Takes a GFF file, and extends the "START" and "END" fields of each gene row, to include intergenic regions
data in:
<some GFF file>
data out:
<the same GFF file, with new START and END fields, to incorporate the intergenic regions>
We want to share the intergenic regions available betwen tandemly occurring feature annotations of a specific type, e.g. exon/transcript/cds/etc., as specified by the input GFF file's row's column's fields: "START" and "END". Where "START" and "END" are measured in nucleotide basepairs, BPs, from left (0) to right (n) of a given chromosome. BPs are hereby represented as ., where ... would be three BPs in tandem. We Then print out a new GFF file with modified "START" and "END" fields to aknowledge the resulting intergenic BP sharings by tandem features.
The following sketch illustrates all possible scenarios we need to account for, and the | shows the precise location along the intergenic regions, where nucleotide basepairs (BPs, shown as .) are shared between tandem gene/transcript/exon/cds annotations of the input GFF file. By precise I mean a common multiple of BPs for 2 and 3 is used leaving no remainders in the example:
| Case | Diagram | Strands | Share | Status |
|---|---|---|---|---|
| 1. Tail-to-Tail | 5'(head)===>3'(tail)...|...3'(tail)<===5'(head) | (+,-) | 1/2:1/2 | Tested |
| 2. Head-to-Head | 3'(tail)<===5'(head)...|...5'(head)===>3'(tail) | (-,+) | 1/2:1/2 | Tested |
| 3. Tail-to-Head | 5'(head)===>3'(tail)..|....5'(head)===>3'(tail) | (+,+) | 1/3:2/3 | Testing:@TODO |
| 4. Head-to-Tail | 3'(tail)<===5'(head)....|..3'(tail)<===5'(head) | (-,-) | 2/3:1/3 | Developing:@TODO |
In the input GFF file, the above data is represented as:
feild: \/start\/end
row 1: ===1===>
row 2: <==2==
row 3: <==3==
row 4: ==4==>
row 5: ===5===>
row 6: <===6===
Specifically, we want to distribute intergenic regions between tandem gene/transcript/exon/cds (@features), according to the following ratios: 1/2:1/2 and 1/3:2/3, inferred using the tandem gene's pairwise "strand" field configurations (see table above). And create a new GFF with modified "start" and "end" fields, which account for the, now shared, BPs (.) as shown above:
after: \/start \/end
row 1: ===1===>...
row 2: ...<==2==....
row 3: ..<==3==...
row 4: ...==4==>....
row 5: ..===5===>...
row 6: ...<===6===
- Python3.5m
- Andy
- Kathrin