Add summaries #105
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Add summaries #105
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What would make sense to do with complexity estimates after merging?.. I think it depends on whether the merged files are separate "lanes" from the same library (then it should be just recalculated from merged duplicates/total mapped reads), or whether the pairs come from different replicates (then they should be summer up, perhaps?). So do we need an argument for that? |
agalitsyna
reviewed
Apr 8, 2022
tests/test_stats.py
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| assert stats['summary/frac_cis_4kb+'] == 0 | ||
| assert stats['summary/frac_cis_10kb+'] == 0 | ||
| assert stats['summary/frac_cis_20kb+'] == 0 | ||
| assert stats['summary/frac_cis_40kb+'] == 0 |
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Wow, these are great tests! Is it possible also to test the deduplication stats?
It's not my idea, though, I found it in #5
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Yeah that's why I didn't notice the recent error in stats with the new dataframe method, because the test file doesn't have an duplicated pairs... SHould be easy to fix
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@Phlya How about throwing a warning if "merge" command is in the header? |
agalitsyna
previously requested changes
Apr 26, 2022
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Thanks, Ilya! This is cool and important. I only suggest some minor improvements and warning to introduce; also suggest to merge into pre 1.0.0 branch and not into master. I still test 1.0.0, thus I will additionally test these options while preparing the release of new version.
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agalitsyna
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Jun 1, 2022
* Separate cli and lib * pairtools flip fix for unannotated chromosomes, resolving #91 * handle empty chromosomes, resolved #76 * fixed rfrags indexing and first rfrag omission, resolved #73 * resolved or deprecated suggestions in #16 * merge improvements, header merge fixed - resolved merge without arguments: #61 - option to add only the first header in merge, resolved #18 * in merge, added option to concatenate instead of merge sorted inputs, resolving: #23 * merge now checks that columns of inputs are the same * I/O improvements - auto_open defaults to stdin/stdout when path evaluates to False. resolved #48 - auto_open defaults to stdin/stdout when the path is "-" - if the stream is optional, it's controlled by the module itself * Parse2 update (#99) (#109) Improved version of parse2 with resolved comments from the previous PR: #96 - Separation of parse and parse2 modules. Parse has an option --walks-policy all, which parses long walks, but always reporting pair orientation and outer positions of 5'-ends, as if each pair was read in paired-end mode independently. Parse2 is specifically designed for long walks, and has options --report-position and --report-orientation, which might be used to report junctions, or reads, or walks. - Parse2 has an option to parse single-end reads, --single-end option, tested on minimap2 output for MC-3C. - Parse2 has the max_fragment_size instead instead of parse's max_molecule_size, which help to determine the overlapping ends of forward and reverse reads. - Recent update simplifies the code: single _parse library used by both parse and parse2, - a number of functions that reduce repetitive code, e.g. push_pair function, - dosctrings and documented structure of _parse library. - Both parse and parse2 have the options to report 5' or 3' ends; to flip alignments according to chromosome coordinate. - Both parse and parse2 have the pysam backend - Improvements of the tests for parse and parse2 - Documentation includes description of various --report-orientation and --report-position cases. * Merge pairlib into pairtools.lib. * CLI for scalings added. * stats output in yaml format * Header CLI (#121) - new module called by `pairtools header` - submodules: - generate : Generate the header - set-columns : Add the columns to the .pairs/pairsam file - transfer : Transfer the header from one pairs file to another - validate-columns : Validate the columns of the .pairs/pairsam file - resolves #119 - option remove-columns for `pairtools select`: Remove the columns from .pairs/pairsam file * pairtools phase critical update (#114) * imporant fixes: - cython dedup with no-parent id forgotten counter reset; - sphinx doc update (added pysam); - header warning if empty and error if try to add a field to empy one * Add summaries (#105) * Add functions for duplication tile and complexity * Make dedup stats! * Benchmarks finalization * [WIP] Stats split by filters (#132) * Markasdup lib removed; markasdup CLI explanation improved * dedup filter stats added and tested Co-authored-by: Aleksandra Galitsyna <[email protected]> Co-authored-by: Ilya Flyamer <[email protected]>
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Adding first support for summary statistics: for now just fraction of cis reads (at all currently calculated minimal separations) and library complexity estimate.