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Releases: jorvis/biocode

v0.12.0

17 Oct 03:33
@jorvis jorvis
v0.12.0
03cd43d
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v0.12.0 Latest
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0.12.0

  • New script: fasta/strip_fasta_headers_after_regex.py
  • New script: fasta/export_fasta_ids.py
  • New script: blast/add_blast_results_to_gff3_product.py
Assets 2
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v0.11.0

17 Nov 05:57
@jorvis jorvis
v0.11.0
3efc84c
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v0.11.0

0.11.0

  • Documentation updates
  • New script: @RPINerd added fasta/fasta_size_report.py
  • New script: fastq/validate_mate_pairing.py
  • New script: general/report_matrix_shape.py
  • New script: gff/remove_fasta_from_gff3.py
  • New script: gtf/convert_stringtie_gtf_to_gff3.py
  • fasta/fasta_simple_stats.py: Critical fix - Script was missing stats on last/only sequence.
  • general/filter_columnar_file.pl renamed to general/filter_columnar_file_by_column_values.pl
  • lib/biocode/utils.py: Added function fasta_file_from_dict()
  • lib/biocode/gff.py: gff.print_gff3_from_assemblies() no longer automatically splits genes with multiple mRNAs
  • lib/biocode/gff.py: Fixed error causing failure if print_gff3_from_assemblies() was called
  • fastq/randomly_subsample_fastq.py: Corrected shebang line which was causing failures
  • fastq/fastq_simple_stats.py: Added (optional) progress interval reporting
  • fastq/fastq_simple_stats.py: Added commas to integer outputs for better human readability
  • blast/calculate_query_coverage_by_blast.py: Added error handling so it reports/dies gracefully if an input seq isn't found
  • fasta/filter_fasta_by_ids.pl: minor: added additional info if in debugging mode
  • general/join_columnar_files.py: Corrected issue where header line was printing to STDOUT rather than output file
  • gff/convert_tRNAScanSE_to_gff3.pl: @pgonzale60 committed improvements to satisfy NCBI's table2asn_GFF requirements
  • fastq/fastq_simple_stats.py: Fixed issues where script would fail if file had no entries
  • Critical bugfix and general improvements to sandbox/export_pasa_unigenes.py

Contributors

RPINerd and pgonzale60
Assets 3
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v0.10.0

01 Sep 15:38
@jorvis jorvis
v0.10.0
7ad8a11
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v0.10.0 
Corrected title underline in README.rst
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v0.3.1

06 Sep 16:41
@jorvis jorvis
v0.3.1
d221c22
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v0.3.1 
Old perl modules now on CPAN as 'TIGR' package
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v0.1.1

06 Jan 03:30
@jorvis jorvis
v0.1.1
8f09d71
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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
Assets 2
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