Skip to main content
https://github.com/svohr/mixemt
20 October 2023, 16:20:37 UTC
sort by:
RevisionAuthorDateMessageCommit Date
be33e2d Sam Vohr06 October 2023, 00:46:11 UTCFix index error for report top proportions (#24)06 October 2023, 00:46:11 UTC
f854cf2 Sam Vohr30 October 2020, 22:18:29 UTCRemove an xrange left over from python 2.7 (#23)30 October 2020, 22:18:29 UTC
954fcf4 Alex Hübner30 May 2020, 00:49:56 UTCPython3 (#20) * Fixed import of SeqRecord and Seq from biopython * Lift to Python3 using 2to3 * Update reading of binary data and module structure of scipy - Decode binary to UTF-8 string of CSV files because pkg_resources.resource_stream reads data in binary mode - Import scipy.special instead of scipy.misc to get access to logsumexp in Scipy >= v1.1 * Remove refs to Python 2.7, change pkg_resources use Remove references to Python 2.7 in mixemt executable and .travis.yml. Change pkg_resources use to get Phylotree as a string to avoid conversion from binary stream and preserve existing tests. Update tests to avoid float comparison. * Change pkg_resource call to get phylotree filename Co-authored-by: svohr <shvohr@gmail.com>30 May 2020, 00:49:56 UTC
397cceb Sam Vohr03 May 2019, 01:55:08 UTCAdd option to set seed for random number generation (#19) * Add option to set seed for random number generation * Add README description of --seed option03 May 2019, 01:55:08 UTC
05746fb Jerrythafast03 May 2019, 01:19:37 UTCAdd option for percentage-of-coverage in addition to -R (#17) * added -p option for percentage next to minimum * PEP8 * Fix assemble_test * Refactor to frac_var_reads and add to README.md * Add README.md changes03 May 2019, 01:19:37 UTC
436ca02 Jerrythafast03 May 2019, 01:17:54 UTCAllow setting -i/--init to infinity for equal priors (#18) * Allow setting -i/--init to infinity for equal priors * Add -i/--init change to README.md03 May 2019, 01:17:54 UTC
e5198aa Sam Vohr20 February 2018, 00:33:02 UTCFixed biopython imports for consensus calling to work (#14)20 February 2018, 00:33:02 UTC
8ff7409 Sam Vohr13 November 2017, 01:57:43 UTCAdded variants to plot_hap_coverage plots. (#13) Using new invocation of plot_hap_coverage, phylotree and novel variants will be added to the plot that is produced.13 November 2017, 01:57:43 UTC
cb14285 Sam Vohr13 November 2017, 00:55:19 UTCCitation (#12) * Added citation information to README.md * Added complete citation including volume and page numbers.13 November 2017, 00:55:19 UTC
fde2fa7 Sam Vohr05 June 2017, 17:35:33 UTCAdded citation information to README.md (#10)05 June 2017, 17:35:33 UTC
51c8ced Sam Vohr08 May 2017, 23:28:42 UTCMerge pull request #8 from svohr/ref-fais Added fasta indexes for reference sequences08 May 2017, 23:28:42 UTC
44d493c svohr08 May 2017, 23:25:49 UTCAdded fasta indexes to package_data in setup.py08 May 2017, 23:25:49 UTC
c451c8f svohr08 May 2017, 23:18:56 UTCChanged ref/README.txt to include more builds of Phylotree.08 May 2017, 23:18:56 UTC
6814283 svohr08 May 2017, 23:06:22 UTCAdded fasta indexes for mtDNA references. User may not always have permission to build fasta indexes (*.fai files) if the package file is installed into the system python package directory. We'll keep the index files here since they're small and they shouldn't change from system to system.08 May 2017, 23:06:22 UTC
e42b503 Sam Vohr05 April 2017, 23:19:34 UTCMerge pull request #6 from svohr/ref-phy-pack-defaults Use Package Ref. Sequence and Phylotree files by default05 April 2017, 23:19:34 UTC
5bee254 svohr05 April 2017, 23:10:27 UTCAdded verbose mesg for reading Phylotree input. Changed order of initial data input so that alignments are read last. This streamlines the verbose output and lets us test the defaults for reference sequence and Phylotree more easily.05 April 2017, 23:10:27 UTC
