0%) + + CDS structure comparison + reference CDS segments.................35 + match prediction.....................35 (100.0%) + don't match prediction...............0 (0.0%) + prediction CDS segments................35 + match reference......................35 (100.0%) + don't match reference................0 (0.0%) + Sensitivity............................1.000 + Specificity............................1.000 + F1 Score...............................1.000 + Annotation edit distance...............0.000 + + Exon structure comparison + reference exons........................38 + match prediction.....................38 (100.0%) + don't match prediction...............0 (0.0%) + prediction exons.......................38 + match reference......................38 (100.0%) + don't match reference................0 (0.0%) + Sensitivity............................1.000 + Specificity............................1.000 + F1 Score...............................1.000 + Annotation edit distance...............0.000 + + UTR structure comparison + reference UTR segments.................12 + match prediction.....................12 (100.0%) + don't match prediction...............0 (0.0%) + prediction UTR segments................12 + match reference......................12 (100.0%) + don't match reference................0 (0.0%) + Sensitivity............................1.000 + Specificity............................1.000 + F1 Score...............................1.000 + Annotation edit distance...............0.000 + + Nucleotide-level comparison CDS UTRs Overall + Matching coefficient: 1.000 1.000 1.000 + Correlation coefficient: 1.000 1.000 -- + Sensitivity: 1.000 1.000 -- + Specificity: 1.000 1.000 -- + F1 Score: 1.000 1.000 -- + Annotation edit distance: 0.000 0.000 -- diff -r 000000000000 -r c4ac24510b55 test-data/parseval_output_test3.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/parseval_output_test3.txt Sun Jan 03 14:58:58 2021 +0000 @@ -0,0 +1,577 @@ +|------------------------------------------------- +|---- Locus: seqid=Chr1 range=3621-5913 +|------------------------------------------------- +| +| reference genes: +| AT1G01010 +| +| prediction genes: +| AT1G01010 +| +|---------- + | + |-------------------------- + |---- Begin comparison ---- + |-------------------------- + | + | reference transcripts: + | AT1G01010.1 + | prediction transcripts: + | AT1G01010.1 + | + | reference GFF3: +##gff-version 3 +Chr1 TAIR9 mRNA 3631 5899 . + . ID=AT1G01010.1;Name=AT1G01010.1;index=1 +Chr1 TAIR9 five_prime_UTR 3631 3759 . + . Parent=AT1G01010.1 +Chr1 TAIR9 exon 3631 3913 . + . Parent=AT1G01010.1 +Chr1 . start_codon 3760 3762 . + . Parent=AT1G01010.1 +Chr1 TAIR9 CDS 3760 3913 . + 0 ID=CDS0;Parent=AT1G01010.1 +Chr1 . intron 3914 3995 . + . Parent=AT1G01010.1 +Chr1 TAIR9 exon 3996 4276 . + . Parent=AT1G01010.1 +Chr1 TAIR9 CDS 3996 4276 . + 2 ID=CDS0;Parent=AT1G01010.1 +Chr1 . intron 4277 4485 . + . Parent=AT1G01010.1 +Chr1 TAIR9 exon 4486 4605 . + . Parent=AT1G01010.1 +Chr1 TAIR9 CDS 4486 4605 . + 0 ID=CDS0;Parent=AT1G01010.1 +Chr1 . intron 4606 4705 . + . Parent=AT1G01010.1 +Chr1 TAIR9 exon 4706 5095 . + . Parent=AT1G01010.1 +Chr1 TAIR9 CDS 4706 5095 . + 0 ID=CDS0;Parent=AT1G01010.1 +Chr1 . intron 5096 5173 . + . Parent=AT1G01010.1 +Chr1 TAIR9 exon 5174 5326 . + . Parent=AT1G01010.1 +Chr1 TAIR9 CDS 5174 5326 . + 0 ID=CDS0;Parent=AT1G01010.1 +Chr1 . intron 5327 5438 . + . Parent=AT1G01010.1 +Chr1 TAIR9 CDS 5439 5630 . + 0 ID=CDS0;Parent=AT1G01010.1 +Chr1 TAIR9 exon 5439 5899 . + . Parent=AT1G01010.1 +Chr1 . stop_codon 5628 5630 . + . Parent=AT1G01010.1 +Chr1 TAIR9 three_prime_UTR 5631 5899 . + . Parent=AT1G01010.1 +### + | prediction GFF3: +##gff-version 3 +Chr1 TAIR10 mRNA 3631 5899 . + . ID=AT1G01010.1;Name=AT1G01010.1;index=1 +Chr1 TAIR10 five_prime_UTR 3631 3759 . + . Parent=AT1G01010.1 +Chr1 TAIR10 exon 3631 3913 . + . Parent=AT1G01010.1 +Chr1 . start_codon 3760 3762 . + . Parent=AT1G01010.1 +Chr1 TAIR10 CDS 3760 3913 . + 0 ID=CDS1;Parent=AT1G01010.1 +Chr1 . intron 3914 3995 . + . Parent=AT1G01010.1 +Chr1 TAIR10 exon 3996 4276 . + . Parent=AT1G01010.1 +Chr1 TAIR10 CDS 3996 4276 . + 2 ID=CDS1;Parent=AT1G01010.1 +Chr1 . intron 4277 4485 . + . Parent=AT1G01010.1 +Chr1 TAIR10 exon 4486 4605 . + . Parent=AT1G01010.1 +Chr1 TAIR10 CDS 4486 4605 . + 0 ID=CDS1;Parent=AT1G01010.1 +Chr1 . intron 4606 4705 . + . Parent=AT1G01010.1 +Chr1 TAIR10 exon 4706 5095 . + . Parent=AT1G01010.1 +Chr1 TAIR10 CDS 4706 5095 . + 0 ID=CDS1;Parent=AT1G01010.1 +Chr1 . intron 5096 5173 . + . Parent=AT1G01010.1 +Chr1 TAIR10 exon 5174 5326 . + . Parent=AT1G01010.1 +Chr1 TAIR10 CDS 5174 5326 . + 0 ID=CDS1;Parent=AT1G01010.1 +Chr1 . intron 5327 5438 . + . Parent=AT1G01010.1 +Chr1 TAIR10 CDS 5439 5630 . + 0 ID=CDS1;Parent=AT1G01010.1 +Chr1 TAIR10 exon 5439 5899 . + . Parent=AT1G01010.1 +Chr1 . stop_codon 5628 5630 . + . Parent=AT1G01010.1 +Chr1 TAIR10 three_prime_UTR 5631 5899 . + . Parent=AT1G01010.1 +### + | + | CDS structure comparison + | 6 reference CDS segments + | 6 prediction CDS segments + | CDS structures match perfectly! + | + | Exon structure comparison + | 6 reference exons + | 6 prediction exons + | Exon structures match perfectly! + | + | UTR structure comparison + | 2 reference UTR segments + | 2 prediction UTR segments + | UTR structures match perfectly! + | + | Gene structures match perfectly! + | + | + |-------------------------- + |----- End comparison ----- + |-------------------------- + +|------------------------------------------------- +|---- Locus: seqid=Chr1 range=5914-8747 +|------------------------------------------------- +| +| reference genes: +| AT1G01020 +| +| prediction genes: +| AT1G01020 +| +|---------- + | + |-------------------------- + |---- Begin comparison ---- + |-------------------------- + | + | reference transcripts: + | AT1G01020.1 + | prediction transcripts: + | AT1G01020.1 + | + | reference GFF3: +##gff-version 3 +Chr1 TAIR9 mRNA 5928 8737 . - . ID=AT1G01020.1;Name=AT1G01020.1;index=1 +Chr1 TAIR9 three_prime_UTR 5928 6263 . - . Parent=AT1G01020.1 +Chr1 TAIR9 exon 5928 6263 . - . Parent=AT1G01020.1 +Chr1 . intron 6264 6436 . - . Parent=AT1G01020.1 +Chr1 TAIR9 three_prime_UTR 6437 6914 . - . Parent=AT1G01020.1 +Chr1 TAIR9 exon 6437 7069 . - . Parent=AT1G01020.1 +Chr1 . stop_codon 6915 6917 . - . Parent=AT1G01020.1 +Chr1 TAIR9 CDS 6915 7069 . - 2 ID=CDS2;Parent=AT1G01020.1 +Chr1 . intron 7070 7156 . - . Parent=AT1G01020.1 +Chr1 TAIR9 CDS 7157 7232 . - 0 ID=CDS2;Parent=AT1G01020.1 +Chr1 TAIR9 exon 7157 7232 . - . Parent=AT1G01020.1 +Chr1 . intron 7233 7383 . - . Parent=AT1G01020.1 +Chr1 TAIR9 CDS 7384 7450 . - 1 ID=CDS2;Parent=AT1G01020.1 +Chr1 TAIR9 exon 7384 7450 . - . Parent=AT1G01020.1 +Chr1 . intron 7451 7563 . - . Parent=AT1G01020.1 +Chr1 TAIR9 CDS 7564 7649 . - 0 ID=CDS2;Parent=AT1G01020.1 +Chr1 TAIR9 exon 7564 7649 . - . Parent=AT1G01020.1 +Chr1 . intron 7650 7761 . - . Parent=AT1G01020.1 +Chr1 TAIR9 CDS 7762 7835 . - 2 ID=CDS2;Parent=AT1G01020.1 +Chr1 TAIR9 exon 7762 7835 . - . Parent=AT1G01020.1 +Chr1 . intron 7836 7941 . - . Parent=AT1G01020.1 +Chr1 TAIR9 CDS 7942 7987 . - 0 ID=CDS2;Parent=AT1G01020.1 +Chr1 TAIR9 exon 7942 7987 . - . Parent=AT1G01020.1 +Chr1 . intron 7988 8235 . - . Parent=AT1G01020.1 +Chr1 TAIR9 CDS 8236 8325 . - 0 ID=CDS2;Parent=AT1G01020.1 +Chr1 TAIR9 exon 8236 8325 . - . Parent=AT1G01020.1 +Chr1 . intron 8326 8416 . - . Parent=AT1G01020.1 +Chr1 TAIR9 CDS 8417 8464 . - 0 ID=CDS2;Parent=AT1G01020.1 +Chr1 TAIR9 exon 8417 8464 . - . Parent=AT1G01020.1 +Chr1 . intron 8465 8570 . - . Parent=AT1G01020.1 +Chr1 TAIR9 CDS 8571 8666 . - 0 ID=CDS2;Parent=AT1G01020.1 +Chr1 TAIR9 exon 8571 8737 . - . Parent=AT1G01020.1 +Chr1 . start_codon 8664 8666 . - . Parent=AT1G01020.1 +Chr1 TAIR9 five_prime_UTR 8667 8737 . - . Parent=AT1G01020.1 +### + | prediction GFF3: +##gff-version 3 +Chr1 TAIR10 mRNA 5928 8737 . - . ID=AT1G01020.1;Name=AT1G01020.1;index=1 +Chr1 TAIR10 three_prime_UTR 5928 6263 . - . Parent=AT1G01020.1 +Chr1 TAIR10 exon 5928 6263 . - . Parent=AT1G01020.1 +Chr1 . intron 6264 6436 . - . Parent=AT1G01020.1 +Chr1 TAIR10 three_prime_UTR 6437 6914 . - . Parent=AT1G01020.1 +Chr1 TAIR10 exon 6437 7069 . - . Parent=AT1G01020.1 +Chr1 . stop_codon 6915 6917 . - . Parent=AT1G01020.1 +Chr1 TAIR10 CDS 6915 7069 . - 2 ID=CDS4;Parent=AT1G01020.1 +Chr1 . intron 7070 7156 . - . Parent=AT1G01020.1 +Chr1 TAIR10 CDS 