Changelog¶
1.1.alpha19¶
- Closed GH-352: Showing percent identity in the CSV file.
1.1.alpha18¶
- Closed GH-346: Adding proper support for ambigious amino acid codes.
1.1.alpha17¶
- Closed GH-340: “malformed row in jplace” after pplacer warning “computed function value is infinite or NaN”.
- Closed GH-339: Better error message concerning strange mass.
1.1.alpha16¶
- Closed GH-334: multiclass_concat.py modifies placement database such that classif_table.py returns accurate tallies.
1.1.alpha15¶
- Closed GH-320: Now compiles fine with Batteries 2.
- Closed GH-327: Ignore sequences that aren’t in both jplace and sequence files.
- Closed GH-312: An improved script for managing classification results, called
classif_table.py
;classif_rect.py
is now deprecated.- Closed GH-315: support
rppr info
on reference packages lacking a taxonomy- Closed GH-316: pplacer warns rather than fails when an alignment looks like nucleotides
- Closed GH-317:
pplacer --write-masked-out
respects--out-dir
- Closed GH-318: Apply alignment mask on a per-placement basis
- Closed GH-319:
pplacer --write-pre-masked
no longer exits after writing mask.- Closed GH-322: Moved to Batteries version 2.1.0. Supports OCaml 4.01.0
- Closed GH-323:
pplacer
,guppy
, andrppr
support gzip-compressed alignment and.jplace
files.- Closed GH-324:
deduplicate_sequences.py
supports gzip-compressed FASTA files.
1.1.alpha14¶
- Closed GH-181: Added
guppy indep_c
; added--leaf-values
toguppy mft
.- Closed GH-215: Added
pca_for_qiime.py
andextract_taxonomy_from_biom.py
; changed guppy and rppr to allow BIOM files to be passed as arguments where placefiles are allowed.- Closed GH-241: On the NBC classifier of
guppy classify
: renamed--target-rank
to--nbc-rank
; added--nbc-rank auto
.- Closed GH-248: Added premasking by default to the NBC classifier of
guppy classify
; correspondingly added--no-pre-mask
.- Closed GH-250: Completely revamped classification.
- Closed GH-251: Added the hybrid5 classifier.
- Closed GH-256: Added
--mmap-file
to pplacer; changed--pretend
in pplacer to show the amount of memory which would be allocated.- Closed GH-259: Added
guppy mcl
and a--mcl
flag toguppy compress
.- Closed GH-260: Added
rooted_pd
toguppy fpd
; Added a--variance
flag toguppy rarefact
.- Closed GH-261: Added
rppr convex_taxids
.- Closed GH-262: Added
--as-mass
toguppy redup
; updatedsort_placefile.py
for the new placefile format; fixed pplacer to better deal with internal edges on a tree with a branch length of 0.- Closed GH-263: Fixed a bug that could sometimes cause failures in
rppr min_adcl
with the PAM algorithm.- Closed GH-265: Fixed a bug that could cometimes cause
rppr reroot
to return a suboptimal rooting.- Closed GH-266: Adding
map_ratio
andmap_overlap
columns toguppy to_csv
.- Closed GH-267: Added a
leaf_count
column torppr convex_taxids
.- Closed GH-268: Merged various minor fixes.
- Closed GH-273: Fix convexify for multifurcating trees
- Closed GH-274: Added
--weight-as-count
toguppy rarefact
.- Closed GH-276: Added
-k
toguppy rarefact
.- Closed GH-277: Added
--weight-as-count
toguppy rarefy
.- Closed GH-278: Changed
guppy rarefact
to allow multiple placefiles to be passed instead of just one.- Closed GH-282: Added a
--inflation
flag toguppy mcl
andguppy compress
.- Closed GH-286: Changed pplacer’s
--mmap-file
to accept a path to either a directory or a file.- Closed GH-287: Added a more informative error message for the case of an input alignment containing some, but not all reference sequence names.
