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CHANGELOG.rst

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Hey, let's keep a change log.

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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

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 improvments 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

0.10.0

  • Added things.Region class for generic genomic regions
  • Updated dependency information for latest Ubuntu
  • Added ORF class and mRNA.longest_orf() method
  • Added script to filter FASTA files from abundance estimation (Salmon) results
  • Added new script for classifying gene coverage in new assemblies
  • Exports to GFF3 updated: tRNAs include anticodon, rRNAs includ product name
  • mRNA.longest_orf() now has require_start option
  • fasta_simple_stats.py now exports N50 and N90 stats
  • fasta_simple_stats.py no longer errors on blank lines

0.9.0

  • Added ncRNA feature class and changed inheritance for all related types (rRNA, tRNA, etc.)
  • gff.parse_annotation_from_column_9() now recognizes both 'product_name' and 'product' in 9th column.

0.8.0

  • This actually should have been what the previous release was called. X.X.N releases should only be for bug fixes.
  • Added dependency support for R in Docker build
  • Added report_go_slim_counts.py script
  • Added metaphlan-parsing R script (though needs major clean-up)

0.7.1

  • NCBI API key now required for all E-Utility calls
  • Added --skip_existing option to batch genbank downloader" download_assemblies_from_genbank.py
  • Changed genbank/download_assemblies_from_genbank.py to export BOTH contig and scaffold range files automatically
  • Bugfix: genbank module was failing if the gene symbol contained a comma
  • Corrected python module dependency from igraph -> python-igraph
  • Updated documentation on taxadb generation in general/filter_uniref_by_taxonomy.py
  • Added taxadb to formal dependencies
  • Changed BED export library to use gene.id for 4th column if no locus is found
  • Added ncbigff module and script to use it for conversions
  • Added general/join_columnar_files.py
  • Added fasta/fasta_simple_stats.py

0.7.0

  • Added script to convert GFF3 to BED
  • Added script to convert BLAST/RAPSearch2 to BED
  • Added script to convert HMMer3 HTAB to BED
  • Added biocode.bed library