7157 7232 . - 0 ID=CDS4;Parent=AT1G01020.1 +Chr1 TAIR10 exon 7157 7232 . - . Parent=AT1G01020.1 +Chr1 . intron 7233 7383 . - . Parent=AT1G01020.1 +Chr1 TAIR10 CDS 7384 7450 . - 1 ID=CDS4;Parent=AT1G01020.1 +Chr1 TAIR10 exon 7384 7450 . - . Parent=AT1G01020.1 +Chr1 . intron 7451 7563 . - . Parent=AT1G01020.1 +Chr1 TAIR10 CDS 7564 7649 . - 0 ID=CDS4;Parent=AT1G01020.1 +Chr1 TAIR10 exon 7564 7649 . - . Parent=AT1G01020.1 +Chr1 . intron 7650 7761 . - . Parent=AT1G01020.1 +Chr1 TAIR10 CDS 7762 7835 . - 2 ID=CDS4;Parent=AT1G01020.1 +Chr1 TAIR10 exon 7762 7835 . - . Parent=AT1G01020.1 +Chr1 . intron 7836 7941 . - . Parent=AT1G01020.1 +Chr1 TAIR10 CDS 7942 7987 . - 0 ID=CDS4;Parent=AT1G01020.1 +Chr1 TAIR10 exon 7942 7987 . - . Parent=AT1G01020.1 +Chr1 . intron 7988 8235 . - . Parent=AT1G01020.1 +Chr1 TAIR10 CDS 8236 8325 . - 0 ID=CDS4;Parent=AT1G01020.1 +Chr1 TAIR10 exon 8236 8325 . - . Parent=AT1G01020.1 +Chr1 . intron 8326 8416 . - . Parent=AT1G01020.1 +Chr1 TAIR10 CDS 8417 8464 . - 0 ID=CDS4;Parent=AT1G01020.1 +Chr1 TAIR10 exon 8417 8464 . - . Parent=AT1G01020.1 +Chr1 . intron 8465 8570 . - . Parent=AT1G01020.1 +Chr1 TAIR10 CDS 8571 8666 . - 0 ID=CDS4;Parent=AT1G01020.1 +Chr1 TAIR10 exon 8571 8737 . - . Parent=AT1G01020.1 +Chr1 . start_codon 8664 8666 . - . Parent=AT1G01020.1 +Chr1 TAIR10 five_prime_UTR 8667 8737 . - . Parent=AT1G01020.1 +### + | + | CDS structure comparison + | 9 reference CDS segments + | 9 prediction CDS segments + | CDS structures match perfectly! + | + | Exon structure comparison + | 10 reference exons + | 10 prediction exons + | Exon structures match perfectly! + | + | UTR structure comparison + | 3 reference UTR segments + | 3 prediction UTR segments + | UTR structures match perfectly! + | + | Gene structures match perfectly! + | + | + |-------------------------- + |----- End comparison ----- + |-------------------------- + | + |-------------------------- + |---- Begin comparison ---- + |-------------------------- + | + | reference transcripts: + | AT1G01020.2 + | prediction transcripts: + | AT1G01020.2 + | + | reference GFF3: +##gff-version 3 +Chr1 TAIR9 mRNA 6790 8737 . - . ID=AT1G01020.2;Name=AT1G01020.2;index=1 +Chr1 TAIR9 three_prime_UTR 6790 7069 . - . Parent=AT1G01020.2 +Chr1 TAIR9 exon 6790 7069 . - . Parent=AT1G01020.2 +Chr1 TAIR9 three_prime_UTR 7157 7314 . - . Parent=AT1G01020.2 +Chr1 TAIR9 exon 7157 7450 . - . Parent=AT1G01020.2 +Chr1 . stop_codon 7315 7317 . - . Parent=AT1G01020.2 +Chr1 TAIR9 CDS 7315 7450 . - 1 ID=CDS3;Parent=AT1G01020.2 +Chr1 TAIR9 CDS 7564 7649 . - 0 ID=CDS3;Parent=AT1G01020.2 +Chr1 TAIR9 exon 7564 7649 . - . Parent=AT1G01020.2 +Chr1 TAIR9 CDS 7762 7835 . - 2 ID=CDS3;Parent=AT1G01020.2 +Chr1 TAIR9 exon 7762 7835 . - . Parent=AT1G01020.2 +Chr1 TAIR9 CDS 7942 7987 . - 0 ID=CDS3;Parent=AT1G01020.2 +Chr1 TAIR9 exon 7942 7987 . - . Parent=AT1G01020.2 +Chr1 TAIR9 CDS 8236 8325 . - 0 ID=CDS3;Parent=AT1G01020.2 +Chr1 TAIR9 exon 8236 8325 . - . Parent=AT1G01020.2 +Chr1 TAIR9 CDS 8417 8464 . - 0 ID=CDS3;Parent=AT1G01020.2 +Chr1 TAIR9 exon 8417 8464 . - . Parent=AT1G01020.2 +Chr1 TAIR9 CDS 8571 8666 . - 0 ID=CDS3;Parent=AT1G01020.2 +Chr1 TAIR9 exon 8571 8737 . - . Parent=AT1G01020.2 +Chr1 . start_codon 8664 8666 . - . Parent=AT1G01020.2 +Chr1 TAIR9 five_prime_UTR 8667 8737 . - . Parent=AT1G01020.2 +### + | prediction GFF3: +##gff-version 3 +Chr1 TAIR10 mRNA 6790 8737 . - . ID=AT1G01020.2;Name=AT1G01020.2;index=1 +Chr1 TAIR10 three_prime_UTR 6790 7069 . - . Parent=AT1G01020.2 +Chr1 TAIR10 exon 6790 7069 . - . Parent=AT1G01020.2 +Chr1 TAIR10 three_prime_UTR 7157 7314 . - . Parent=AT1G01020.2 +Chr1 TAIR10 exon 7157 7450 . - . Parent=AT1G01020.2 +Chr1 . stop_codon 7315 7317 . - . Parent=AT1G01020.2 +Chr1 TAIR10 CDS 7315 7450 . - 1 ID=CDS5;Parent=AT1G01020.2 +Chr1 TAIR10 CDS 7564 7649 . - 0 ID=CDS5;Parent=AT1G01020.2 +Chr1 TAIR10 exon 7564 7649 . - . Parent=AT1G01020.2 +Chr1 TAIR10 CDS 7762 7835 . - 2 ID=CDS5;Parent=AT1G01020.2 +Chr1 TAIR10 exon 7762 7835 . - . Parent=AT1G01020.2 +Chr1 TAIR10 CDS 7942 7987 . - 0 ID=CDS5;Parent=AT1G01020.2 +Chr1 TAIR10 exon 7942 7987 . - . Parent=AT1G01020.2 +Chr1 TAIR10 CDS 8236 8325 . - 0 ID=CDS5;Parent=AT1G01020.2 +Chr1 TAIR10 exon 8236 8325 . - . Parent=AT1G01020.2 +Chr1 TAIR10 CDS 8417 8464 . - 0 ID=CDS5;Parent=AT1G01020.2 +Chr1 TAIR10 exon 8417 8464 . - . Parent=AT1G01020.2 +Chr1 TAIR10 CDS 8571 8666 . - 0 ID=CDS5;Parent=AT1G01020.2 +Chr1 TAIR10 exon 8571 8737 . - . Parent=AT1G01020.2 +Chr1 . start_codon 8664 8666 . - . Parent=AT1G01020.2 +Chr1 TAIR10 five_prime_UTR 8667 8737 . - . Parent=AT1G01020.2 +### + | + | CDS structure comparison + | 7 reference CDS segments + | 7 prediction CDS segments + | CDS structures match perfectly! + | + | Exon structure comparison + | 8 reference exons + | 8 prediction exons + | Exon structures match perfectly! + | + | UTR structure comparison + | 3 reference UTR segments + | 3 prediction UTR segments + | UTR structures match perfectly! + | + | Gene structures match perfectly! + | + | + |-------------------------- + |----- End comparison ----- + |-------------------------- + +|------------------------------------------------- +|---- Locus: seqid=Chr1 range=11639-13724 +|------------------------------------------------- +| +| reference genes: +| AT1G01030 +| +| prediction genes: +| AT1G01030 +| +|---------- + | + |-------------------------- + |---- Begin comparison ---- + |-------------------------- + | + | reference transcripts: + | AT1G01030.1 + | prediction transcripts: + | AT1G01030.1 + | + | reference GFF3: +##gff-version 3 +Chr1 TAIR9 mRNA 11649 13714 . - . ID=AT1G01030.1;Name=AT1G01030.1;index=1 +Chr1 TAIR9 three_prime_UTR 11649 11863 . - . Parent=AT1G01030.1 +Chr1 TAIR9 exon 11649 13173 . - . Parent=AT1G01030.1 +Chr1 . stop_codon 11864 11866 . - . Parent=AT1G01030.1 +Chr1 TAIR9 CDS 11864 12940 . - 0 Parent=AT1G01030.1 +Chr1 . start_codon 12938 12940 . - . Parent=AT1G01030.1 +Chr1 TAIR9 five_prime_UTR 12941 13173 . - . Parent=AT1G01030.1 +Chr1 . intron 13174 13334 . - . Parent=AT1G01030.1 +Chr1 TAIR9 five_prime_UTR 13335 13714 . - . Parent=AT1G01030.1 +Chr1 TAIR9 exon 13335 13714 . - . Parent=AT1G01030.1 +### + | prediction GFF3: +##gff-version 3 +Chr1 TAIR10 mRNA 11649 13714 . - . ID=AT1G01030.1;Name=AT1G01030.1;index=1 +Chr1 TAIR10 three_prime_UTR 11649 11863 . - . Parent=AT1G01030.1 +Chr1 TAIR10 exon 11649 13173 . - . Parent=AT1G01030.1 +Chr1 . stop_codon 11864 11866 . - . Parent=AT1G01030.1 +Chr1 TAIR10 CDS 11864 12940 . - 0 Parent=AT1G01030.1 +Chr1 . start_codon 12938 12940 . - . Parent=AT1G01030.1 +Chr1 TAIR10 five_prime_UTR 12941 13173 . - . Parent=AT1G01030.1 +Chr1 . intron 13174 13334 . - . Parent=AT1G01030.1 +Chr1 TAIR10 five_prime_UTR 13335 13714 . - . Parent=AT1G01030.1 +Chr1 TAIR10 exon 13335 13714 . - . Parent=AT1G01030.1 +### + | + | CDS structure comparison + | 1 reference CDS segments + | 1 prediction CDS segments + | CDS structures match perfectly! + | + | Exon structure comparison + | 2 reference exons + | 2 prediction exons + | Exon structures match perfectly! + | + | UTR structure comparison + | 3 reference UTR segments + | 3 prediction UTR segments + | UTR structures match perfectly! + | + | Gene structures match perfectly! + | + | + |-------------------------- + |----- End comparison ----- + |-------------------------- + +|------------------------------------------------- +|---- Locus: seqid=Chr1 range=23136-31237 +|------------------------------------------------- +| +| reference genes: +| AT1G01040 +| +| prediction genes: +| AT1G01040 +| +|---------- + | + |-------------------------- + |---- Begin comparison ---- + |-------------------------- + | + | reference transcripts: + | AT1G01040.1 + | prediction transcripts: + | AT1G01040.1 + | + | reference GFF3: +##gff-version 3 +Chr1 TAIR9 mRNA 23146 31227 . + . ID=AT1G01040.1;Name=AT1G01040.1;index=1 +Chr1 TAIR9 five_prime_UTR 23146 23518 . + . Parent=AT1G01040.1 +Chr1 TAIR9 exon 23146 24451 . + . Parent=AT1G01040.1 +Chr1 . start_codon 23519 23521 . + . Parent=AT1G01040.1 +Chr1 TAIR9 CDS 23519 24451 . + 0 ID=CDS6;Parent=AT1G01040.1 +Chr1 . intron 24452 24541 . + . Parent=AT1G01040.1 +Chr1 TAIR9 exon 24542 24655 . + . Parent=AT1G01040.1 +Chr1 TAIR9 CDS 24542 24655 . + 0 ID=CDS6;Parent=AT1G01040.1 +Chr1 . intron 24656 24751 . + . Parent=AT1G01040.1 +Chr1 TAIR9 exon 24752 24962 . + . Parent=AT1G01040.1 +Chr1 TAIR9 CDS 24752 24962 . + 