Skip to content

Latest commit

 

History

History
225 lines (203 loc) · 9.99 KB

NEWS.rst

File metadata and controls

225 lines (203 loc) · 9.99 KB

PyPop Release History

Notes towards next release

(unreleased)

New features

  • Updated to Python 3
  • Implement new assymetric LD (ALD) measure
  • New wrapper module Haplostats. This wraps a portion of the haplo.stats R package haplo-stats for haplotype estimation. [Implementation in alpha-phase].
  • popmeta: now accepts the -o/--outputdir option for saving generated files.
  • pypop: renamed --generate-tsv to --enable-tsv

Release Notes for PyPop 0.7.0

(2008-09-09)

New features

  • makeNewPopFile option has been changed. This option allows user to generate intermediate output of filtered files. Now option should be of the format: type:order where type is one of separate-loci or all-loci so that the user can specify whether a separate file should be generated for each locus (separate-loci) or a single file with all loci (all-loci). order should be the order in the filtering chain where the matrix is generated, there is no default, for example, for generating files after the first filter operation use 1.
  • New command-line option --generate-tsv, will generate the .dat tab-separated values (TSV) files on the the generated -out.xml files (aka "popmeta") directly from pypop without needing to run additional script. Now output from pypop can be directly read into spreadsheet.
  • New feature: add individual genotype tests to Hardy-Weinberg module (gthwe), now computes statistics based on individual genotypes in the HWP table. The [HardyWeinbergGuoThompson] or [HardyWeinbergGuoThompsonMonteCarlo] options must be enabled in the configuration ".ini" file in order for these tests to be carried out.
  • Major improvements to custom and random binning filters (Owen Solberg).
  • New feature: generate homozygosity values using the Ewens-Watterson test for all pairwise loci, or all sites within a gene for sequence data ([homozygosityEWSlatkinExactPairwise] in .ini file). Note: this really only works for sequence data where the phase for sites within an allele are known.
  • Haplotype and LD estimation module emhaplofreq improvements
    • improved memory usage and speed for emhaplofreq module.
    • maximum sample size for emhaplofreq module increased from 1023 to 5000 individuals.
    • maximum length of allele names increased to 20

Bug fixes

  • Support Python 2.4 on GCC 4.0 platforms.
  • Add missing initialisation for non-sequence data when processing haplotypes. Thanks to Jill Hollenbach for the report.
  • Fix memory leak in xslt translation.
  • Various fixes relating to parsing XML output.
  • Fixed an incorrect parameter name.
  • Handle some missing sections in .ini better. Thanks to Owen Solberg for report.
  • Various build and installation fixes (SWIG, compilation flags)
  • Make name of source package be lowercase "pypop".
  • Change data directory: /usr/share/pypop/ to /usr/share/PyPop/
  • Print out warning when maximum length of allele exceeded, rather than crashing. Thanks to Steve Mack for report.

Other issues

  • Sequence filter
    • In the Sequence filter, add special case for Anthony Nolan HLA data: mark null alleles ending in "N" (e.g. HLA-B*5127N) as "missing data" (****).
    • Also in Sequence, keep track of unsequenced sites separately (via unsequencedSites variable) from "untyped" (aka "missing data"). Treat unsequencedSite as a unique allele to make sure that those sites don't get treated as having a consensus sequence if only one of the sequences in the the set of matches is typed.
    • If no matching sequence is found in the MSF files, then return a sequence of * symbols (ie, will be treated as truly missing data, not untyped alleles.
    • Add another special case for HLA data: test for 7 digits in allele names (e.g. if 2402101 is not found insert a zero after the first 4 digits to form 24020101, and check for that). This is to cope with yet-another HLA nomenclature change.
  • Change semantics of batchsize, make "0" (default) process files separately if only R dat files is enabled. If batchsize not set explicitly (and therefore 0) set batchsize to 1 is PHYLIP mode is enabled.

