fix yeast additions, with dual exons

[nathandunn]

fixes #51

• [x] fix test_other_yeast_types_bulk, (a client submission error)

• [ ] fix test_multiexon_yeastI, multiple errors

• [x] fix test_single_trna_test, casts tRNA to ncRNA incorrectly on GFF3 export (maybe adds them that way as well?)

• [x] fix test_bulk_mix_transcript, casts tRNA to ncRNA incorrectly on GFF3 export (maybe adds them that way as well?)

• [x] fix test_mix_bulk_safe, casts tRNA to ncRNA incorrectly on GFF3 export (maybe adds them that way as well?)

• [x] add breaking (double-exon) annotation test to yeast

• [x] add other relevant parts of yeastI test to annotation_test (psuedogenes, transposable_elements, etc. etc.) and validate counts

• [x] add yeastI organism to bootstrap

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• [x] add merlin case with 2 exons (confirm), i.e., an intron on the isoform (confirm what we have now)
  • [x] add test if does not exist
• add test with two isoforms, each with 2 exons, but in different posistions, (verify on Apollo2)

---

• [x] add test data for add yeast on Chromosome 1 (gff3 and fasta)
• [x] fix deleteFeatureAndChildren
• [x] add logging exception for all

[nathandunn]

All of the other mRNA's work, but not this one:

I   sgd gene    87286   87752   .   +   .   ID=gene:YAL030W;Name=SNC1;biotype=protein_coding;description=Vesicle membrane receptor protein (v-SNARE)%3B involved in the fusion between Golgi-derived secretory vesicles with the plasma membrane%3B proposed to be involved in endocytosis%3B member of the synaptobrevin/VAMP family of R-type v-SNARE proteins%3B SNC1 has a paralog%2C SNC2%2C that arose from the whole genome duplication [Source:SGD%3BAcc:S000000028];gene_id=YAL030W;logic_name=sgd
I   sgd mRNA    87286   87752   .   +   .   ID=transcript:YAL030W_mRNA;Parent=gene:YAL030W;Name=SNC1;biotype=protein_coding;transcript_id=YAL030W_mRNA
I   sgd exon    87286   87387   .   +   .   Parent=transcript:YAL030W_mRNA;Name=YAL030W_mRNA-E1;constitutive=1;ensembl_end_phase=0;ensembl_phase=0;exon_id=YAL030W_mRNA-E1;rank=1
I   sgd CDS 87286   87387   .   +   0   ID=CDS:YAL030W;Parent=transcript:YAL030W_mRNA;protein_id=YAL030W
I   sgd exon    87501   87752   .   +   .   Parent=transcript:YAL030W_mRNA;Name=YAL030W_mRNA-E2;constitutive=1;ensembl_end_phase=0;ensembl_phase=0;exon_id=YAL030W_mRNA-E2;rank=2
I   sgd CDS 87501   87752   .   +   0   ID=CDS:YAL030W;Parent=transcript:YAL030W_mRNA;protein_id=YAL030W

[nathandunn]

Add 3 tests to a new "yeast_test" file adding and dropping yeast organism (not in bootstrap):

1. bulk_load_yeastI.gff, 51 genes, mRNA, CDS, exons, each
2. other_types_yeastI.gff, 23 genes, 20 mRNA, 25 exons (one tRNA has two exons), 2 transposable_elements, 1 pseudogene, 3 tRNA (to genes), 20 CDS's
3. multiexon_yeastI.gff, . . . 1 gene, 1 mRNA, 2 exons, and one CDS (input is 2)