e202704 svohr05 April 2017, 21:28:02 UTCminor spelling fixes in README.md05 April 2017, 21:28:02 UTC
a00a892 svohr05 April 2017, 21:25:47 UTCMinor spelling fixes in help output.05 April 2017, 21:25:47 UTC
187fc9c svohr05 April 2017, 18:43:16 UTCMinor re-word in README.md05 April 2017, 18:43:16 UTC
2885078 svohr05 April 2017, 18:24:53 UTCAdded output option descriptions05 April 2017, 18:24:53 UTC
0d6ce99 svohr04 April 2017, 23:28:05 UTCAdded descriptions of contributor and assembly options.04 April 2017, 23:28:05 UTC
3a33904 svohr04 April 2017, 22:18:14 UTCFixed incorrectly formatted verbatim/code block04 April 2017, 22:18:14 UTC
af7cf66 svohr04 April 2017, 22:11:31 UTCAdded description of EM options to README.md04 April 2017, 22:11:31 UTC
446d9b5 svohr04 April 2017, 21:49:57 UTCAdded descriptions of customization and quality filtering options04 April 2017, 21:49:57 UTC
06be425 svohr04 April 2017, 18:46:17 UTCAdded descriptions of basic options to README.md04 April 2017, 18:46:17 UTC
bf45e00 svohr03 April 2017, 23:14:26 UTCREADME.md updated for installation and new usage. mixemt now uses the reference sequence and Phylotree representation included in the repository by default and the README has been updated to reflect that.03 April 2017, 23:14:26 UTC
ed30a70 Sam Vohr14 March 2017, 18:01:13 UTCUpdated .gitignore with new path to ref/14 March 2017, 18:01:13 UTC
e7a39c0 Sam Vohr14 March 2017, 17:59:46 UTCPhylotree input now read from package data by default.14 March 2017, 17:59:46 UTC
bc12c11 Sam Vohr13 March 2017, 21:03:33 UTCcmdline args Ref and Phylotree now options. Reference sequence now read from package data by default.13 March 2017, 21:03:33 UTC
4c4d92b Sam Vohr10 March 2017, 21:56:36 UTCTurn off Travis CI email notifications.10 March 2017, 21:56:36 UTC
c222910 Sam Vohr10 March 2017, 19:51:21 UTCChanged shebang line to use env for portability.10 March 2017, 19:51:21 UTC
d745cba svohr08 March 2017, 01:59:00 UTCRemoved osx from Travis config.08 March 2017, 01:59:00 UTC
98900dd svohr07 March 2017, 23:14:07 UTCAdded Travis CI badge to README.md07 March 2017, 23:14:07 UTC
d8644bc svohr07 March 2017, 22:41:42 UTCChanged testing call from pytest to py.test07 March 2017, 22:41:42 UTC
1ae25ba svohr07 March 2017, 22:34:11 UTCUpgrade pip to use --only-binary.07 March 2017, 22:34:11 UTC
3e726c6 svohr07 March 2017, 21:30:23 UTCUsing pre-compiled numpy/scipy with Travis.07 March 2017, 21:30:23 UTC
52ce279 svohr07 March 2017, 21:22:22 UTCOnly test with Python 2.707 March 2017, 21:22:22 UTC
75d9ff6 svohr07 March 2017, 19:46:45 UTCAdded config file for Travis CI.07 March 2017, 19:46:45 UTC
99cdd9c Sam Vohr07 March 2017, 00:00:34 UTCMerge pull request #4 from svohr/re-org-dirs Reorganized Directories, added mixemt package, setup.py07 March 2017, 00:00:34 UTC
46941ca svohr06 March 2017, 23:54:53 UTCAdded description to setup.py06 March 2017, 23:54:53 UTC
8d130e5 svohr06 March 2017, 23:41:39 UTCUpdated test script to use new paths and pytest.06 March 2017, 23:41:39 UTC
54a86c7 svohr06 March 2017, 23:22:12 UTCAdded docstring for mixemt/__init__.py06 March 2017, 23:22:12 UTC
45f4e41 svohr03 March 2017, 19:47:22 UTCorder of imports changed to fit convention03 March 2017, 19:47:22 UTC
0489c63 svohr03 March 2017, 19:24:00 UTCRemoved R scripts (not used). Added requirements.03 March 2017, 19:24:00 UTC
1bc3fac svohr03 March 2017, 19:23:33 UTCChanged mixemt imports to use full path.03 March 2017, 19:23:33 UTC
3722941 svohr03 March 2017, 17:58:40 UTCSetuptools works in setup.py now.03 March 2017, 17:58:40 UTC
bbb22fc svohr03 March 2017, 17:57:49 UTCFixed imports for new mixemt package.03 March 2017, 17:57:49 UTC
46c5cfc svohr03 March 2017, 17:47:10 UTCAdded entries for additional files to setup.py03 March 2017, 17:47:10 UTC
9e240a8 svohr03 March 2017, 17:46:19 UTCRenamed ref/README as it does not use markdown.03 March 2017, 17:46:19 UTC
