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JCVI Genome Annotation

note

Computes statistics on genome annotation.

https://pypi.org/project/jcvi/

The JCVI module parses the output of python -m jcvi.annotation.stats genestats <input.gff>. The file name is used as the sample name. If the output from the python -m jcvi.annotation.stats stats <input.gff> is present in the same directory, it is used to draw complementary plots.

A typical result directory will contain:

├── Exon_Count
│   ├── sample1.txt
│   └── sample2.txt
├── Exon_Length
│   ├── sample1.txt
│   └── sample2.txt
├── Gene_Length
│   ├── sample1.txt
│   └── sample2.txt
├── Intron_Length
│   ├── sample1.txt
│   └── sample2.txt
├── sample1_genestats.txt
└── sample2_genestats.txt

The JCVI module has been tested with output from JCVI v1.0.9.

File search patterns​

jcvi:
  contents: '     o    % GC    % of genome    Average size (bp)    Median size (bp)    Number    Total
    length (Mb)'