- Closed GH-288: Added
guppy placemat
- Closed GH-290: Random tie breaking in NBC classifier
- Closed GH-291: Added qD(T) alpha diversity measure from Chao et. al., 2010 (doi:10.1098/rstb.2010.0272)
- Closed GH-293: Switched build system to use OPAM
- Closed GH-294: Added
--unitize
option toguppy squash
- Closed GH-297: Support multiprocessing during squash cluster bootstrapping
- Closed GH-298: Faster upper-limit finding during integration
- Closed GH-299: Fix NaN likelihoods for empirical frequencies + unseen state
- Closed GH-303: Updated Batteries dependency to version 2.0.0
- Closed GH-305: Eliminate compilation warnings from CDD
- Closed GH-306: Random tie breaking is default in NBC
- Closed GH-307: Renamed
--kappa
to--theta
,awpd
tobwpd
inguppy fpd
- Closed GH-309: Support overlap minimization (SOM) added to
guppy epca
(see also GH-221)
1.1.alpha13¶
- Fixed a bug where pplacer would sometimes fail abruptly with a Child_error of EBADF on close(2). [rc2]
- Added missing
-o
and related flags toguppy to_csv
. [rc3]- Fixed minor errors in the documentation [r2]
- Closed GH-216: Added
guppy trim
andguppy check
.- Closed GH-225: Added
rppr vorotree
.- Closed GH-235: Added
--rep-edges
flag for the splitify subcommands.- Closed GH-237: Added a multiplicity column to
guppy diplac
.- Closed GH-238: Added
--epsilon
for splitify commands to filter constant edges out of the resulting splitify matrices.- Closed GH-239: Added the
pam
algorithm to voronoi commands; cleaned up voronoi full algorithm and implementation.- Closed GH-240: Added a
-o
flag for pplacer.- Closed GH-242: Renamed ECLD to ADCL; added –max-adcl to voronoi commands.
- Closed GH-243: Updated
rppr reroot
so it can run on reference packages which have unannotated sequences.- Closed GH-244: Updated
rppr infer
to handle sequences which could not be reasonably placed anywhere on the tree.- Closed GH-245: Updated code to allow refpkgs to be passed as .zip files as well as directories.
- Closed GH-246: Added –always-include to voronoi commands.
- Closed GH-247: Added
guppy unifrac
.- Closed GH-249: Added
guppy rarefy
.- Closed GH-252: Added
--all-alternates
torppr convexify
.- Closed GH-253: Added
--no-collapse
toguppy diplac
.- Closed GH-255: Added
guppy to_csv
.- Closed GH-257: Renamed
rppr voronoi
torppr min_adcl
,rppr vorotree
torppr min_adcl_tree
, andguppy diplac
toguppy adcl
. Added--seed
torppr min_adcl
andrppr min_adcl_tree
.- Closed GH-280: Fixed a bug in which pplacer would fail if passed -t and -s flags without also passing a -c or -r flag.
1.1.alpha12¶
- Added
guppy to_rdp
andguppy classify_rdp
.- Closed GH-113: Updated the
best_classification
andmulticlass
SQL views; correspondingly changed the flags torppr prep_db
; added theplacement_evidence
table for bayes classification.- Closed GH-183: Added documentation for more functions.
- Closed GH-189: Added
guppy pentropy
.- Closed GH-191: Added -m to
guppy redup
; bumped the jplace format version to 3 with the ability to give each name for a pquery a different mass.- Closed GH-192: Added
rppr infer
.- Closed GH-193: Added
rppr reclass
.- Closed GH-194: Added a
mass
column toplacement_names
to parallel new features in the jplace format.- Closed GH-195: Added a –groups flag to pplacer for placing metagenomic sequences onto trees built from very wide alignments.
- Closed GH-196: Added code to pplacer to better handle errors raised when calling fork(2).
- Closed GH-198: Added progress reporting code to
guppy compress
.- Closed GH-199: Renamed
guppy pentropy
toguppy entropy
; added quadratic entropy calculation.- Closed GH-200: Added –discard-below to
guppy {islands,compress}
.- Closed GH-201: Added a setup.py file to the scripts directory.
- Closed GH-202: Added
rppr prepsim
; added –include-pendant toguppy diplac
.- Closed GH-204: Added more columns to
rppr reclass
.- Closed GH-205: Added
guppy error
.- Closed GH-206: Updated some pplacer documentation.
- Closed GH-207: Added CSV output to
guppy edpl
.- Closed GH-208: Fixed the -o flag to reflect the actual file written to for
guppy {sing,tog,edpl}
.- Closed GH-209: Fixed a bug preventing Gcat_model refinement if the supplied alignment had a different number of sites from the refpkg; added –always-refine to pplacer.