0 ID=CDS6;Parent=AT1G01040.1 +Chr1 . intron 24963 25040 . + . Parent=AT1G01040.1 +Chr1 TAIR9 exon 25041 25435 . + . Parent=AT1G01040.1 +Chr1 TAIR9 CDS 25041 25435 . + 2 ID=CDS6;Parent=AT1G01040.1 +Chr1 . intron 25436 25523 . + . Parent=AT1G01040.1 +Chr1 TAIR9 exon 25524 25743 . + . Parent=AT1G01040.1 +Chr1 TAIR9 CDS 25524 25743 . + 0 ID=CDS6;Parent=AT1G01040.1 +Chr1 . intron 25744 25824 . + . Parent=AT1G01040.1 +Chr1 TAIR9 exon 25825 25997 . + . Parent=AT1G01040.1 +Chr1 TAIR9 CDS 25825 25997 . + 2 ID=CDS6;Parent=AT1G01040.1 +Chr1 . intron 25998 26080 . + . Parent=AT1G01040.1 +Chr1 TAIR9 exon 26081 26203 . + . Parent=AT1G01040.1 +Chr1 TAIR9 CDS 26081 26203 . + 0 ID=CDS6;Parent=AT1G01040.1 +Chr1 . intron 26204 26291 . + . Parent=AT1G01040.1 +Chr1 TAIR9 exon 26292 26452 . + . Parent=AT1G01040.1 +Chr1 TAIR9 CDS 26292 26452 . + 0 ID=CDS6;Parent=AT1G01040.1 +Chr1 . intron 26453 26542 . + . Parent=AT1G01040.1 +Chr1 TAIR9 exon 26543 26776 . + . Parent=AT1G01040.1 +Chr1 TAIR9 CDS 26543 26776 . + 1 ID=CDS6;Parent=AT1G01040.1 +Chr1 . intron 26777 26861 . + . Parent=AT1G01040.1 +Chr1 TAIR9 exon 26862 27012 . + . Parent=AT1G01040.1 +Chr1 TAIR9 CDS 26862 27012 . + 1 ID=CDS6;Parent=AT1G01040.1 +Chr1 . intron 27013 27098 . + . Parent=AT1G01040.1 +Chr1 TAIR9 exon 27099 27281 . + . Parent=AT1G01040.1 +Chr1 TAIR9 CDS 27099 27281 . + 0 ID=CDS6;Parent=AT1G01040.1 +Chr1 . intron 27282 27371 . + . Parent=AT1G01040.1 +Chr1 TAIR9 exon 27372 27533 . + . Parent=AT1G01040.1 +Chr1 TAIR9 CDS 27372 27533 . + 0 ID=CDS6;Parent=AT1G01040.1 +Chr1 . stop_codon 27531 27533 . + . Parent=AT1G01040.1 +### + | prediction GFF3: +##gff-version 3 +Chr1 TAIR10 mRNA 23146 31227 . + . ID=AT1G01040.1;Name=AT1G01040.1;index=1 +Chr1 TAIR10 five_prime_UTR 23146 23518 . + . Parent=AT1G01040.1 +Chr1 TAIR10 exon 23146 24451 . + . Parent=AT1G01040.1 +Chr1 . start_codon 23519 23521 . + . Parent=AT1G01040.1 +Chr1 TAIR10 CDS 23519 24451 . + 0 ID=CDS7;Parent=AT1G01040.1 +Chr1 . intron 24452 24541 . + . Parent=AT1G01040.1 +Chr1 TAIR10 exon 24542 24655 . + . Parent=AT1G01040.1 +Chr1 TAIR10 CDS 24542 24655 . + 0 ID=CDS7;Parent=AT1G01040.1 +Chr1 . intron 24656 24751 . + . Parent=AT1G01040.1 +Chr1 TAIR10 exon 24752 24962 . + . Parent=AT1G01040.1 +Chr1 TAIR10 CDS 24752 24962 . + 0 ID=CDS7;Parent=AT1G01040.1 +Chr1 . intron 24963 25040 . + . Parent=AT1G01040.1 +Chr1 TAIR10 exon 25041 25435 . + . Parent=AT1G01040.1 +Chr1 TAIR10 CDS 25041 25435 . + 2 ID=CDS7;Parent=AT1G01040.1 +Chr1 . intron 25436 25523 . + . Parent=AT1G01040.1 +Chr1 TAIR10 exon 25524 25743 . + . Parent=AT1G01040.1 +Chr1 TAIR10 CDS 25524 25743 . + 0 ID=CDS7;Parent=AT1G01040.1 +Chr1 . intron 25744 25824 . + . Parent=AT1G01040.1 +Chr1 TAIR10 exon 25825 25997 . + . Parent=AT1G01040.1 +Chr1 TAIR10 CDS 25825 25997 . + 2 ID=CDS7;Parent=AT1G01040.1 +Chr1 . intron 25998 26080 . + . Parent=AT1G01040.1 +Chr1 TAIR10 exon 26081 26203 . + . Parent=AT1G01040.1 +Chr1 TAIR10 CDS 26081 26203 . + 0 ID=CDS7;Parent=AT1G01040.1 +Chr1 . intron 26204 26291 . + . Parent=AT1G01040.1 +Chr1 TAIR10 exon 26292 26452 . + . Parent=AT1G01040.1 +Chr1 TAIR10 CDS 26292 26452 . + 0 ID=CDS7;Parent=AT1G01040.1 +Chr1 . intron 26453 26542 . + . Parent=AT1G01040.1 +Chr1 TAIR10 exon 26543 26776 . + . Parent=AT1G01040.1 +Chr1 TAIR10 CDS 26543 26776 . + 1 ID=CDS7;Parent=AT1G01040.1 +Chr1 . intron 26777 26861 . + . Parent=AT1G01040.1 +Chr1 TAIR10 exon 26862 27012 . + . Parent=AT1G01040.1 +Chr1 TAIR10 CDS 26862 27012 . + 1 ID=CDS7;Parent=AT1G01040.1 +Chr1 . intron 27013 27098 . + . Parent=AT1G01040.1 +Chr1 TAIR10 exon 27099 27281 . + . Parent=AT1G01040.1 +Chr1 TAIR10 CDS 27099 27281 . + 0 ID=CDS7;Parent=AT1G01040.1 +Chr1 . intron 27282 27371 . + . Parent=AT1G01040.1 +Chr1 TAIR10 exon 27372 27533 . + . Parent=AT1G01040.1 +Chr1 TAIR10 CDS 27372 27533 . + 0 ID=CDS7;Parent=AT1G01040.1 +Chr1 . stop_codon 27531 27533 . + . Parent=AT1G01040.1 +### + | + | CDS structure comparison + | 12 reference CDS segments + | 12 prediction CDS segments + | CDS structures match perfectly! + | + | Exon structure comparison + | 12 reference exons + | 12 prediction exons + | Exon structures match perfectly! + | + | UTR structure comparison + | 1 reference UTR segments + | 1 prediction UTR segments + | UTR structures match perfectly! + | + | Gene structures match perfectly! + | + | + |-------------------------- + |----- End comparison ----- + |-------------------------- + +============================================================ +========== ParsEval Summary +============================================================ + +Started: 31 Dec 2020, 08:39PM +Reference annotations: /tmp/tmpuaspc0eb/files/a/5/5/dataset_a554f401-58a7-425c-88d9-4da452d77344.dat +Prediction annotations: /tmp/tmpuaspc0eb/files/9/5/a/dataset_95aee753-49cb-406a-a66f-13f51ef7a287.dat +Executing command: parseval -l 10 -t 10 -w -f text -o /tmp/tmpuaspc0eb/files/f/7/e/dataset_f7ec07dd-99dc-47f5-b69e-b01cec68543f.dat /tmp/tmpuaspc0eb/files/a/5/5/dataset_a554f401-58a7-425c-88d9-4da452d77344.dat /tmp/tmpuaspc0eb/files/9/5/a/dataset_95aee753-49cb-406a-a66f-13f51ef7a287.dat + + Sequences compared + Chr1 + + Gene loci................................4 + shared.................................4 + unique to reference....................0 + unique to prediction...................0 + + Reference annotations + genes..................................4 + average per locus....................1.000 + transcripts............................5 + average per locus....................1.250 + average per gene.....................1.250 + + Prediction annotations + genes..................................4 + average per locus....................1.000 + transcripts............................5 + average per locus....................1.250 + average per gene.....................1.250 + + Total comparisons........................5 + perfect matches........................5 (100.0%) + avg. length..........................3629.80 bp + avg. # refr exons....................7.60 + avg. # pred exons....................7.60 + avg. refr CDS length.................449.40 aa + avg. pred CDS length.................449.40 aa + perfect matches with mislabeled UTRs...0 (0.0%) + CDS structure matches..................0 (0.0%) + exon structure matches.................0 (0.0%) + UTR structure matches..................0 (0.0%) + non-matches............................0 (0.0%) + + CDS structure comparison + reference CDS segments.................35 + match prediction.....................35 (100.0%) + don't match prediction...............0 (0.0%) + prediction CDS segments................35 + match reference......................35 (100.0%) + don't match reference................0 (0.0%) + Sensitivity............................1.000 + Specificity............................1.000 + F1 Score...............................1.000 + Annotation edit distance...............0.000 + + Exon structure comparison + reference exons........................38 + match prediction.....................38 (100.0%) + don't match prediction...............0 (0.0%) + prediction exons.......................38 + match reference......................38 (100.0%) + don't match reference................0 (0.0%) + Sensitivity............................1.000 + Specificity............................1.000 + F1 Score...............................1.000 + Annotation edit distance...............0.000 + + UTR structure comparison + reference UTR segments.................12 + match prediction.....................12 (100.0%) + don't match prediction...............0 (0.0%) + prediction UTR segments................12 + match reference......................12 (100.0%) + don't match reference................0 (0.0%) + Sensitivity............................1.000 + Specificity............................1.000 + F1 Score...............................1.000 + Annotation edit distance...............0.000 + + Nucleotide-level comparison CDS UTRs Overall + Matching coefficient: 1.000 1.000 1.000 + Correlation coefficient: 1.000 1.000 -- + Sensitivity: 1.000 1.000 -- + Specificity: 1.000 1.000 -- + F1 Score: 1.000 1.000 -- + Annotation edit distance: 0.000 0.000 -- diff -r 000000000000 -r c4ac24510b55 test-data/parseval_output_test4.html --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/parseval_output_test4.html Sun Jan 03 14:58:58 2021 +0000 @@ -0,0 +1,146 @@ + + + + + ParsEval Summary + + + + + + +

