Changelog

Version 0.8.4 (2021-06-30)

  • Added slice feature to FastaKeys

  • Fixed FastaKeys and FastqKeys iteration memory leak

  • Optimized FastaKeys and FastqKeys creation

Version 0.8.3 (2021-04-25)

  • Fixed Fastx iteration for next function

  • Fixed Fastx uppercase for reading fasta

Version 0.8.2 (2021-01-02)

  • Fixed sample segfault error caused by fastq iteration error

  • Fixed gzip index import error in multiple processes

  • Fixed fastq iteration segfault error with full_name=True

  • Fixed all objects iteration to support built-in next function

Version 0.8.1 (2020-12-16)

  • Fixed pip install error from source code

  • Removed support for python39 32bit due to dll load error

Version 0.8.0 (2020-12-15)

  • Added Fastx object as a simple sequence iterator

  • Added FastqKeys object to obtain read names

  • Added full_name option to Fastq object

  • Added support for Python 3.9

  • Fixed Fasta object error identifier order

  • Optimized speed of containing test and iteration

  • Changed Identifier object to FastaKeys object

Version 0.7.0 (2020-09-20)

  • Added support for extracting flank sequences

  • Added support for indexing super large gzip file

  • Reduced memory consumption when building gzip index

  • Improved the speed of random access to reads from fastq

  • Fixed sequence dealloc error cuasing no fasta delloc trigger

  • Fixed fastq max and min quality score return value

Older versions

Version 0.6.17 (2020-08-31)

  • Fixed gzip index loading error when no write permission

Version 0.6.16 (2020-08-27)

  • Increased the buff size of kseq to speedup sequence iteration

  • Removed warning message from fasta.c when building full index

Version 0.6.15 (2020-08-25)

  • Fixed key_func error caused by free operation

  • Fixed full name error when reading sequence without whitespace in names

  • Fixed a hidden bug in fasta/q iteration when reading attributes (not seq)

  • Fixed fasta/fastq size and sequence count error on Windows when parsing large file

  • Fixed zlib 2gb and 4gb limit on windows x64 to support large file

  • Reduced seek point span size to speedup random access from gzip file

Version 0.6.14 (2020-07-31)

  • Added support for using full header as identifier without building index

  • Improved the speed of fasta sequence iteration

  • Improved the speed of gzipped fastq read iteration

  • Fixed a bug in fastq read reader

Version 0.6.13 (2020-07-09)

  • Fixed fastq read iteration error

  • Fixed fastq cache buffer reader

  • Added cache for mean, median and N50 length

  • Speedup fasta iteration by reduced seeks

Version 0.6.12 (2020-06-14)

  • Fixed DeprecationWarning on py38 caused by ‘#’ formats args

  • Fixed some memory leak bugs

  • Cached sequence name to speedup fetch method

  • Used random string as gzip index temp file to support multiple processes

Version 0.6.11 (2020-05-18)

  • Fixed iteration error on Windows

  • Fixed test error on Windows

  • Fixed fastq composition error on 32bit OS

  • Improved the speed of fasta identifier sort and filter

Version 0.6.10 (2020-04-22)

  • Improved the speed of sequence reading

  • Improved the speed of sequence line iteration

  • Added avglen, minlen, maxlen, minqual and maxqual to Fastq object

  • Fixed read retrieval error

  • Fixed some hidden memory leaks

  • Changed fastq index file structure to save more information

Version 0.6.9 (2020-04-12)

  • Added buffreader to improve speed for reading from gzipped file

  • Added extract subcommand to extract sequences from fasta/q file

  • Added build subcommand to just build index

  • Changed info subcommand output to a tab seperated table

  • Changed Fastq object composition parameter to full_index

Version 0.6.8 (2020-03-14)

  • Fixed large offset seek error on windows

  • Fixed PyUnicode_AsUTF8 const char type warning

  • Changed sequence read line by line function

  • Changed gzread to fread for fastq information

Version 0.6.7 (2020-03-03)

  • Added check for fasta/q format when open file

  • Added benchmark scripts for evaluating performance

  • Speed up the fasta/q object iteration

  • Optimzed str length warning caused by strlen

Version 0.6.6 (2020-02-15)

  • Fixed incorrect sliced sequence name

  • Fixed seq,identifier,read object memory dealloc

  • Changed description text into description length in index file

Version 0.6.5 (2020-01-31)

  • Reduced memory usage when building index for large fasta

  • Removed rebuild_index method from Fasta object due to segmentation fault

  • Optimized compatibility between sqlite3 and python GIL

Version 0.6.4 (2020-01-14)

  • Fixed last sequence fetching error caused by missing n

  • Improved fasta/q object key error message to make it more human

Version 0.6.3 (2020-01-08)

  • Added .raw attribute to sequence object to get seq raw string

  • Added .raw attribute to read object to get read raw string

  • Added .description to read object to get full header line

  • Added iteration for sequence object from FASTA object

  • Added iteration for tuple from FASTQ object

  • Changed FASTA class parameter composition to full_index

Version 0.6.2 (2020-01-04)

  • Fixed sample sequence index error

  • Fixed ci deploy error

Version 0.6.1 (2020-01-03)

  • Added sample sequences command line

  • Added get subsequence command line

Version 0.6.0 (2020-01-02)

  • Fixed FASTA object parameter error

  • Fixed identifier sprintf warning

  • Fixed fasta description end r retained

  • Fixed error byte length when slice sequence

  • Removed support for python2.7 and python3.4

  • Removed python2 compat

  • Disabled export gzip index when building memory index

Version 0.5.10 (2019-11-20)

