count_reads.py fix when library could be a tsv - #6
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…les the file downstream decide what to do, and don't let the function return None
… with `--overwrite` In a previous commit, the behaviour that the pipeline skips over existing analysis files was removed, but existing analysis files were still checked for. I have re-enabled the behaviour and made it the default. This is so that additional analyses can be easily added without running everything again. Overwriting existing analysis files can be achieved with `--overwrite`.
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All planned changes have been committed and I have completed my tests. This pull request is ready to merge :) |
Support Chronos, amend requirements, bump version
make output dir if it doesn't exist in count_batch
version 3.0.1 with improved Chronos calling
fix chronos crashes
Fix chronos obtaining the unintended differential levels
Improve Chronos creation of sequencemap
Chronos deal properly when replicates are used in more than one comparison
Add Trajectory column in replicate details xlsx for Chronos analysis
If supplied, detect guide lengths. If guide length is not constant or slice width is not equal to guide length, slide a window along the slice and count individually. Retain support when library not supplied
Support variable guides and mismatched slice in count_reads
… in a library with variable length guides
Warn instead of fail when using a slice shorter than max guide length in count_reads
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In count_reads.py:576,
pd.read_table()in favour overpd.read_csv()so as to allow if the library is a tsv