- Closed GH-210: Merged
guppy {pd,wpd,entropy}
intoguppy fpd
.- Closed GH-212: Changed parsing error messages to be more specific.
- Closed GH-213: Added PyNAST support to refpkg_align.py.
- Closed GH-214: Added
guppy ograph
.- Closed GH-218: Added –split-csv to
guppy merge
.- Closed GH-219: Fixed some guppy commands which needed a zero root branch length.
- Closed GH-220: Added error messages for some exceptions; fixed
guppy rarefact
.- Closed GH-222: Added a -c flag to
guppy bary
.- Closed GH-236: Fixed support for numeric leaf names when writing out XML.
1.1.alpha11¶
- Fixed a bug with parsing MAP identity from a jplace file.
- Fixed a bug that occurred sometimes when running
rppr convexify
on a tree where not every leaf had a corresponding tax_id at a particular rank.- Fixed a bug with fasttree placements which caused failure when the site categories had to be calculated (ie. when using a combined reference + query alignment)
- Changed versions to be parsed only out of git tags.
- Closed GH-42: Added –edpl flag to
guppy fat
for EDPL coloring in fat trees.- Closed GH-146: Added an –unweighted flag to
guppy pca
.- Closed GH-168: Changed guppy and rppr to list the subcommands in –help; reformatted the options flags to be more readable.
- Closed GH-169: Fixed all commands that work on reference packages to use the -c flag to specify the reference package.
- Closed GH-176: Fixed
rppr reroot
to handle cases where not all tax_ids are specified under the rank the rerooting is happening at.- Closed GH-177: Added –mass-gt and –mass-le flags to
guppy filter
.- Closed GH-178: Fixed
guppy compress
to add a zero root branch length.- Closed GH-179: Changed the JSON emitter to be able to represent a wider range of floats.
- Closed GH-182: Changed ‘weighted’ to ‘spread’ and ‘unweighted’ to ‘point’ across all the guppy and rppr commands.
- Closed GH-184: Added a placement_median_identites table for guppy classify.
- Closed GH-188: Added support for a reference package to be able to specify that some reference sequences are unclassified.
1.1.alpha10¶
- Closed GH-126: Split Glv/Model into Gmix_model and Gcat_model with the option of adding more models to pplacer later.
- Closed GH-154: Added
guppy islands
.- Closed GH-156: Added functionality for calculating multiple KR distances with only one tree traversal.
- Closed GH-157: Added
guppy compress
.- Closed GH-162: Added fig ranking to pplacer.
- Closed GH-163: Added a –node-numbers flag to every command that emits a phyloxml tree which adds the tree’s node numbers to the phyloxml output as bootstrap values.
- Closed GH-172: Switched from using xml-light to xmlm.
1.1.alpha09¶
- Fixed a bug that was making classifications appear too specific when the placement was on the edge just proximal to an MRCA.
- Fixed a bug wherein the Newick parser would add a ‘.’ to the end of leaf names if the name was an integer.
- In fixing a bug, made
guppy diplac
only emit the first name in a pquery in its results.- Fixed a bug that caused the trailing } in a JSON file to be omitted when the file was large enough.
- Added a
multiclass
view and associated parameters torppr prep_db
.- Fixed a bug where sometimes placements that fell too close to the root would vanish with the –map-identity flag on.
- Fixed identity to give 0% sequence identity in the case of no overlap between sequences.
- Fixed a bug by flushing all output buffers before forking, so that the same data isn’t written multiple times.
- Fixed a bug in pplacer in which it wouldn’t write the original reference tree when creating a placefile.
- Fixed some issues with phyloxml generation.
- Closed GH-27: Reorganized functions that operate on alignments.
- Closed GH-67: Added
guppy wpd
.- Closed GH-72: Added new features to
rppr convexify
and fixed the implementation of the convexify algorithm, as it cut too many leaves in some corner cases.- Closed GH-75: Changed mass maps to use records types instead of tuples.
- Closed GH-76: Added a check in
guppy classify
to ensure that the sqlite database has been properly initialized.- Closed GH-78: Added an –average flag to
guppy fat
.- Closed GH-81: Removed old code that was deprecated by batteries; changed most code to be using batteries.