ParsEval Summary

+Started:                03 Jan 2021, 02:54PM
+Reference annotations:  /tmp/tmpok6hen4l/files/7/2/c/dataset_72c6fa9a-e400-4213-a1ef-ac6fc6ab18e7.dat
+Prediction annotations: /tmp/tmpok6hen4l/files/d/2/0/dataset_d20b7bb7-e832-4eb2-917e-7b76fdb1a0cb.dat
+Executing command:      parseval --delta 0 --maxtrans 32 -w -f html -o /tmp/tmpok6hen4l/job_working_directory/000/43/working/dataset_63abed3a-aaab-41d9-b66b-4030368d9362_files /tmp/tmpok6hen4l/files/7/2/c/dataset_72c6fa9a-e400-4213-a1ef-ac6fc6ab18e7.dat /tmp/tmpok6hen4l/files/d/2/0/dataset_d20b7bb7-e832-4eb2-917e-7b76fdb1a0cb.dat

+ +

Sequences compared

Click on a sequence ID below to see comparison results for individual loci.

+ + + + + + + + + + + + +

Sequence	Refr genes	Pred genes	Loci
Chr1	4	4	4

+ +

Gene loci [?]If a gene annotation overlaps with another gene annotation, those annotations are associated with the same gene locus. See this page for a formal definition of a locus annotation.

+ + + + + +

shared	4
unique to reference	0
unique to prediction	0
Total	4

+ +

Reference annotations

+ + + + + + +

genes	4
average per locus	1.000
transcripts	5
average per locus	1.250
average per gene	1.250

+ +

Prediction annotations

+ + + + + + +

genes	4
average per locus	1.000
transcripts	5
average per locus	1.250
average per gene	1.250

+ +

Comparisons

+ + + + + + + + + + + + + +

Total comparisons	5
(+) perfect matches [?]Prediction transcripts (exons, coding sequences, and UTRs) line up perfectly with reference transcripts.	5 (100.0%)
average length	3607.40 bp
average # refr exons	7.60
average # pred exons	7.60
average refr CDS length	449.40 aa
average pred CDS length	449.40 aa
(+) perfect matches with mislabeled UTRs [?]5'/3' orientation of UTRs is reversed between reference and prediction, but a perfect match in all other aspects.	0 (0.0%)
(+) CDS structure matches [?]Not a perfect match, but prediction coding sequence(s) line up perfectly with reference coding sequence(s).	0 (0.0%)
(+) exon structure matches [?]Not a perfect match or CDS match, but prediction exon structure is identical to reference exon structure.	0 (0.0%)
(+) UTR structure matches [?]Not a perfect match, CDS match, or exon structure match, but prediction UTRs line up perfectly with reference UTRs.	0 (0.0%)
(+) non-matches [?]Differences in CDS, exon, and UTR structure.	0 (0.0%)

+ +

CDS structure comparison

+ + + + + + + + + + + +

reference CDS segments	35
match prediction	35 (100.0%)
don't match prediction	0 (0.0%)
prediction CDS segments	35
match prediction	35 (100.0%)
don't match prediction	0 (0.0%)
Sensitivity	1.000
Specificity	1.000
F1 score	1.000
Annotation edit distance	0.000

+ +

Exon structure comparison

+ + + + + + + + + + + +

reference exons	38
match prediction	38 (100.0%)
don't match prediction	0 (0.0%)
prediction exons	38
match prediction	38 (100.0%)
don't match prediction	0 (0.0%)
Sensitivity	1.000
Specificity	1.000
F1 score	1.000
Annotation edit distance	0.000