  • Added identifier filter function

  • Remove tp_new for Read, Sequence and Identifier

  • Fixed module method error

Version 0.5.9 (2019-11-17)

  • Added get longest and shortest sequence object

  • Added composition argument to speedup getting GC content

  • Added memory index to keep index in memory rather than local file

  • Fixed command line error

  • Changed sqlite to higher version

  • Removed journal_mode OFF

  • Speedup index building

Version 0.5.8 (2019-11-10)

  • Fixed fasta NL function parameter check

  • Fixed read id error when fastq iteration

Version 0.5.7 (2019-11-09)

  • Fixed SystemError caused caused by Python 2.7 seperated int and long type

  • Fixed String type check on Python 2.7

  • Fixed objects memory deallocation

Version 0.5.6 (2019-11-08)

  • Optimized random access from plain file

  • Reduced memory consumption

Version 0.5.5 (2019-11-07)

  • Added Support for IUPAC code complement

  • Speedup reverse complement

  • Speedup space removing and uppercase

Version 0.5.4 (2019-11-04)

  • Added guess fasta type (DNA, RNA, protein)

  • Added support for calculating protein sequence composition

  • Optimized the speed of index building

  • Calculate sequence composition when get gc content or composition

  • Fixed char return in python 2.7

Version 0.5.3 (2019-10-23)

  • Added support for coverting fastq to fasta

  • Updated command line interface docs

  • Fixed command line entry points

Version 0.5.2 (2019-10-18)

  • Fixed command line interface running error

Version 0.5.1 (2019-10-17)

  • Added key function for custom sequence identifier

  • Optimized speed of fasta indexing

  • Fixed bool args parsing error in py2.7

Version 0.5.0 (2019-10-13)

  • Added support for python 2.7 and 3.4

  • Added command line tool to manipulate fasta and fastq file

  • Added gzip attribute to fasta and fastq object to check whether compressed

  • Added sort function for identifier object

  • Fixed python bool argument parsing error caused by uint16_t

  • Fixed identifier sort key initialization

Version 0.4.1 (2019-10-05)

  • Fixed fastq quality encoding system guesser

  • Fixed gzip index insertion error

Version 0.4.0 (2019-09-29)

  • Added support for parsing FASTQ

  • Added random access to reads from FASTQ

Version 0.3.10 (2019-09-27)

  • Fixed GC skew exception caused by mixing unsigned with signed for division

Version 0.3.9 (2019-09-26)

  • Fixed sequence read line by line error

  • Fixed last sequence build index error when fasta file ended without n

  • Fixed GC skew error

Version 0.3.8 (2019-09-25)

  • Fixed large offset became negative error

  • Fixed slice step

  • Fixed uncorrect median length

  • Fixed strand compare error

  • Added GC skew calculation

  • Updated test script

Version 0.3.7 (2019-09-24)

  • Changed int type to standard type

  • Added support for processing large fasta file

  • Added id number for each sequence

  • Fixed SQL fetch error

  • Used 50 as default value of nl to calculate N50 and L50

Version 0.3.6 (2019-09-20)

  • Added support for searching subsequence from a sequence

  • Added support for checking subsequence weather in a sequence

  • Fixed gzip index import error

  • Fixed subsequence parent length for full sequence extraction

Version 0.3.5 (2019-09-08)

  • Fixed unicode error caused by sqlite3_finalize

Version 0.3.4 (2019-09-07)

  • Fixed seq description unicode string error

Version 0.3.3 (2019-09-07)

  • Fixed sequence description encoding error

Version 0.3.2 (2019-09-07)

Deleted

Version 0.3.1 (2019-09-07)

  • Added support for geting sequence description

Version 0.3.0 (2019-09-07)

  • Added read sequence from fasta file line by line

  • Added support for calculating assembly N50 and L50

  • Added support for calculating median and average length

  • Added support for getting longest and shortest sequence

  • Added support for calculating counts of sequence

  • removed support for Python34

Version 0.2.11 (2019-08-31)

  • Support for Python 3.4

Version 0.2.10 (2019-08-28)

  • Changed fseek and fread into gzseek and gzread

  • Fixed sequence cache name comparision

  • Fixed last sequence read error without line end

  • Fixed subsequence slice error in normal FASTA file

Version 0.2.9 (2019-08-27)

  • Fixed bad line calculate error

  • Changed rewind to fseek for subsequence extraction

Version 0.2.8 (2019-08-26)

  • Changed kseq.h library from li to attractivechaos

  • Improved fasta parser

Version 0.2.7 (2019-08-26)

  • Fixed no gzip index wrote to sqlite index file

Version 0.2.6 (2019-08-26)

  • Optimized speed of gzip random access

Version 0.2.5 (2019-08-25)

  • Fixed segmentation fault raised when loading gzip index

  • Changed fasta object method get_seq to fetch

Version 0.2.4 (2019-08-25)

  • Fixed fasta iter error after building new index

Version 0.2.3 (2019-08-24)

  • Fixed fasta iter error when end of file is not n

Version 0.2.2 (2019-07-19)

  • Fixed identifier contain error

Version 0.2.1 (2019-07-15)

  • Fixed sequence name always end with 0

  • Fixed fasta iterable for flat fasta

Version 0.2.0 (2019-07-09)

  • First release to PyPI