This is the v1.4 release of khmer featuring the results of our March and April (PyCon) coding sprints and the 16 new contributors; the use of the new v0.8 release of screed (the library we use for pure Python reading of nucleotide sequence files); and the addition of @luizirber’s HyperLogLog counter for quick cardinality estimation.
Documentation is at https://khmer.readthedocs.org/en/v1.4/
Casava 1.8 read naming is now fully supported and in general the scripts
no longer mangle read names. Side benefits: split-paired-reads.py
will no longer drop reads with ‘bad’ names; count-median.py can
generate output in CSV format. #759 #818 @ctb #873 @ahaerpfer
Most scripts now support a “broken” interleaved paired-read format for
FASTA/ FASTQ nucleotide sequence files.
`trim-low-abund.py <http://khmer.readthedocs.org/en/v1.4/user/scripts.html#trim-low-abund-py>`__
has been promoted from the sandbox as well (with streaming support).
#759 @ctb #963 @sguermond #933 @standage
The script to transform an interleaved paired-read nucleotide sequence file into two files now allows one to name the output files which can be useful in combination with named pipes for streaming processing #762 @ctb
Streaming everywhere: thanks to screed v0.8 we now support streaming of almost all inputs and outputs. #830 @aditi9783 #812 @mr-c #917 @bocajnotnef #882 @standage
Need a quick way to count total number of unique k-mers in very low
memory? the unique-kmers.py script in the sandbox uses a HyperLogLog
counter to quickly (and with little memory) provide an estimate with a
controllable error rate. #257 #738 #895 #902 @luizirber
normalize-by-median.py can now process both a paired interleaved
sequence file and a file of unpaired reads in the same invocation thus
removing the need to write the counting table to disk as required in the
workaround. #957 @susinmotion
Paired-end reads from Casava 1.8 no longer require renaming for use in
normalize-by-median.py and abund-filter.py when used in paired
mode #818 @ctb
Python version support clarified. We do not (yet) support Python 3.x #741 @mr-c
If a single output file mode is chosen for normalize-by-median.py we now default to overwriting the output. Appending the output is available by using the append redirection operator from the shell. #843 @drtamermansour
Scripts that consume sequence data using C++ will now properly throw an error on truncated files. #897 @kdmurray91 And while writing to disk we properly check for errors #856 #962 @mr-c
abundance-dist-single.py no longer fails with small files and many
threads. #900 @mr-c
Many documentation updates #753 @PamelaM, #782 @bocajnotnef, #845 @alameldin, #804 @ctb, #870 @SchwarzEM, #953 #942 @safay, #929,@davelin1, #687 #912 #926 @mr-c
Installation instructions for Conda, Arch Linux, and Mac Ports have been added #723 @reedacartwright #952 @elmbeech #930 @ahaerpfer
The example script for the STAMPS database has been fixed to run correctly #781 @drtamermansour
split-paired-reads.py: added -o option to allow specification of
an output directory #752 @bede
Fixed a string formatting and a boundary error in
sample-reads-randomly.py #773 @qingpeng #995 @ctb
CSV output added to abundance-dist.py, abundance-dist-single.py,
and count-overlap.py, and readstats.py #831 #854 #855
@drtamermansour #959 @anotherthomas
TSV/JSON output of load-into-counting.py enhanced with the total
number of reads processed #996 @kdmurray91 Output files are now also
checked to be writable before loading the input files #672 @pgarland
@bocajnotnef
interleave-reads.py now prints the output filename nicely #827
@kdmurray91
Cleaned up error for input file not existing #772 @jessicamizzi #851 @ctb
Fixed error in find-knots.py #860 @TheOneHyer
The help text for load-into-counting.py for the
--no-bigcounts/-b flag has been clarified #857 @kdmurray91
@lexnederbragt confirmed an old bug has been fixed with his test for
whitespace in sequence identifiers interacting with the
extract-partitions.py script #979
Now safe to copy-and-paste from the user documentation as the smart quotes have been turned off. #967 @ahaerpfer
The script make-coverage.py has been restored to the sandbox. #920
@SherineAwad
normalize-by-median.py will warn if two of the input files have the
