Mercurial > repos > iuc > aegean_gaeval
diff test-data/parseval_output_test1.txt @ 0:1dd7adc21b6d draft
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/aegean commit e6c01517075cab35e620fe1bbdb5fd68e4d1359f"
| author | iuc |
|---|---|
| date | Sun, 03 Jan 2021 14:59:26 +0000 |
| parents | |
| children |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/parseval_output_test1.txt Sun Jan 03 14:59:26 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 --