Recent Releases of biocode
biocode - v0.11.0
0.11.0
- Documentation updates
- New script: @RPINerd added fasta/fastasizereport.py
- New script: fastq/validatematepairing.py
- New script: general/reportmatrixshape.py
- New script: gff/removefastafrom_gff3.py
- New script: gtf/convertstringtiegtftogff3.py
- fasta/fastasimplestats.py: Critical fix - Script was missing stats on last/only sequence.
- general/filtercolumnarfile.pl renamed to general/filtercolumnarfilebycolumn_values.pl
- lib/biocode/utils.py: Added function fastafilefrom_dict()
- lib/biocode/gff.py: gff.printgff3from_assemblies() no longer automatically splits genes with multiple mRNAs
- lib/biocode/gff.py: Fixed error causing failure if printgff3from_assemblies() was called
- fastq/randomlysubsamplefastq.py: Corrected shebang line which was causing failures
- fastq/fastqsimplestats.py: Added (optional) progress interval reporting
- fastq/fastqsimplestats.py: Added commas to integer outputs for better human readability
- blast/calculatequerycoveragebyblast.py: Added error handling so it reports/dies gracefully if an input seq isn't found
- fasta/filterfastaby_ids.pl: minor: added additional info if in debugging mode
- general/joincolumnarfiles.py: Corrected issue where header line was printing to STDOUT rather than output file
- gff/converttRNAScanSEtogff3.pl: @pgonzale60 committed improvements to satisfy NCBI's table2asnGFF requirements
- fastq/fastqsimplestats.py: Fixed issues where script would fail if file had no entries
- Critical bugfix and general improvements to sandbox/exportpasaunigenes.py
- Python
Published by jorvis over 2 years ago
biocode - v0.1.1
v0.1.0 was the first release made to PyPi and involved renaming a lot of the modules to better follow conventions there. v0.1.1 contains some corrections where Pycharm didn't quite get the name refactoring right.
The structure here doesn't match that on PyPi. A simple pip install should work:
$ pip3 install biocode
- Python
Published by jorvis over 9 years ago