0cedff9 svohr01 March 2017, 23:54:00 UTCAdded basic info to setup.py Still untested.01 March 2017, 23:54:00 UTC
9a1b650 svohr01 March 2017, 23:37:40 UTCAdded empty setup.py file01 March 2017, 23:37:40 UTC
8aa50b0 svohr01 March 2017, 23:35:49 UTCAdded __init__.py Hope this works!01 March 2017, 23:35:49 UTC
57600c4 svohr01 March 2017, 23:14:57 UTCRe-organized the directory structure This will make it easier to write the setup.py01 March 2017, 23:14:57 UTC
7c20b04 svohr01 March 2017, 22:46:56 UTCstyle: removed escaped \n01 March 2017, 22:46:56 UTC
11fd1f0 svohr28 February 2017, 23:19:33 UTCStyle-fixes after linting. Mostly fixing indentation for continued lines.28 February 2017, 23:19:33 UTC
d1dbfad svohr09 February 2017, 18:44:44 UTCchanged multi-em logaddexp to in-place operation09 February 2017, 18:44:44 UTC
e2686d4 svohr08 February 2017, 22:54:47 UTCRefactored em_step() for speed. em_step() now uses in place operations when possible and no longer uses for loops.08 February 2017, 22:54:47 UTC
87aa436 svohr08 February 2017, 00:38:21 UTCEM multi run now works the same as before. Multi run could probably be refactored to be more memory efficient and it would be better if it kept track of the variance in mixture proportions as well as the average.08 February 2017, 00:38:21 UTC
9319479 svohr07 February 2017, 21:41:11 UTCUpdated README requirements and links07 February 2017, 21:41:11 UTC
551d42b svohr07 February 2017, 21:27:08 UTCUpdated read assignment to use log-probs, and tests.07 February 2017, 21:27:08 UTC
ada5da7 svohr07 February 2017, 20:59:34 UTCUpdated docstring for em functions.07 February 2017, 20:59:34 UTC
6fdbb28 svohr07 February 2017, 19:19:12 UTCTests for em.py updated to work with log-probs. Multi EM run is still not fixed.07 February 2017, 19:19:12 UTC
2d83fd6 svohr07 February 2017, 18:24:07 UTCrun_em() now returns mixture props (linear) For handing around the results of em, mixture proportions are stored as linear while the read probabilities remain in log form. We only need to do math with the proportions and read probablity matrix one more time so this will avoid lots of exp(props) in the post-em functions.07 February 2017, 18:24:07 UTC
d23e0e4 svohr04 February 2017, 02:36:31 UTCEM now performed with log-probs. Need to fix mulit-run EM and could reduce redundant exp calls.04 February 2017, 02:36:31 UTC
af544e7 svohr04 February 2017, 01:35:20 UTCRefactored EM single step to log-probs. This change introduces a dependency for scipy in order to the the log(sum(exp())) operation.04 February 2017, 01:35:20 UTC
01ed649 svohr03 February 2017, 18:41:13 UTCpreprocess now produces log-prob input matrix Updated preprocess tests to match new ownput03 February 2017, 18:41:13 UTC
5834464 svohr01 February 2017, 18:09:54 UTCcorrected README headings01 February 2017, 18:09:54 UTC
93ccd5f svohr31 January 2017, 22:58:27 UTCREADME edits31 January 2017, 22:58:27 UTC
00446a6 svohr30 January 2017, 23:48:13 UTCMerge branch 'master' of https://github.com/svohr/mixemt Fixed conflict in title.30 January 2017, 23:48:13 UTC
41971dd svohr30 January 2017, 23:45:45 UTCAdded usage and preparing input to README.md30 January 2017, 23:45:45 UTC
0c5344f Sam Vohr27 January 2017, 22:12:58 UTCAdded check and error message for 0 contributors detected.27 January 2017, 22:12:58 UTC
be889c2 Sam Vohr24 January 2017, 17:18:15 UTCUpdate README.md spelling: deconvolving rather than deconvoluting24 January 2017, 17:18:15 UTC
a05cacb svohr13 January 2017, 22:04:31 UTCAdded overview of program13 January 2017, 22:04:31 UTC
8acb375 Sam Vohr31 December 2016, 02:11:30 UTCCreate LICENSE31 December 2016, 02:11:30 UTC
3ede038 Sam Vohr05 October 2016, 00:16:14 UTCMerge branch 'em-refine'05 October 2016, 00:16:14 UTC