same name #932 @elmbeech
Switched away from using --user install for developers #740 @mr-c
@drtamermansour & #883 @standage
Developers can now see a summary of important Makefile targets via
make help #783 @standage
The unused khmer.load_pe module has been removed #828 @kdmurray91
Versioneer bug due to new screed release was squashed #835 @mr-c
A Python 2.6 and 2.7.2 specific bug was worked around #869 @kdmurray91 @ctb
Added functions hash_find_all_tags_list and hash_get_tags_and_positions to CountingHash objects #749 #765 @ctb
The make diff-cover and ChangeLog formatting requirements have been
added to checklist #766 @mr-c
A useful message is now presented if large tables fail to allocate enough memory #704 @mr-c
A checklist for developers adding new CPython types was added #727 @mr-c
The sandbox graduation checklist has been updated to include streaming support #951 @sguermond
Specific policies for sandbox/ and scripts/ content, and a process for adding new command line scripts into scripts/ have been added to the developer documentation #799 @ctb
Sandbox scripts update: corrected #! Python invocation #815 @Echelon9, executable bits, copyright headers, no underscores in filenames #823 #826 #850 @alameldin several scripts deleted, docs + requirements updated #852 @ctb
Avoid running big-memory tests on OS X #819 @ctb
Unused callback code was removed #698 @mr-c
The CPython code was updated to use the new checklist and follow additional best practices #785 #842 @luizirber
Added a read-only view of the raw counting tables #671 @camillescott #869 @kdmurray91
Added a Python method for quickly getting the number of underlying tables in a counting or presence table #879 #880 @kdmurray91
The C++ library can now be built separately for the brave and curious developer #788 @kdmurray91
The ReadParser object now keeps track of the number of reads processed #877 @kdmurray91
Documentation is now reproducible #886 @mr-c
Python future proofing: specify floor division #863 @mr-c
Miscellaneous spelling fixes; thanks codespell! #867 @mr-c
Debian package list update #984 @mr-c
khmer.kfile.check_file_status() has been renamed to
check_input_files() #941 @proteasome filter-abund.py now uses it
to check the input counting table #931 @safay
normalize-by-median.py was refactored to not pass the ArgParse
object around #965 @susinmotion
Developer communication has been clarified #969 @sguermond
Tests using the ‘fail_okay=true’ parameter to runscript have been
updated to confirm the correct error occurred. 3 faulty tests were fixed
and the docs were clarified #968 #971 @susinmotion
FASTA test added for extract-long-sequences.py #901 @jessicamizzi
‘added silly test for empty file warning’ #557 @wltrimbl @bocajnotnef
A couple tests were made more resilient and some extra error checking added in CPython land #889 @mr-c
Copyright added to pull request checklist #940 @sguermond
khmer_exceptions are now based on std::strings which plugs a
memory leak #938 @anotherthomas
Python docstrings were made PEP257 compliant #936 @ahaerpfer
Some C++ comments were converted to be Doxygen compliant #950 @josiahseaman
The counting and presence table warning logic was refactored and centralized #944 @susinmotion
The release checklist was updated to better run the post-install tests #911 @mr-c
The unused method find_all_tags_truncate_on_abundance was removed
from the CPython API #924 @anotherthomas
OS X warnings quieted #887 @mr-c
All of these are pre-existing.
Some users have reported that normalize-by-median.py will utilize more memory than it was configured for. This is being investigated in https://github.com/dib-lab/khmer/issues/266
Some scripts only output FASTA even if given a FASTQ file. This issue is being tracked in https://github.com/dib-lab/khmer/issues/46
@ctb, @kdmurray91, @mr-c, @drtamermansour, @luizirber, @standage, @bocajnotnef, ‡@susinmotion, @jessicamizzi, ‡@elmbeech, ‡@anotherthomas, ‡@sguermond, ‡@ahaerpfer, ‡@alameldin, ‡@TheOneHyer, ‡@aditi9783, ‡@proteasome, ‡@bede, ‡@davelin1, @Echelon9, ‡@reedacartwright, @qingpeng, ‡@SchwarzEM, ‡@scottsievert, @PamelaM, @SherineAwad, ‡@josiahseaman, ‡@lexnederbragt,
‡ Indicates new contributors
@moorepants, @teshomem, @macmanes, @lexnederbragt, @r-gaia-cs, @magentashades