Version History and Changes

Version 3.0.0 (2024-03-18)

  • Add option to compute distances from gene TES only (--edge=tes) (PR #77).

  • Add CITATION.cff file and updated information on how to cite RnaChipIntegrator (PR #78).

  • Update the installation documentation and metadata (PR #85,

  • Add automated CI testing and deployment to PyPI via GitHub Actions, and add support for Python 3.9 (PR #74).

  • Drop support for Python 2.7 (PR #76).

Version 2.0.0 (2020-01-06)

  • Add support for Python 3 (3.5, 3.6, 3.7 and 3.8) (PR #69,

Version 1.2.0 (2019-07-19)

  • Implement batch mode operation which allows a single run of RnaChipIntegrator to iterate over any combination of multiple cutoffs (via new --cutoffs option) and multiple peaks and genes files (via new --peaks and --genes options) (PR #58).

  • Drop support for Python 2.6 (PR #66).

Version 1.1.0 (2018-08-06)

  • Fix bug in gene-centric analysis when using --edge=both, which meant valid peaks could sometimes be dropped from the results (PR #60).

  • New --peak_id option enables peak names to be read from an ID column in the peaks file, which will be carried through to the output files (PR #56).

  • New --analyses option enables specific analyses to be selected (i.e. either peak-centric only, gene-centric only, or both peak- and gene-centric) (PR #46).

Version 1.0.3 (2018-01-23)

  • Update description of ‘direction’ in the documentation and the XLSX file, to clarify the meaning of the terms ‘upstream’ and downstream’ in the program outputs.

  • Update documentation to explain how comments, header lines, and lines with ‘bad’ data, are handled by the program when reading in the input files.

  • Add a section on ‘known problems’ to the documentation.

Version 1.0.2 (2016-08-17)

  • Bugfix release: fixes bug which crashed the program if --cutoff=0 was specified together with --xlsx.

Version 1.0.1 (2016-06-16)

  • Bugfix release: fixes bug which crashed the program if --cutoff=0 was specified.

Version 1.0.0 (2016-02-24)

  • Complete reimplementation of RnaChipIntegrator to unify internal algorithms, simplify usage and substantially update the documentation.

  • Installs using pip; can be obtained directly from PyPI using pip install RnaChipIntegrator.

  • Executable now installs as RnaChipIntegrator (i.e. no .py extension)

  • Documentation now available via ReadTheDocs: http://rnachipintegrator.readthedocs.org/en/latest/

  • No distinction is now made between ‘summits’ and ‘peaks’; the same algorithm is applied in each case.

  • The program always finds the nearest genes to each peak, and vice versa. The same distance cutoff and maximum number of hits are applied to both and can be specified using the --cutoff and --number options.

  • By default all pairs within the cut-off distance are reported unless the user explicitly restricts this to a subset by specifying the --number option (i.e. --number now turned off by default).

  • By default nearest distances between peaks and gene are calculated from the TSS of the feature to whichever of the peak edges are closer; alternatively distances can be calculated between the nearest pair of peak/gene edges by specifying the --edge=both option.

  • Any differential expression flags in the input genes file are ignored unless the --only-DE option is specified, in which case only the differentially expressed genes are considered in the analyses.

  • By default each peak/gene pair is reported on a separate line; the --compact option reports all nearest gene/peaks on a single line of output.

  • New direction field in output indicates whether hits are up- or downstream from reference.

  • Specify arbitrary columns from input peaks file using new --peak_cols options to set chromosome, start and end.

  • Output file names now end with gene-centric and peak-centric.

  • Excel output is only produced if the --xlsx option is specified; spreadsheets are now output in XLSX format (instead of XLS).

  • Summary output is only produced if --summary is specified.

  • The rearrange_columns.py utility has been dropped.

Version 0.5.0-alpha.8 (2016-02-18)

  • Fix typo in XLSX ‘notes’ sheet.

Version 0.5.0-alpha.7 (2016-02-03)

  • Update --xls option to --xlsx and generate XLSX files (instead of XLS); as XLSX has much greater limits on the number of rows and columns allowed in a worksheet this should address previous problems with having data split over multiple sheets.

  • Correct headers and placeholders now output when using --compact option when --number is not specified.

  • Pre-existing output files are explicitly removed before analysis is run (rather than relying on overwrite).

Version 0.5.0-alpha.6 (2016-01-29)

  • Fix broken --xls option (crashed program if specified).

Version 0.5.0-alpha.5 (2016-01-29)

  • Rename ‘feature’ to ‘gene’ in program output, documentation etc NB this doesn’t affect the program function.

  • By default all pairs within the cut-off distance are reported unless the user explicitly restricts this to a subset by specifying the --number option (i.e. --number now turned off by default).

  • Output file names changed to feature-centric and peak-centric.

  • Options are grouped into subsets when displayed by -h/--help.

  • Parameter defaults are also given in the documentation.

  • Peaks in the input have ‘start’ and ‘end’ positions which aren’t at least 1bp apart cause the program to raise an error.

Version 0.5.0-alpha.4 (2015-12-01)

  • Fix the broken --promoter_region option which was being ignored.