69bbf78 Sam Vohr05 October 2016, 00:07:22 UTCAdded option to skip contribution estimate refinement Also added backwards compatibility for old results where the initial EM input matrix was not saved.05 October 2016, 00:07:22 UTC
d413dbe Sam Vohr22 September 2016, 20:32:55 UTCFixed issue with diagnostic variant check and custom haplogroups Ran into a problem with the steps that fill in ancestral bases after a haplogroup has been detected and the variant bases it carries are removed from consideration as evidence for another haplogroup. In the case that a variant that defines a custom haplogroup that is not at a known variant position, we previously tried to delete that position from the list of ancestral pos/bases. We now check to see if this position is included in the list before removing it now. We may need to revisit this later.22 September 2016, 20:32:55 UTC
8041df7 Sam Vohr20 September 2016, 00:27:17 UTCChanged save/load to also include the input matrix for EM. In order to implement the second EM run to refine the contribution estimates, we need to know the original input matrix for EM. We could rebuild it but it would take a long time and not necessarily match. Instead, the input matrix is now output with the -s flag, and read in using the -l flag. This is a little annoying since it means that any previous results will not be usable, unless I add in some backwards compatibility checks.20 September 2016, 00:27:17 UTC
8acf899 Sam Vohr19 September 2016, 23:33:43 UTCChanged contribution estimate refinement to replace intial values.19 September 2016, 23:33:43 UTC
e6bc240 Sam Vohr16 September 2016, 04:19:16 UTCOutput table now reports only final contribution estimate.16 September 2016, 04:19:16 UTC
307d35d Sam Vohr15 September 2016, 18:57:22 UTCTweaks to get estimate refinement working. Changed when verbose mode initial results are reported. Changed main output to include both initial and refined estimates.15 September 2016, 18:57:22 UTC
e216722 Sam Vohr15 September 2016, 04:59:43 UTCAdded parts for refined contribution estimates Added function to update contributor table and updated main workflow to include second EM run to refine contribution estimates. Output updated to include both contribution estimates. Not running just yet.15 September 2016, 04:59:43 UTC
7570552 Sam Vohr15 September 2016, 03:51:38 UTCmoved reduce_em_matrix to preprocess.py15 September 2016, 03:51:38 UTC
d9f795c Sam Vohr15 September 2016, 03:38:05 UTCAdded function to reduce EM input matrix to only identified contributors15 September 2016, 03:38:05 UTC
d0dd278 Sam Vohr07 September 2016, 22:46:22 UTCwrite_variants() output overhauled to be more useful. write_variants used to report a list of polymorphic positions from phylotree and whether they were expected to be polymorphic or fixed in the sample, given the haplogroups that were detected. This has been changed to be more useful in interpretting the results of mixemt. write_variants now reports for each position in the reference, the number of A,C,G,Ts, whether this position is expected to be polymorphic, whether this position would be called a variant position under our scheme (i.e. whether there exist more than 1 base that pass the minimum variant count cutoff) and, finally, the variants that are known for this position from our detected haplogroups. This should make it much easier to see how the results are affected by what bases are found in the sample.07 September 2016, 22:46:22 UTC
42ff20e Sam Vohr07 September 2016, 18:47:57 UTCFormatting of the verbose output for _check_contrib_phy_vars() now cleaner Verbose output for _check_contrib_phy_vars() is now sorted on reference position and is justified to line up a little nice now.07 September 2016, 18:47:57 UTC
