IGVF-DACC / igvf-catalog / 010b0933-60af-4b6c-91b5-3349d9af7faa

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DSERV-1242-more-perturb-seq-clean (#729)

* more data files + adjusted adapter

* more normalization

* tests for CRUDO tap-seq

* sample file

* reworking the adapter

* mixed dataset adjustments

* safeguard against duplicates

* stuff

* added config

* teloHAEC datasets

* rename p_value_adj to adj_p_value

* hardcoding TSS as significant = True

* removed teloHAEC

* skip rows explicit

* don't use catalog_notes

* remove ai

* FRACTEL_effect_size is a log2fc

* teloHAEC is comma-deliminated

* some notes adjustments

* more lines to skip

* hon dataset

* renamed n_guides to num_guides

* files_filesets

* rename

* rename

* moved around some stuff in config

* spaces

* clean up config

* NOS3 data is erroneous

* updating wording

* adjusting config

* rename target gene to perturbed gene

* p_value_adj

* significant

* adapter_calculated_fields

* neg_log10_p_value_adj

* neg_log10_p_value and neg_log10_p_value_adj

* stuff

* pyspade corrections

* API stuff

* comments no longer needed

* updated pyspade p-values

* flip mapping

* revert changes to API

* code review

* context + prompted cleanup of adapter

* fixed rebase

* parsed data

* parsed data update

* neg_log10_pvalue --> neg_log10_p_value

* significance always uses threshold

* updated following Mpathi feedback

* fix test

* updated files_filesets

283 of 360 branches covered (78.61%)

Branch coverage included in aggregate %.

13724 of 16211 relevant lines covered (84.66%)

1.05 hits per line