Version 0.5.0-alpha.3 (2015-12-20)

  • --compact now only changes the output format from “multi-line” (i.e. one hit pair per line) to “single-line” (i.e. all hits on the same line). The same fields are reported in both modes.

  • The explanatory text for the dist_closest field has been updated to make it clearer what this means.

Version 0.5.0-alpha.2 (2015-10-28)

  • Executable now installs as RnaChipIntegrator (i.e. no .py extension)

  • Specify feature type (e.g. gene, transcript etc) to be used in output using --feature option.

  • New direction field in output indicates whether hits are up- or downstream from reference.

  • Specify arbitrary columns from input peaks file using new --peak_cols options to set chromosome, start and end.

  • --pad option is automatically implied by the --compact option (i.e. single line output is always padded).

Version 0.5.0-alpha.1 (2015-09-01)

  • Complete reimplementation of RnaChipIntegrator to unify internal algorithms, simplify usage and substantially update the documentation.

  • No distinction is now made between ‘summits’ and ‘peaks’; the same algorithm is applied in each case.

  • The program always finds the nearest features to each peak, and vice versa. The same distance cutoff and maximum number of hits are applied to both and can be specified using the --cutoff and --number options.

  • By default nearest distances between peaks and features are calculated from the TSS of the feature to whichever of the peak edges are closer; alternatively distances can be calculated between the nearest pair of peak/feature edges by specifying the --edge=both option.

  • Any differential expression flags in the input features file are ignored unless the --only-DE option is specified, in which case only the differentially expressed features are considered in the analyses.

  • By default each peak/feature pair is reported on a separate line; the --compact option reports all nearest features/peaks on a single line of output.

  • Excel output is only produced if the --xls option is specified; summary output is only produced if --summary is specified.

  • The rearrange_columns.py utility has been dropped.

Version 0.4.4 (2015-06-10)

  • Use /usr/bin/env rather than /bin/env to invoke Python interpreter in RnaChipIntegrator.py (was broken for e.g. Ubuntu linux).

Version 0.4.3 (2014-05-08)

  • Update --pad output so that requested number of lines appears for peaks even when there are no hits, and “empty” lines contain the chromosome, start and end positions for the peak in question.

Version 0.4.2 (2014-05-02)

  • Truncate worksheet titles if they exceed maximum length as defined by the spreadsheet writing libraries.

Version 0.4.1 (2014-01-20)

  • Add --pad option: for ‘NearestTranscriptsToPeakEdge’ and ‘NearestTSSToPeakEdge’ analyses, where necessary adds blank lines to output files and spreadsheet so that each reported peak has the same number of lines associated regardless of the number of hits.

Version 0.4.0 (2014-01-20)

  • Fixed bug in overlap determination, which manifested when a gene was on the negative strand and was also wider than the peak. In those cases the start and end of the gene were being assigned incorrectly way around.

    (The bug didn’t affect results for other genes on the negative strand which were narrower than the peak.)

    Note that this bug would have a similar effect on determining whether a peak was within the promoter region of a gene on the negative strand. However the lists of nearest genes/peaks were not affected and the results should otherwise have been correct.

Version 0.3.3 (2012-02-16)

  • Added explanatory text to the “notes” page of the output XLS spreadsheet and standardised naming of output files to match XLS page titles.

  • Minor updates to READMEs/documentation.

Version 0.3.2 (2012-01-27)

  • Output files now use <Rna-Seq-file>_vs_<ChIP-Seq-file> as the default basename (unless overridden by the --project option).

  • Added example data files in new examples directory.

Version 0.3.1 (2012-01-20)

  • Added setup.py into an installable Python package.

  • Updated documentation.

Version 0.3.0 (2012-01-05)

  • Rename ID column to geneID (using ID has the potential to clash with other programs where this is a reserved word).

  • Various improvements to some of the column descriptions on the “notes” page of the output XLS file.

  • In all analyses, now only use those genes flagged as differentially expressed (use all if no flag was specified on the input gene data).

Version 0.2.0 (2011-12-19)

  • Only performs analyses which are appropriate for the supplied ChIP peak data i.e. ignore “region”-based analyses if ChIP data are summits, or summit-based analyses if data are regions.

Version 0.1.4 (2011-12-08)

  • Program will stop if it encounters any ‘bad’ lines in the RNA-seq/transcipt input data, with the exception of the first line (which is treated as a header and skipped if it contains bad data).

  • New option --no-xls: suppresses output of XLS spreadsheet.

Version 0.1.3 (2011-12-07)

  • Skip input transcripts where ‘start’ position is higher than ‘end’.

  • In output spreadsheet, splits the lists of transcripts inbetween across multiple columns in the TSSToSummits sheet if they exceed 250 characters, and creates multiple sheets for result sets that exceed 65536 rows.

Version 0.1.2 (2011-12-05)

  • Fixed failure when using with Python 2.4 (optparse.OptionParser “epilog” argument is unsupported)

Version 0.1.1 (2011-11-24)

  • Updated to use optparse library to process command line arguments, and substantially expanded help text (available using -h or --help option).

Version 0.1.0 (2011-11-21)

  • Baseline version of RnaChIPIntegrator.py.