gwlilabmit / gwlilabmit/rendseq
Adapt to bedgraph or multi-chromosome wig
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Description
Any genome with multiple contigs or chromosomes can be represented in a multi-line wig file like this:
```
track type=wiggle_0
variableStep chrom=chrI
...
1 10
2 10
3 10
...
variableStep chrom=chrII
...
7 5
8 5
9 5
....
```
or as a bedgraph file like this:
```
chrI 1 3 10
...
chrII 7 9 5
...
```
This applies to yeast data and to Jenny's cyano data.
When I was extending Cassandra's peak calling script ([see here](https://github.com/gwlilabmit/CORE_Transcription-Isoform-Analysis/blob/main/evaluate_peaks.py)) I preferred to accommodate multi-chromosome files as bedgraph files, and had separate `load_reads_wig()` and `load_reads_bedgraph()` functions.
Maybe we can do something similar here? However we do it, it should be relatively straightforward to add some functions to [file_funcs.py](https://github.com/miraep8/rendseq/blob/main/rendseq/file_funcs.py) to accommodate multiple chromosomes.
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