README.md of /blobology/dev
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Input formats
legacy format:
| columns | ID | len | gc | cov1 | cov2 | cov3 | taxlevel1 | taxlevel2 | taxlevel3 | taxlevel4 |
|---|---|---|---|---|---|---|---|---|---|---|
| type | str | int | float | float | float | float | str | str | str | str |
| example | ID | len | gc | cov1 | cov2 | cov3 | taxlevel_species | taxlevel_order | taxlevel_phylum | taxlevel_superkingdom |
| contig1 | 1000 | 0.56 | 100 | 150.2 | 80.3 | Danio rerio | Cypriniformes | Chordata | Eukaryota | |
| contig2 | 500 | 0.54 | 12.9 | 11.1 | 15.7 | Not Annotated | Not Annotated | Not Annotated | Not Annotated |
- eval format as in gc_cov_annotate_v1.pl --evalue (requires BLAST -outfmt '6 qseqid taxid std')
| columns | ID | len | gc | cov1 | cov2 | cov3 | taxlevel1 | taxlevel2 | taxlevel3 | taxlevel4 | eval |
|---|---|---|---|---|---|---|---|---|---|---|---|
| type | str | int | float | float | float | float | str | str | str | str | scientific |
| example | ID | len | gc | cov1 | cov2 | cov3 | taxlevel_species | taxlevel_order | taxlevel_phylum | taxlevel_superkingdom | eval |
| contig1 | 1000 | 0.56 | 100 | 150.2 | 80.3 | Danio rerio | Cypriniformes | Chordata | Eukaryota | 1e-25 | |
| contig2 | 500 | 0.54 | 12.9 | 11.1 | 15.7 | Not Annotated | Not Annotated | Not Annotated | Not Annotated | N/A |
- novel format (to be inplemented)
| columns | ID | len | gc | cov | tax | eval |
|---|---|---|---|---|---|---|
| type | str | int | float | float | str | scientific |
| example | ID | len | gc | cov | tax | eval |
| contig1 | 1000 | 0.56 | cov1=100;cov2=150.2;cov3=80.3 | species=Danio rerio;order=Cypriniformes;phylum=Chordata;superkingdom=Eukaryota | 1e-25 | |
| contig2 | 500 | 0.54 | cov1=12.9;cov2=11.1;cov3=15.7 | species=Not Annotated;order=Not Annotated;phylum=Not Annotated;superkingdom=Not Annotated | N/A |