+ +

UTR structure comparison

+ + + + + + + + + + + +

reference UTR segments	12
match prediction	12 (100.0%)
don't match prediction	0 (0.0%)
prediction UTR segments	12
match prediction	12 (100.0%)
don't match prediction	0 (0.0%)
Sensitivity	1.000
Specificity	1.000
F1 score	1.000
Annotation edit distance	0.000

+ +

Nucleotide-level comparison

+ + + + + + + + +

	CDS	UTRs	Overall
matching coefficient	1.000	1.000	1.000
correlation coefficient	1.000	1.000	--
sensitivity	1.000	1.000	--
specificity	1.000	1.000	--
F1 score	1.000	1.000	--
annotation edit distance	0.000	0.000	--

+ + +

diff -r 000000000000 -r c4ac24510b55 test-data/parseval_output_test5.html --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/parseval_output_test5.html Sun Jan 03 14:58:58 2021 +0000 @@ -0,0 +1,146 @@ + + + + + ParsEval Summary + + + + + + +

ParsEval Summary

+Started:                03 Jan 2021, 02:54PM
+Reference annotations:  /tmp/tmpok6hen4l/files/3/2/4/dataset_324b4f7b-e4b1-45d0-a543-be63ae960b43.dat
+Prediction annotations: /tmp/tmpok6hen4l/files/b/4/0/dataset_b4066664-7777-4c30-9e37-820e44194617.dat
+Executing command:      parseval --delta 10 --maxtrans 10 -w -f html -o /tmp/tmpok6hen4l/job_working_directory/000/46/working/dataset_1f07132b-8f99-4a03-8305-5c4c5a68089c_files /tmp/tmpok6hen4l/files/3/2/4/dataset_324b4f7b-e4b1-45d0-a543-be63ae960b43.dat /tmp/tmpok6hen4l/files/b/4/0/dataset_b4066664-7777-4c30-9e37-820e44194617.dat

+ +

Sequences compared

Click on a sequence ID below to see comparison results for individual loci.

+ + + + + + + + + + + + +

Sequence	Refr genes	Pred genes	Loci
Chr1	4	4	4

+ +

Gene loci [?]If a gene annotation overlaps with another gene annotation, those annotations are associated with the same gene locus. See this page for a formal definition of a locus annotation.

+ + + + + +

shared	4
unique to reference	0
unique to prediction	0
Total	4

+ +

Reference annotations

+ + + + + + +

genes	4
average per locus	1.000
transcripts	5
average per locus	1.250
average per gene	1.250

+ +

Prediction annotations

+ + + + + + +

genes	4
average per locus	1.000
transcripts	5
average per locus	1.250
average per gene	1.250

+ +

Comparisons

+ + + + + + + + + + + + + +

Total comparisons	5
(+) perfect matches [?]Prediction transcripts (exons, coding sequences, and UTRs) line up perfectly with reference transcripts.	5 (100.0%)
average length	3629.80 bp
average # refr exons	7.60
average # pred exons	7.60
average refr CDS length	449.40 aa
average pred CDS length	449.40 aa
(+) perfect matches with mislabeled UTRs [?]5'/3' orientation of UTRs is reversed between reference and prediction, but a perfect match in all other aspects.	0 (0.0%)
(+) CDS structure matches [?]Not a perfect match, but prediction coding sequence(s) line up perfectly with reference coding sequence(s).	0 (0.0%)
(+) exon structure matches [?]Not a perfect match or CDS match, but prediction exon structure is identical to reference exon structure.	0 (0.0%)
(+) UTR structure matches [?]Not a perfect match, CDS match, or exon structure match, but prediction UTRs line up perfectly with reference UTRs.	0 (0.0%)
(+) non-matches [?]Differences in CDS, exon, and UTR structure.	0 (0.0%)

+ +

CDS structure comparison

+ + + + + + + + + + + +

reference CDS segments	35
match prediction	35 (100.0%)
don't match prediction	0 (0.0%)
prediction CDS segments	35
match prediction	35 (100.0%)
don't match prediction	0 (0.0%)
Sensitivity	1.000
Specificity	1.000
F1 score	1.000
Annotation edit distance	0.000

+ +

Exon structure comparison

+ + + + + + + + + + + +

reference exons	38
match prediction	38 (100.0%)
don't match prediction	0 (0.0%)
prediction exons	38
match prediction	38 (100.0%)
don't match prediction	0 (0.0%)
Sensitivity	1.000
Specificity	1.000
F1 score	1.000
Annotation edit distance	0.000

+ +

UTR structure comparison

+ + + + + + + + + + + +

reference UTR segments	12
match prediction	12 (100.0%)
don't match prediction	0 (0.0%)
prediction UTR segments	12
match prediction	12 (100.0%)
don't match prediction	0 (0.0%)
Sensitivity	1.000
Specificity	1.000
F1 score	1.000
Annotation edit distance	0.000

+ +

Nucleotide-level comparison

+ + + + + + + + +

	CDS	UTRs	Overall
matching coefficient	1.000	1.000	1.000
correlation coefficient	1.000	1.000	--
sensitivity	1.000	1.000	--
specificity	1.000	1.000	--
F1 score	1.000	1.000	--
annotation edit distance	0.000	0.000	--

