Update Tests - Githubissues

dib-lab / dammit

just annotate it, dammit!

http://dib-lab.github.io/dammit/

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Update Tests #188

Closed camillescott closed 4 years ago

camillescott commented 4 years ago

CLI Components

Primary annotation and configuration commands:

[x] config Show dammit configuration information.

FASTA munging commands:

[x] rename-fasta Copy a FASTA file and rename the headers.
[x] transcriptome-stats Run basic metrics on a transcriptome
[x] annotate-fasta Annotate a FASTA file from a GFF3 file.

Filtering commands:

[x] best-hits Filter query best-hits from a MAF file.

Conversion commands:

[x] maf-to-gff3 Convert MAF to GFF3.
[x] shmlast-to-gff3 Convert shmlast CSV output to GFF3.
[x] hmmscan-to-gff3 Convert HMMER to GFF3.
[x] cmscan-to-gff3 Convert Infernal's cmscan output to GFF3.

Transformation commands:

[x] merge-gff3 Merge a collection of GFF3 files.
[ ] remap-hmmer-coords Remap hmmscan coordinates using TransDecoder ORF...