- Closed GH-82: Merged the
pick
branch into dev.- Closed GH-84: Renamed .json to .jplace for new-format placefiles.
- Closed GH-85: Added better error messages for potential premasking failures.
- Closed GH-86: Dropped support for older versions of the reference package format.
- Closed GH-88: Improved handling very small alphas in pplacer, working around a problem with the GSL that wasn’t allowing us to invert the CDF for the gamma distribution.
- Closed GH-89: Fixed some bugs in the convexify algorithm.
- Closed GH-90: Added an error message for if pplacer is invoked with no arguments.
- Closed GH-91: Added more documentation to .mli files.
- Closed GH-92: Added searching and alignment scripts.
- Closed GH-94: Improved the leaf selection criteria in
rppr voronoi
.- Closed GH-96: Now using colors from colorbrewer2.org for heat.
- Closed GH-98: Added a –map-identity flag to pplacer.
- Closed GH-99: Added more examples for guppy batchfiles.
- Closed GH-101: Added virtual placefiles to guppy batchfiles.
- Closed GH-103: Added batteries as a dependency.
- Closed GH-104: Added a naive reference implementation of convexify, accessible with a –naive flag.
- Closed GH-105: Added parameter substitution to guppy batchfiles.
- Closed GH-108: Added more data from jplace files into the taxtable schema; added a way to change the cutoff for best_classifications.
- Closed GH-109: Added a
rppr info
subcommand.- Closed GH-110: Added a –no-early flag to
rppr convexify
.- Closed GH-111: Added a script to update reference packages to version 1.1.
- Closed GH-112: Improved some of pplacer’s error messages.
- Closed GH-114: Changed MAP identity in placefiles to be stored flat instead of nested.
- Closed GH-115: Updated the documentation to reflect changes to the SQL schema in
rppr prep_db
.- Closed GH-116: Added –keep-at-most and –keep-factor flags to pplacer.
- Closed GH-117: Added the output of
git describe
to –version output.- Closed Gh-118: Added a –quiet flag to guppy and rppr.
- Closed GH-119: Added a
rppr reroot
subcommand.- Closed GH-120: Added a –rank-limit flag to
rppr convexify
.- Closed GH-122: Renamed
rppr taxtable
torppr prep_db
.- Closed GH-124: Rewrote the Newick parser.
- Closed GH-125: Added a –rooted flag to
rppr convexify
.- Closed GH-128: Added informative priors to pplacer integration.
- Closed GH-129: Added the ability for
rppr convexify
to convexify a tree not in a reference package.- Closed GH-130: Added
guppy pd
.- Closed GH-131: Changed pplacer to set some defaults with the -p flag.
- Closed GH-133: Added edge painting classification by default to pplacer and a corresponding –painted flag to
rppr ref_tree
.- Re-closed GH-133: Added checks for the case when not all ranks are represented by some sequence in the reference package.
- Closed GH-135: Generally improved error messages in pplacer, guppy, and rppr.
- Closed GH-138: Removed the –transform flag from everything except
guppy mft
; removed the –unweighted flag from commands which don’t respect it.- Closed GH-139: Added a check to pplacer to ensure all query sequences have at least some overlap with some reference sequence.
- Closed GH-140: Allowed pplacer to be run with -t and without -r or -c.
- Closed GH-141: Removed
compare_placements.py
; addedcheck_placements.py
; documented the rest of the python scripts.- Closed GH-143: Changed the –leaves argument to
rppr voronoi
to specify the number of leaves to keep in the tree instead of the number of leaves to prune.- Closed GH-144: Changed pplacer to explicitly disallow unplaced sequences from being written out; changed
best_classifications
andmulticlass
views to yield NULL for rows where no placements match all the criteria.- Closed GH-149: Updated the jplace version to 2; changed the Newick parser and emitter to allow for the new format of trees with edge numbers specified in braces instead of brackets.
- Closed GH-153: Changed
guppy mft
to not squash name lists to mass by default.- Closed GH-155: Changed pplacer to always check for invalid bases when pre-masking sequences.
- Closed GH-159: Updated to use the v2 batteries API.
- Closed GH-164: Fixed some bugs related to various APIs not knowing how to deal with node labels on non-leaves.
- Closed GH-167: Fixed an issue where
rppr reroot
wasn’t updating the bark of trees correctly.