48e40bb Sam Vohr07 September 2016, 18:28:28 UTCAdded much more verbose output to haplogroup diagnostic checks. The verbose output for the haplogroup diagnostic position checks now includes a report for every position considered so that weird things can be picked out more easily. Added a method to ObservedBases to get the total number of observed bases at a reference position more easily.07 September 2016, 18:28:28 UTC
a83ca2e Sam Vohr08 August 2016, 22:54:09 UTCMinor spelling fix.08 August 2016, 22:54:09 UTC
abfaa5f Sam Vohr06 August 2016, 23:17:31 UTCFor coverage plots, Y axis always starts at 0 now.06 August 2016, 23:17:31 UTC
dbbfa35 Sam Vohr03 August 2016, 21:39:45 UTCFixed missing empty-line for consistent formatting.03 August 2016, 21:39:45 UTC
2d4b926 Sam Vohr03 August 2016, 16:42:55 UTCMerge branch 'master' of https://github.com/svohr/mixemt Conflicts: preprocess.py Removed TODO note for precomputing mutation weights because it is now done.03 August 2016, 16:42:55 UTC
223377a svohr03 August 2016, 04:24:31 UTCHapVarBaseMatrix now pre-computes site instability score. Big win. We now compute the site-specific instability frequency score for every variant position and store it a dictionary at initialization. The values are used later to find the probability of observing a read from a haplogroup. This change cuts the time needed to build the initial EM input matrix in half.03 August 2016, 04:24:31 UTC
1e8a09d Sam Vohr02 August 2016, 22:36:12 UTCAdded TODO to speed up building initial matrix.02 August 2016, 22:36:12 UTC
49ad26c Sam Vohr02 August 2016, 22:34:27 UTCUpdated docstring for _check_contrib_phy_vars02 August 2016, 22:34:27 UTC
768c446 Sam Vohr28 July 2016, 21:33:03 UTCFix for problem in using ancestral bases as evidence for haplogroup. Previously, we only checked positions with defining mutations to see if a haplogroup was present in the sample. This led to problems where the defining mutations on a branch we actually back mutations to the ancestral base. We did not account for the fact that these ancestral bases were likely introduced by haplogroups at higher proportions and that they should only be used as evidence if the previous haplogroups did not carry the ancestral base. To fix this, we now keep track of ancestral bases (positions where no mutation is inferred to have occurred) so that they can be ignore when checking for the defining mutations for a haplogroup/contributor. Added, modified 2 tests to match new behavior and added 2 new ones.28 July 2016, 21:33:03 UTC
ee0d877 Sam Vohr28 July 2016, 20:30:54 UTCAdded reference sequence to phylotree object at init. stats.write_statistics() now uses the reference sequence stored in phylotree rather than passing it separately. PhyloTree.polymorphic_sites() now uses the internal reference sequence by default. New unit tests for PhyloTree.get_ancestral()28 July 2016, 20:30:54 UTC
a479494 Sam Vohr28 July 2016, 18:27:13 UTCAdded new method get_ancestral() Phylotree now stores a reference to the reference sequence that the tree is based on. This is used by get_ancestral() to return the ancestral bases for all sites not affected by a mutation in a lineage. We can refactor some of the code now so we do not have to pass a phylotree object and a reference sequence string around all of the time.28 July 2016, 18:27:13 UTC
f02efd0 Sam Vohr28 July 2016, 18:09:33 UTCUpped default max number of iterations in EM to 10,00028 July 2016, 18:09:33 UTC
33d6eb2 Sam Vohr15 July 2016, 21:56:37 UTCAdjusted coverage plot so lines stop at 0 when coverage reaches 0 Lines in coverage plot now drop to 0 when coverage reaches 0 but lines do not extend across the entirety of 0 coverage stretch. Plot size also adjusted to not look so stretched out.15 July 2016, 21:56:37 UTC
1c29a82 Sam Vohr09 July 2016, 23:41:19 UTCAdded correction for 0 to 1 based coords to unassigned coverage too.09 July 2016, 23:41:19 UTC
back to top