Release Notes for PyPop 0.6.0

(2005-04-13)

New features

  • Allow for odd allele counts when processing an allele count data (i.e "semi"-typing). When PyPop is dealing with data that is originally genotyped, the current default is preserved i.e. we dis-allow individuals that are typed at only allele, and set allowSemiTyped to false.
  • New command-line option -f (long version --filelist) which accepts a file containing a list of files (one per line) to process (note that this is mutually exclusive with supplying INPUTFILEs, and will abort with an error message if you supply both simultaneously).
  • In batch version, handle multiple INPUTFILEs supplied as command-line arguments and support Unix shell-globbing syntax (e.g. pypop.py -c config.ini *.pop). (NOTE: This is supported only in batch version, not in the interactive version, which expects one and only one file supplied by user.
  • Allele count files can now be filtered through the filter apparatus (particularly the Sequence and AnthonyNolan) in the same was as genotype files transparently. [This has been enabled via a code refactor that treats allele count files as pseudo-genotype files for the purpose of filtering]. This change also resulted in the removal of the obsolete lookup-table-based homozygosity test.
  • Add --disable-ihwg option to popmeta script to disable hardcoded generation of the IHWG header output, and use the output as defined in the header in the original .pop input text file. This is disabled by default to preserve backwards compatibility.
  • Add --batchsize (-b short version) option for popmeta. Does the processing in "batches". If set and greater than one, list of XML files is split into batchsize group. For example, if there are 20 XML files and option is via using ("-b 2" or "--batchsize=2") then the files will be processed in two batches, each consisting of 10 files. If the number does not divide evenly, the last list will contain all the "left-over" files. This option is particularly useful with large XML files that may not fit in memory all at once. Note this option is mutually exclusive with the --enable-PHYLIP option because the PHYLIP output needs to calculate allele frequencies across all populations before generating files.
  • New .ini file option: [HardyWeinbergGuoThompsonMonteCarlo]: add a plain Monte-Carlo (randomization, without the Markov chain test) test for the HardyWeinberg "exact test". Add code for Guo & Thompson test to distribution (now under GNU GPL).

Bug fixes

  • HardyWeinbergGuoThompson overall p-value test was numerically unstable because it attempted to check for equality in greater than or equal to constructs ("<=") which is not reliable in C. Replaced this with a GNU Scientific Library (GSL) function gsl_fcmp() which compares floats to within an EPSILON (defaults to 1e-6).
  • Allow HardyWeinbergGuoThompson` test to be run if at least two alleles present (test was originally failing with a ``too-few-alleles message if there were not at least 3 alleles). Thanks to Kristie Mather for the report.
  • Checks to see if a locus is monomorphic, if it is, it generates an allele summary report, but skips the rest of the single locus analyses which do not make sense for monomorphic locus. Thanks to Steve Mack and Owen Solberg for the bug report(s).
  • Now builds against recent versions of SWIG (no longer stuck at version 1.3.9), should be compatible with versions of SWIG > 1.3.10. (Tested against SWIG 1.3.21).
  • Homozygosity module: Prevent math errors by in Slatkin's exact test by forcing the homozygosity to be positive (only a problem for rare cases, when the result is so close to zero that the floating point algorithms cause a negative result.)

Release Notes for PyPop 0.5.2 (public beta)

(2004-03-09)

Bug fixes

  • Add missing RandomBinning.py file to source distribution Thanks to Hazael Maldonado Torres for the bug report.
  • Fixed line endings for .bat scripts for Win32 so they work under Windows 98 thanks to Wendy Hartogensis for the bug report.

Release Notes for PyPop 0.5.1 (public beta)

(2004-02-26)

Changes

  • New parameter numInitCond, number of initial conditions by the haplotype estimation and LD algorithm used before performing permutations. Defaults to 50.
  • Remove some LOG messages/diagnostics that were erroneously implying an error to the user (if nothing is wrong, don't say anything). Add some more useful messages for what is being done in haplo/LD estimation step.
  • Add popmeta.py to the distribution: this is undocumented and unsupported as yet, it is at alpha stage only, use at your own risk!

Bug fixes

  • Remember to output plaintext version of LD for specified loci.

Release Notes for PyPop 0.5 (public beta)

(2003-12-31)

Changes

  • All Linux wrapper scripts no longer have .sh file suffixes for consistency with DOS (all DOS bat files can be executed without specifying the .bat extension).

Bug fixes

  • Add wrapper scripts for interactive and batch mode for both DOS and Linux so that correct shared libraries are called.
  • Pause and wait for user to press a key at end of DOS .bat file so that output can be viewed before window close.
  • Set PYTHONHOME in wrapper scripts to prevent messages about missing <prefix> being displayed.

Release Notes for PyPop 0.4.3beta

Bug fixes

  • Fixed bug in processing of popname field. Thanks to Richard Single for the report.