+ + +

diff -r 000000000000 -r c4ac24510b55 test-data/parseval_output_test6.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/parseval_output_test6.txt Sun Jan 03 14:58:58 2021 +0000 @@ -0,0 +1,577 @@ +|------------------------------------------------- +|---- Locus: seqid=Chr1 range=3631-5899 +|------------------------------------------------- +| +| reference genes: +| AT1G01010 +| +| prediction genes: +| AT1G01010 +| +|---------- + | + |-------------------------- + |---- Begin comparison ---- + |-------------------------- + | + | reference transcripts: + | AT1G01010.1 + | prediction transcripts: + | AT1G01010.1 + | + | reference GFF3: +##gff-version 3 +Chr1 TAIR9 mRNA 3631 5899 . + . ID=AT1G01010.1;Name=AT1G01010.1;index=1 +Chr1 TAIR9 five_prime_UTR 3631 3759 . + . Parent=AT1G01010.1 +Chr1 TAIR9 exon 3631 3913 . + . Parent=AT1G01010.1 +Chr1 . start_codon 3760 3762 . + . Parent=AT1G01010.1 +Chr1 TAIR9 CDS 3760 3913 . + 0 ID=CDS0;Parent=AT1G01010.1 +Chr1 . intron 3914 3995 . + . Parent=AT1G01010.1 +Chr1 TAIR9 exon 3996 4276 . + . Parent=AT1G01010.1 +Chr1 TAIR9 CDS 3996 4276 . + 2 ID=CDS0;Parent=AT1G01010.1 +Chr1 . intron 4277 4485 . + . Parent=AT1G01010.1 +Chr1 TAIR9 exon 4486 4605 . + . Parent=AT1G01010.1 +Chr1 TAIR9 CDS 4486 4605 . + 0 ID=CDS0;Parent=AT1G01010.1 +Chr1 . intron 4606 4705 . + . Parent=AT1G01010.1 +Chr1 TAIR9 exon 4706 5095 . + . Parent=AT1G01010.1 +Chr1 TAIR9 CDS 4706 5095 . + 0 ID=CDS0;Parent=AT1G01010.1 +Chr1 . intron 5096 5173 . + . Parent=AT1G01010.1 +Chr1 TAIR9 exon 5174 5326 . + . Parent=AT1G01010.1 +Chr1 TAIR9 CDS 5174 5326 . + 0 ID=CDS0;Parent=AT1G01010.1 +Chr1 . intron 5327 5438 . + . Parent=AT1G01010.1 +Chr1 TAIR9 CDS 5439 5630 . + 0 ID=CDS0;Parent=AT1G01010.1 +Chr1 TAIR9 exon 5439 5899 . + . Parent=AT1G01010.1 +Chr1 . stop_codon 5628 5630 . + . Parent=AT1G01010.1 +Chr1 TAIR9 three_prime_UTR 5631 5899 . + . Parent=AT1G01010.1 +### + | prediction GFF3: +##gff-version 3 +Chr1 TAIR10 mRNA 3631 5899 . + . ID=AT1G01010.1;Name=AT1G01010.1;index=1 +Chr1 TAIR10 five_prime_UTR 3631 3759 . + . Parent=AT1G01010.1 +Chr1 TAIR10 exon 3631 3913 . + . Parent=AT1G01010.1 +Chr1 . start_codon 3760 3762 . + . Parent=AT1G01010.1 +Chr1 TAIR10 CDS 3760 3913 . + 0 ID=CDS1;Parent=AT1G01010.1 +Chr1 . intron 3914 3995 . + . Parent=AT1G01010.1 +Chr1 TAIR10 exon 3996 4276 . + . Parent=AT1G01010.1 +Chr1 TAIR10 CDS 3996 4276 . + 2 ID=CDS1;Parent=AT1G01010.1 +Chr1 . intron 4277 4485 . + . Parent=AT1G01010.1 +Chr1 TAIR10 exon 4486 4605 . + . Parent=AT1G01010.1 +Chr1 TAIR10 CDS 4486 4605 . + 0 ID=CDS1;Parent=AT1G01010.1 +Chr1 . intron 4606 4705 . + . Parent=AT1G01010.1 +Chr1 TAIR10 exon 4706 5095 . + . Parent=AT1G01010.1 +Chr1 TAIR10 CDS 4706 5095 . + 0 ID=CDS1;Parent=AT1G01010.1 +Chr1 . intron 5096 5173 . + . Parent=AT1G01010.1 +Chr1 TAIR10 exon 5174 5326 . + . Parent=AT1G01010.1 +Chr1 TAIR10 CDS 5174 5326 . + 0 ID=CDS1;Parent=AT1G01010.1 +Chr1 . intron 5327 5438 . + . Parent=AT1G01010.1 +Chr1 TAIR10 CDS 5439 5630 . + 0 ID=CDS1;Parent=AT1G01010.1 +Chr1 TAIR10 exon 5439 5899 . + . Parent=AT1G01010.1 +Chr1 . stop_codon 5628 5630 . + . Parent=AT1G01010.1 +Chr1 TAIR10 three_prime_UTR 5631 5899 . + . Parent=AT1G01010.1 +### + | + | CDS structure comparison + | 6 reference CDS segments + | 6 prediction CDS segments + | CDS structures match perfectly! + | + | Exon structure comparison + | 6 reference exons + | 6 prediction exons + | Exon structures match perfectly! + | + | UTR structure comparison + | 2 reference UTR segments + | 2 prediction UTR segments + | UTR structures match perfectly! + | + | Gene structures match perfectly! + | + | + |-------------------------- + |----- End comparison ----- + |-------------------------- + +|------------------------------------------------- +|---- Locus: seqid=Chr1 range=5928-8737 +|------------------------------------------------- +| +| reference genes: +| AT1G01020 +| +| prediction genes: +| AT1G01020 +| +|---------- + | + |-------------------------- + |---- Begin comparison ---- + |-------------------------- + | + | reference transcripts: + | AT1G01020.1 + | prediction transcripts: + | AT1G01020.1 + | + | reference GFF3: +##gff-version 3 +Chr1 TAIR9 mRNA 5928 8737 . - . ID=AT1G01020.1;Name=AT1G01020.1;index=1 +Chr1 TAIR9 three_prime_UTR 5928 6263 . - . Parent=AT1G01020.1 +Chr1 TAIR9 exon 5928 6263 . - . Parent=AT1G01020.1 +Chr1 . intron 6264 6436 . - . Parent=AT1G01020.1 +Chr1 TAIR9 three_prime_UTR 6437 6914 . - . Parent=AT1G01020.1 +Chr1 TAIR9 exon 6437 7069 . - . Parent=AT1G01020.1 +Chr1 . stop_codon 6915 6917 . - . Parent=AT1G01020.1 +Chr1 TAIR9 CDS 6915 7069 . - 2 ID=CDS2;Parent=AT1G01020.1 +Chr1 . intron 7070 7156 . - . Parent=AT1G01020.1 +Chr1 TAIR9 CDS 7157 7232 . - 0 ID=CDS2;Parent=AT1G01020.1 +Chr1 TAIR9 exon 7157 7232 . - . Parent=AT1G01020.1 +Chr1 . intron 7233 7383 . - . Parent=AT1G01020.1 +Chr1 TAIR9 CDS 7384 7450 . - 1 ID=CDS2;Parent=AT1G01020.1 +Chr1 TAIR9 exon 7384 7450 . - . Parent=AT1G01020.1 +Chr1 . intron 7451 7563 . - . Parent=AT1G01020.1 +Chr1 TAIR9 CDS 7564 7649 . - 0 ID=CDS2;Parent=AT1G01020.1 +Chr1 TAIR9 exon 7564 7649 . - . Parent=AT1G01020.1 +Chr1 . intron 7650 7761 . - . Parent=AT1G01020.1 +Chr1 TAIR9 CDS 7762 7835 . - 2 ID=CDS2;Parent=AT1G01020.1 +Chr1 TAIR9 exon 7762 7835 . - . Parent=AT1G01020.1 +Chr1 . intron 7836 7941 . - . Parent=AT1G01020.1 +Chr1 TAIR9 CDS 7942 7987 . - 0 ID=CDS2;Parent=AT1G01020.1 +Chr1 TAIR9 exon 7942 7987 . - . Parent=AT1G01020.1 +Chr1 . intron 7988 8235 . - . Parent=AT1G01020.1 +Chr1 TAIR9 CDS 8236 8325 . - 0 ID=CDS2;Parent=AT1G01020.1 +Chr1 TAIR9 exon 8236 8325 . - . Parent=AT1G01020.1 +Chr1 . intron 8326 8416 . - . Parent=AT1G01020.1 +Chr1 TAIR9 CDS 8417 8464 . - 0 ID=CDS2;Parent=AT1G01020.1 +Chr1 TAIR9 exon 8417 8464 . - . Parent=AT1G01020.1 +Chr1 . intron 8465 8570 . - . Parent=AT1G01020.1 +Chr1 TAIR9 CDS 8571 8666 . - 0 ID=CDS2;Parent=AT1G01020.1 +Chr1 TAIR9 exon 8571 8737 . - . Parent=AT1G01020.1 +Chr1 . start_codon 8664 8666 . - . Parent=AT1G01020.1 +Chr1 TAIR9 five_prime_UTR 8667 8737 . - . Parent=AT1G01020.1 +### + | prediction GFF3: +##gff-version 3 +Chr1 TAIR10 mRNA 5928 8737 . - . ID=AT1G01020.1;Name=AT1G01020.1;index=1 +Chr1 TAIR10 three_prime_UTR 5928 6263 . - . Parent=AT1G01020.1 +Chr1 TAIR10 exon 5928 6263 . - . Parent=AT1G01020.1 +Chr1 . intron 6264 6436 . - . Parent=AT1G01020.1 +Chr1 TAIR10 three_prime_UTR 6437 6914 . - . Parent=AT1G01020.1 +Chr1 TAIR10 exon 6437 7069 . - . Parent=AT1G01020.1 +Chr1 . stop_codon 6915 6917 . - . Parent=AT1G01020.1 +Chr1 TAIR10 CDS 6915 7069 . - 2 ID=CDS4;Parent=AT1G01020.1 +Chr1 . intron 7070 7156 . - . Parent=AT1G01020.1 +Chr1 TAIR10 CDS 7157 7232 . - 0 ID=CDS4;Parent=AT1G01020.1 +Chr1 TAIR10 exon 7157 7232 . - . Parent=AT1G01020.1 +Chr1 . intron 7233 7383 . - . Parent=AT1G01020.1 +Chr1 TAIR10 CDS 7384 7450 . - 1 ID=CDS4;Parent=AT1G01020.1 +Chr1 TAIR10 exon 7384 7450 . - . Parent=AT1G01020.1 +Chr1 . intron 7451 7563 . - . Parent=AT1G01020.1 +Chr1 TAIR10 CDS 7564 7649 . - 0 ID=CDS4;Parent=AT1G01020.1 +Chr1 TAIR10 exon 7564 7649 . - . Parent=AT1G01020.1 +Chr1 . intron 7650 7761 . - . Parent=AT1G01020.1 +Chr1 TAIR10 CDS 7762 7835 . - 2 ID=CDS4;Parent=AT1G01020.1 +Chr1 TAIR10 exon 7762 7835 . - . Parent=AT1G01020.1 +Chr1 . intron 7836 7941 . - . Parent=AT1G01020.1 +Chr1 TAIR10 CDS 7942 7987 . - 0 ID=CDS4;Parent=AT1G01020.1 +Chr1 TAIR10 exon 7942 7987 . - . Parent=AT1G01020.1 +Chr1 . intron 7988 8235 . - . Parent=AT1G01020.1 +Chr1 TAIR10 CDS 8236 8325 . - 0 ID=CDS4;Parent=AT1G01020.1 +Chr1 TAIR10 exon 8236 8325 . - . Parent=AT1G01020.1 +Chr1 . intron 8326 8416 . - . Parent=AT1G01020.1 +Chr1 TAIR10 CDS 8417 8464 . - 0 ID=CDS4;Parent=AT1G01020.1 +Chr1 TAIR10 exon 8417 8464 . - . Parent=AT1G01020.1 +Chr1 . intron 8465 8570 . - . Parent=AT1G01020.1 +Chr1 TAIR10 CDS 8571 8666 . - 0 ID=CDS4;Parent=AT1G01020.1 +Chr1 TAIR10 exon 8571 8737 . - . Parent=AT1G01020.1 +Chr1 . start_codon 8664 8666 . - . Parent=AT1G01020.1 +Chr1 TAIR10 five_prime_UTR 8667 8737 . - . Parent=AT1G01020.1 +### + | + | CDS structure comparison + | 9 reference CDS segments + | 9 prediction CDS segments + | CDS structures match perfectly! + | + | Exon structure comparison + | 10 reference exons + | 10 prediction exons + | Exon structures match perfectly! + | + | UTR structure comparison + | 3 reference UTR segments + | 3 prediction UTR segments + | UTR structures match perfectly! + | + | Gene structures match perfectly! + | + | + |-------------------------- + |----- End comparison ----- + |-------------------------- + | + |-------------------------- + |---- Begin comparison ---- + |-------------------------- + | + | reference transcripts: + | AT1G01020.2 + | prediction transcripts: + | AT1G01020.2 + | + | reference GFF3: +##gff-version 3 +Chr1 TAIR9 mRNA 6790 8737 . - . ID=AT1G01020.2;Name=AT1G01020.2;index=1 +Chr1 TAIR9 three_prime_UTR 6790 7069 . - . Parent=AT1G01020.2 +Chr1 TAIR9 exon 6790 7069 . - . Parent=AT1G01020.2 +Chr1 TAIR9 three_prime_UTR 7157 7314 . - . Parent=AT1G01020.2 +Chr1 TAIR9 exon 7157 7450 . - . Parent=AT1G01020.2 +Chr1 . stop_codon 7315 7317 . - . Parent=AT1G01020.2 +Chr1 TAIR9 CDS 7315 7450 . - 1 ID=CDS3;Parent=AT1G01020.2 +Chr1 TAIR9 CDS 7564 7649 . - 0 ID=CDS3;Parent=AT1G01020.2 +Chr1 TAIR9 exon 7564 7649 . - . Parent=AT1G01020.2 +Chr1 TAIR9 CDS 7762 7835 . - 2 ID=CDS3;Parent=AT1G01020.2 +Chr1 TAIR9 exon 7762 7835 . - . Parent=AT1G01020.2 +Chr1 TAIR9 CDS 7942 7987 . - 0 ID=CDS3;Parent=AT1G01020.2 +Chr1 TAIR9 exon 7942 7987 . - . Parent=AT1G01020.2 +Chr1 TAIR9 CDS 8236 8325 . - 0 ID=CDS3;Parent=AT1G01020.2 +Chr1 TAIR9 exon 8236 8325 . - . Parent=AT1G01020.2 +Chr1 TAIR9 CDS 8417 8464 . - 0 ID=CDS3;Parent=AT1G01020.2 +Chr1 TAIR9 exon 8417 8464 . - . Parent=AT1G01020.2 +Chr1 TAIR9 CDS 8571 8666 . - 0 ID=CDS3;Parent=AT1G01020.2 +Chr1 TAIR9 exon 8571 8737 . - . Parent=AT1G01020.2 +Chr1 . start_codon 8664 8666 . - . Parent=AT1G01020.2 +Chr1 TAIR9 five_prime_UTR 8667 8737 . - . Parent=AT1G01020.2 +### + | prediction GFF3: +##gff-version 3 +Chr1 TAIR10 mRNA 6790 8737 . - . ID=AT1G01020.2;Name=AT1G01020.2;index=1 +Chr1 TAIR10 three_prime_UTR 6790 7069 . - . Parent=AT1G01020.2 +Chr1 TAIR10 exon 6790 7069 . - . Parent=AT1G01020.2 +Chr1 TAIR10 three_prime_UTR 7157 7314 . - . Parent=AT1G01020.2 +Chr1 TAIR10 exon 7157 7450 . - . Parent=AT1G01020.2 +Chr1 . stop_codon 7315 7317 . - . Parent=AT1G01020.2 +Chr1 TAIR10 CDS 7315 7450 . - 1 ID=CDS5;Parent=AT1G01020.2 +Chr1 TAIR10 CDS 7564 7649 . - 0 ID=CDS5;Parent=AT1G01020.2 +Chr1 TAIR10 exon 7564 7649 . - . Parent=AT1G01020.2 +Chr1 TAIR10 CDS 7762 7835 . - 2 ID=CDS5;Parent=AT1G01020.2 +Chr1 TAIR10 exon 7762 7835 . - . Parent=AT1G01020.2 +Chr1 TAIR10 CDS 7942 7987 . - 0 ID=CDS5;Parent=AT1G01020.2 +Chr1 TAIR10 exon 7942 7987 . - . Parent=AT1G01020.2 +Chr1 TAIR10 CDS 8236 8325 . - 0 ID=CDS5;Parent=AT1G01020.2 +Chr1 TAIR10 exon 8236 8325 . - . Parent=AT1G01020.2 +Chr1 TAIR10 CDS 8417 8464 . - 0 ID=CDS5;Parent=AT1G01020.2 +Chr1 TAIR10 exon 8417 8464 . - . Parent=AT1G01020.2 +Chr1 TAIR10 CDS 8571 8666 . - 0 ID=CDS5;Parent=AT1G01020.2 +Chr1 TAIR10 exon 8571 8737 . - . Parent=AT1G01020.2 +Chr1 . start_codon 8664 8666 . - . Parent=AT1G01020.2 +Chr1 TAIR10 five_prime_UTR 8667 8737 . - . Parent=AT1G01020.2 +### + | + | CDS structure comparison + | 7 reference CDS segments + | 7 prediction CDS segments + | CDS structures match perfectly! + | + | Exon structure comparison + | 8 reference exons + | 8 prediction exons + | Exon structures match perfectly! + | + | UTR structure comparison + | 3 reference UTR segments + | 3 prediction UTR segments + | UTR structures match perfectly! + | + | Gene structures match perfectly! + | + | + |-------------------------- + |----- End comparison ----- + |-------------------------- + +|------------------------------------------------- +|---- Locus: seqid=Chr1 range=11649-13714 +|------------------------------------------------- +| +| reference genes: +| AT1G01030 +| +| prediction genes: +| AT1G01030 +| +|---------- + | + |-------------------------- + |---- Begin comparison ---- + |-------------------------- + | + | reference transcripts: + | AT1G01030.1 + | prediction transcripts: + | AT1G01030.1 + | + | reference GFF3: +##gff-version 3 +Chr1 TAIR9 mRNA 11649 13714 . - . ID=AT1G01030.1;Name=AT1G01030.1;index=1 +Chr1 TAIR9 three_prime_UTR 11649 11863 . - . Parent=AT1G01030.1 +Chr1 TAIR9 exon 11649 13173 . - . Parent=AT1G01030.1 +Chr1 . stop_codon 11864 11866 . - . Parent=AT1G01030.1 +Chr1 TAIR9 CDS 11864 12940 . - 0 Parent=AT1G01030.1 +Chr1 . start_codon 12938 12940 . - . Parent=AT1G01030.1 +Chr1 TAIR9 five_prime_UTR 12941 13173 . - . Parent=AT1G01030.1 +Chr1 . intron 13174 13334 . - . Parent=AT1G01030.1 +Chr1 TAIR9 five_prime_UTR 13335 13714 . - . Parent=AT1G01030.1 +Chr1 TAIR9 exon 13335 13714 . - . Parent=AT1G01030.1 +### + | prediction GFF3: +##gff-version 3 +Chr1 TAIR10 mRNA 11649 13714 . - . ID=AT1G01030.1;Name=AT1G01030.1;index=1 +Chr1 TAIR10 three_prime_UTR 11649 11863 . - . Parent=AT1G01030.1 +Chr1 TAIR10 exon 11649 13173 . - . Parent=AT1G01030.1 +Chr1 . stop_codon 11864 11866 . - . Parent=AT1G01030.1 +Chr1 TAIR10 CDS 11864 12940 . - 0 Parent=AT1G01030.1 +Chr1 . start_codon 12938 12940 . - . Parent=AT1G01030.1 +Chr1 TAIR10 five_prime_UTR 12941 13173 . - . Parent=AT1G01030.1 +Chr1 . intron 13174 13334 . - . Parent=AT1G01030.1 +Chr1 TAIR10 five_prime_UTR 13335 13714 . - . Parent=AT1G01030.1 +Chr1 TAIR10 exon 13335 13714 . - . Parent=AT1G01030.1 +### + | + | CDS structure comparison + | 1 reference CDS segments + | 1 prediction CDS segments + | CDS structures match perfectly! + | + | Exon structure comparison + | 2 reference exons + | 2 prediction exons + | Exon structures match perfectly! + | + | UTR structure comparison + | 3 reference UTR segments + | 3 prediction UTR segments + | UTR structures match perfectly! + | + | Gene structures match perfectly! + | + | + |-------------------------- + |----- End comparison ----- + |-------------------------- + +|------------------------------------------------- +|---- Locus: seqid=Chr1 range=23146-31227 +|------------------------------------------------- +| +| reference genes: +| AT1G01040 +| +| prediction genes: +| AT1G01040 +| +|---------- + | + |-------------------------- + |---- Begin comparison ---- + |-------------------------- + | + | reference transcripts: + | AT1G01040.1 + | prediction transcripts: + | AT1G01040.1 + | + | reference GFF3: +##gff-version 3 +Chr1 TAIR9 mRNA 23146 31227 . + . ID=AT1G01040.1;Name=AT1G01040.1;index=1 +Chr1 TAIR9 five_prime_UTR 23146 23518 . + . Parent=AT1G01040.1 +Chr1 TAIR9 exon 23146 24451 . + . Parent=AT1G01040.1 +Chr1 . start_codon 23519 23521 . + . Parent=AT1G01040.1 +Chr1 TAIR9 CDS 23519 24451 . + 0 ID=CDS6;Parent=AT1G01040.1 +Chr1 . intron 24452 24541 . + . Parent=AT1G01040.1 +Chr1 TAIR9 exon 24542 24655 . + . Parent=AT1G01040.1 +Chr1 TAIR9 CDS 24542 24655 . + 0 ID=CDS6;Parent=AT1G01040.1 +Chr1 . intron 24656 24751 . + . Parent=AT1G01040.1 +Chr1 TAIR9 exon 24752 24962 . + . Parent=AT1G01040.1 +Chr1 TAIR9 CDS 24752 24962 . + 0 ID=CDS6;Parent=AT1G01040.1 +Chr1 . intron 24963 25040 . + . Parent=AT1G01040.1 +Chr1 TAIR9 exon 25041 25435 . + . Parent=AT1G01040.1 +Chr1 TAIR9 CDS 25041 25435 . + 2 ID=CDS6;Parent=AT1G01040.1 +Chr1 . intron 25436 25523 . + . Parent=AT1G01040.1 +Chr1 TAIR9 exon 25524 25743 . + . Parent=AT1G01040.1 +Chr1 TAIR9 CDS 25524 25743 . + 0 ID=CDS6;Parent=AT1G01040.1 +Chr1 . intron 25744 25824 . + . Parent=AT1G01040.1 +Chr1 TAIR9 exon 25825 25997 . + . Parent=AT1G01040.1 +Chr1 TAIR9 CDS 25825 25997 . + 2 ID=CDS6;Parent=AT1G01040.1 +Chr1 . intron 25998 26080 . + . Parent=AT1G01040.1 +Chr1 TAIR9 exon 26081 26203 . + . Parent=AT1G01040.1 +Chr1 TAIR9 CDS 26081 26203 . + 0 ID=CDS6;Parent=AT1G01040.1 +Chr1 . intron 26204 26291 . + . Parent=AT1G01040.1 +Chr1 TAIR9 exon 26292 26452 . + . Parent=AT1G01040.1 +Chr1 TAIR9 CDS 26292 26452 . + 0 ID=CDS6;Parent=AT1G01040.1 +Chr1 . intron 26453 26542 . + . Parent=AT1G01040.1 +Chr1 TAIR9 exon 26543 26776 . + . Parent=AT1G01040.1 +Chr1 TAIR9 CDS 26543 26776 . + 1 ID=CDS6;Parent=AT1G01040.1 +Chr1 . intron 26777 26861 . + . Parent=AT1G01040.1 +Chr1 TAIR9 exon 26862 27012 . + . Parent=AT1G01040.1 +Chr1 TAIR9 CDS 26862 27012 . + 1 ID=CDS6;Parent=AT1G01040.1 +Chr1 . intron 27013 27098 . + . Parent=AT1G01040.1 +Chr1 TAIR9 exon 27099 27281 . + . Parent=AT1G01040.1 +Chr1 TAIR9 CDS 27099 27281 . + 0 ID=CDS6;Parent=AT1G01040.1 +Chr1 . intron 27282 27371 . + . Parent=AT1G01040.1 +Chr1 TAIR9 exon 27372 27533 . + . Parent=AT1G01040.1 +Chr1 TAIR9 CDS 27372 27533 . + 0 ID=CDS6;Parent=AT1G01040.1 +Chr1 . stop_codon 27531 27533 . + . Parent=AT1G01040.1 +### + | prediction GFF3: +##gff-version 3 +Chr1 TAIR10 mRNA 23146 31227 . + . ID=AT1G01040.1;Name=AT1G01040.1;index=1 +Chr1 TAIR10 five_prime_UTR 23146 23518 . + . Parent=AT1G01040.1 +Chr1 TAIR10 exon 23146 24451 . + . Parent=AT1G01040.1 +Chr1 . start_codon 23519 23521 . + . Parent=AT1G01040.1 +Chr1 TAIR10 CDS 23519 24451 . + 0 ID=CDS7;Parent=AT1G01040.1 +Chr1 . intron 24452 24541 . + . Parent=AT1G01040.1 +Chr1 TAIR10 exon 24542 24655 . + . Parent=AT1G01040.1 +Chr1 TAIR10 CDS 24542 24655 . + 0 ID=CDS7;Parent=AT1G01040.1 +Chr1 . intron 24656 24751 . + . Parent=AT1G01040.1 +Chr1 TAIR10 exon 24752 24962 . + . Parent=AT1G01040.1 +Chr1 TAIR10 CDS 24752 24962 . + 0 ID=CDS7;Parent=AT1G01040.1 +Chr1 . intron 24963 25040 . + . Parent=AT1G01040.1 +Chr1 TAIR10 exon 25041 25435 . + . Parent=AT1G01040.1 +Chr1 TAIR10 CDS 25041 25435 . + 2 ID=CDS7;Parent=AT1G01040.1 +Chr1 . intron 25436 25523 . + . Parent=AT1G01040.1 +Chr1 TAIR10 exon 25524 25743 . + . Parent=AT1G01040.1 +Chr1 TAIR10 CDS 25524 25743 . + 0 ID=CDS7;Parent=AT1G01040.1 +Chr1 . intron 25744 25824 . + . Parent=AT1G01040.1 +Chr1 TAIR10 exon 25825 25997 . + . Parent=AT1G01040.1 +Chr1 TAIR10 CDS 25825 25997 . + 2 ID=CDS7;Parent=AT1G01040.1 +Chr1 . intron 25998 26080 . + . Parent=AT1G01040.1 +Chr1 TAIR10 exon 26081 26203 . + . Parent=AT1G01040.1 +Chr1 TAIR10 CDS 26081 26203 . + 0 ID=CDS7;Parent=AT1G01040.1 +Chr1 . intron 26204 26291 . + . Parent=AT1G01040.1 +Chr1 TAIR10 exon 26292 26452 . + . Parent=AT1G01040.1 +Chr1 TAIR10 CDS 26292 26452 . + 0 ID=CDS7;Parent=AT1G01040.1 +Chr1 . intron 26453 26542 . + . Parent=AT1G01040.1 +Chr1 TAIR10 exon 26543 26776 . + . Parent=AT1G01040.1 +Chr1 TAIR10 CDS 26543 26776 . + 1 ID=CDS7;Parent=AT1G01040.1 +Chr1 . intron 26777 26861 . + . Parent=AT1G01040.1 +Chr1 TAIR10 exon 26862 27012 . + . Parent=AT1G01040.1 +Chr1 TAIR10 CDS 26862 27012 . + 1 ID=CDS7;Parent=AT1G01040.1 +Chr1 . intron 27013 27098 . + . Parent=AT1G01040.1 +Chr1 TAIR10 exon 27099 27281 . + . Parent=AT1G01040.1 +Chr1 TAIR10 CDS 27099 27281 . + 0 ID=CDS7;Parent=AT1G01040.1 +Chr1 . intron 27282 27371 . + . Parent=AT1G01040.1 +Chr1 TAIR10 exon 27372 27533 . + . Parent=AT1G01040.1 +Chr1 TAIR10 CDS 27372 27533 . + 0 ID=CDS7;Parent=AT1G01040.1 +Chr1 . stop_codon 27531 27533 . + . Parent=AT1G01040.1 +### + | + | CDS structure comparison + | 12 reference CDS segments + | 12 prediction CDS segments + | CDS structures match perfectly! + | + | Exon structure comparison + | 12 reference exons + | 12 prediction exons + | Exon structures match perfectly! + | + | UTR structure comparison + | 1 reference UTR segments + | 1 prediction UTR segments + | UTR structures match perfectly! + | + | Gene structures match perfectly! + | + | + |-------------------------- + |----- End comparison ----- + |-------------------------- + +============================================================ +========== ParsEval Summary +============================================================ + +Started: 31 Dec 2020, 08:39PM +Reference annotations: example_ref_label +Prediction annotations: example_pred_label +Executing command: parseval -l 0 -t 32 -w -x example_ref_label -y example_pred_label -f text -o /tmp/tmpuaspc0eb/files/1/7/a/dataset_17a21c9f-5e47-48fb-b467-1d022f11befc.dat /tmp/tmpuaspc0eb/files/2/d/4/dataset_2d46af81-606d-4a91-bdad-a08bfdbc2b2b.dat /tmp/tmpuaspc0eb/files/8/d/9/dataset_8d95a475-34f5-4968-a3a0-653b7a5efb86.dat + + Sequences compared + Chr1 + + Gene loci................................4 + shared.................................4 + unique to reference....................0 + unique to prediction...................0 + + Reference annotations + genes..................................4 + average per locus....................1.000 + transcripts............................5 + average per locus....................1.250 + average per gene.....................1.250 + + Prediction annotations + genes..................................4 + average per locus....................1.000 + transcripts............................5 + average per locus....................1.250 + average per gene.....................1.250 + + Total comparisons........................5 + perfect matches........................5 (100.0%) + avg. length..........................3607.40 bp + avg. # refr exons....................7.60 + avg. # pred exons....................7.60 + avg. refr CDS length.................449.40 aa + avg. pred CDS length.................449.40 aa + perfect matches with mislabeled UTRs...0 (0.0%) + CDS structure matches..................0 (0.0%) + exon structure matches.................0 (0.0%) + UTR structure matches..................0 (0.0%) + non-matches............................0 (0.0%) + + CDS structure comparison + reference CDS segments.................35 + match prediction.....................35 (100.0%) + don't match prediction...............0 (0.0%) + prediction CDS segments................35 + match reference......................35 (100.0%) + don't match reference................0 (0.0%) + Sensitivity............................1.000 + Specificity............................1.000 + F1 Score...............................1.000 + Annotation edit distance...............0.000 + + Exon structure comparison + reference exons........................38 + match prediction.....................38 (100.0%) + don't match prediction...............0 (0.0%) + prediction exons.......................38 + match reference......................38 (100.0%) + don't match reference................0 (0.0%) + Sensitivity............................1.000 + Specificity............................1.000 + F1 Score...............................1.000 + Annotation edit distance...............0.000 + + UTR structure comparison + reference UTR segments.................12 + match prediction.....................12 (100.0%) + don't match prediction...............0 (0.0%) + prediction UTR segments................12 + match reference......................12 (100.0%) + don't match reference................0 (0.0%) + Sensitivity............................1.000 + Specificity............................1.000 + F1 Score...............................1.000 + Annotation edit distance...............0.000 + + Nucleotide-level comparison CDS UTRs Overall + Matching coefficient: 1.000 1.000 1.000 + Correlation coefficient: 1.000 1.000 -- + Sensitivity: 1.000 1.000 -- + Specificity: 1.000 1.000 -- + F1 Score: 1.000 1.000 -- + Annotation edit distance: 0.000 0.000 --