1.1.alpha08¶
- Closed GH-46: Added a –timing flag to pplacer to show where time was spent during placements.
- Closed GH-47: Added unit tests for gaussian kr distance.
- Closed GH-49: Added a more informative error message to pplacer if reference sequences occur multiple times in a query file.
- Closed GH-52: Fixed padding in
guppy squash
.- Closed GH-58: Improved navigation for the documentation on guppy commands.
- Closed GH-59: Improved documentation for guppy commands using sqlite.
- Closed GH-60: Improved documentation for
guppy classify
.- Closed GH-65: Released alpha08.
- Closed GH-66: Added a FAQ to the documentation.
- Closed GH-68: Changed
guppy info
to show multiplicity.- Closed GH-69: Changed
guppy tog
to use polytomy instead of a _ delimiter joining sequence names.- Closed GH-70: Added documentation for how to compile pplacer.
- Closed GH-73: Added a pre-masking feature to cut out irrelevant columns of the alignment.
- Closed GH-74: Improved how pplacer dedupes sequences before a placerun.
- Added a script to sort placefiles for easier visual diffs.
- Added more informative error messages when the length of the query alignment and reference alignment don’t match.
guppy edpl
now calculates the EDPL (expected distance between placement locations) for placements
1.1.alpha07¶
- Fixed a serious issue with any command that used a
--prefix
flag.
1.1.alpha06¶
- Closed GH-20: efficiency of kr_distance evaluated and approved.
- Closed GH-44: improved sqlite3 support in guppy.
- Closed GH-45: better consistency of output flags across all guppy commands.
- Closed GH-48: better error reporting when loading json placefiles.
- Closed GH-50: fixed the output of
guppy classify
.- Closed GH-51: only parsing the first word as a sequence name in a fasta file.
- Renamed the
--normal
flag forguppy kr
to--gaussian
to avoid confusion with normalization.- Only one shuffle at a time is now stored in memory (big savings, obviously).
- Fixed bug that was throwing off
guppy kr
shuffling significance estimation.guppy pca
now defaults to scaling eigenvalues to percent variance; now has a –raw-eval flag to specify otherwise.- Fixed all of the sequence parsers to be tail-recursive, so parsing large files no longer causes segfaults.
- Added a
guppy redup
command for re-adding duplicate sequences to placefiles generated from deduplicated sequence files.
1.1.alpha05¶
- Closed GH-11: options for the tree-generating subcommands are more uniform.
- Closed GH-22: added more unit tests for
guppy kr
.- Closed GH-32: using power iteration rather than full eigendecomposition. Leads to 60x speedup for PCA on demo data.
- Closed GH-35: added a remark in the documentation about multiple comparison.
- Closed GH-41: added docs for the json placefile format.
- Added
guppy splitify
. Spits out differences of mass across splits.- Changed default behavior of
guppy kr
to not normalize, and correspondingly added in a--normalize
command line flag.- Improved documentation.
- Moved
guppy heat
toguppy kr_heat
.- The
guppy heat
subcommand now maps an arbitrary vector to a phylogenetic tree contained in a reference package.- Removed redundant
classic
subcommand from guppy.- Changed
guppy round
to use the new placefile format.- Added support for posterior probabilities in json placefiles.
- Removed csv and old-placefile-format generation from pplacer.
- Added the ability to run pplacer in multiple processes in parallel with the -j flag.
- Removed friend-finding from pplacer, as it was superseded by some of the multiprocessing code.
1.1.alpha03 to 1.1.alpha04¶
Closed GH-12: removed Placement.classif, and renamed Placement.contain_classif to Placement.classif.
Closed GH-29: added
guppy merge
to merge multiple placefiles.Closed GH-30: accepting r, n, and rn as delimiters everywhere in pplacer and guppy.
Closed GH-36: added
guppy {classic,tog,sing,filter}
. The former three were originally a part of placeviz, and the lattermost filters placefiles to only a specific subset of their placements.Closed GH-37: added a trailing newline to the end of json files.
Closed GH-38: added this changelog.
- Bugfix in
guppy classify
. From the commit:Previously, a file was being opened and closed for every pquery in every placerun. This resulted in only the last pquery being classified and written out. Now only one file is being opened for each placerun.