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So we currently read annotations from .trinotate into memory, then pull from them on the fly when writing .tbl files. I propose that we store annotations as a component of genes/mRNAs/CDSs, that we ad…
bruab updated
10 years ago
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I'm guessing it needs some sort of "if strand is reversed lookit indices[1] instead of indices[0]" magic, will look into later
bruab updated
10 years ago
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Add a 'FASTA' item under the 'Save as' menu, which when clicked brings up a model dialog that lets the user select what kind of sequence will be in the FASTA file, and has a 'Download' button. When t…
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The last thread got pretty silly (my fault). Here are the stats that still need adding:
### Exon
shortest, longest, total length (each line in the gff is an exon, so a single mRNA should contain mult…
bruab updated
10 years ago
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What _should_ happen is:
remove bases in question from sequence.
if the bases intersect a gene, trim the gene (update its indices)
BUT if the bases intersect a CDS, remove the CDS (and its mRNA, and …
bruab updated
10 years ago
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min/max CDS length
min/max protein length
remove terminal Ns ("terminal" means initial or final in NCBI-speak)
min/max intron length
min/max exon length
bruab updated
10 years ago
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bruab updated
10 years ago
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Seqmasker creates an interval format that looks like
> sp|Q9BS26|ERP44_HUMAN Endoplasmic reticulum resident
> 6 - 18
If no other BLAST tool is using it as input, I would propose to include an python…
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Jimmy and I prototyped related GFF3 tidy scripts for the iLocus analysis. Once the VIGA analysis confirms things have worked like we hoped, it shouldn't be too difficult to implement this functionalit…
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Issue #64 was the result of having lots of output files open simultaneously. Output is only written to one output file (per thread) at a time, so there may not be any reason for keeping all these file…