Parse2 update (#99) #109
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Parse2 update (#99) #109
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1. parse is now fully pysam-powered, which is propagated to dependencies and setup. 2. Novel classes for simplified access to alignments with pysam: AlignmentFilePairtoolized, AlignedSegmentPairtoolized in _parse_pysam.pyx. 2. Tests updated; test sam files can be parsed by pysam.
* Parse2: created. Improved version of parse2 with resolved comments from the previous PR: #96 Major changes: * Single-end mode of parse2 added, --single-end option. Tested on minimap2 output for MC-3C. * parse2 now has three possible coordinate systems for reporting: read, walk and pair (described in the docstring). Default coord system "read" tested. * demo notebook with MC-3C and Arima datasets * simplified code of parse2, e.g. push_pair function added instead of repetitive code improved docstrings * Max molecule size replaced with max fragment size. * parse2(docs): Documentation improved, #96 (comment) resolved. * Option to report 5' or 3' ends option added.
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* simple parse supports complex walks * parse2 supports single-end and coordinate system options
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* 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 <agalitzina@gmail.com> Co-authored-by: Ilya Flyamer <flyamer@gmail.com>
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parse2 is a module specifically designed for parsing long Hi-C reads.
This is an improved version of parse2 with resolved comments from the previous PR: #96
Major changes:
Separation of parse and parse2 modules. Parse has an option
--walks-policy all, which parses long walks, but always reportingpairorientation andouterpositions 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-positionand--report-orientation, which might be used to report junctions, or reads, or walks.Parse2 has an option to parse single-end reads,
--single-endoption, tested on minimap2 output for MC-3C.Parse2 has the
max_fragment_size insteadinstead of parse'smax_molecule_size, which help to determine the overlapping ends of forward and reverse reads.Recent update simplifies the code:
single _parselibrary used by both parse and parse2,push_pairfunction,_parselibrary.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
Important improvements of the tests for parse and parse2