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CHANGELOG.rst

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Changes for bioy

1.12-dev

  • new bioy ssearch_count output columns [tax_name, position, A, T, G, C, N, expected, naligns, nseqs, rank, id]

1.12

  • bioy classifier --best-n-hits argument looks at each query sequence's Nth best blast hit, based on (GH 46) number of mismatches, and disregards all hits for that query with greater mismatches
  • bioy --split-condensed-assignments to retain assignment threshold assignments regardless of common condense ids assignments (GH 53)
  • bioy classifier --include-ref-rank $RANK will pull in ${RANK}_id and ${RANK}_name columns from taxonomy into details.
  • Fixed bioy --split-condensed-assignments centroid bug (GH 58)

1.11

  • bioy --version outputs git tag release plus a count of additional commits above tag release (GH 44)
  • bioy classifier --hits-below-threshold switch will append hits below the threshold to --details-out file (GH 41)

1.10

  • updated classifier to work with Python Pandas >=0.17.0
  • fixed classifier bug where assignment_id assignment was being unordered
  • classifier has new argument for emitting blast results normally discarded as below assignment threshold

1.9.4

  • fixed a bug when duplicate values are in the specimen map cause duplicate entries in details (GH 38)

1.9.3

  • added a workaround to get past a datatype inference bug in Pandas (GH 36)

1.9.2

  • dynamically assigning rank thresholds and refreshed the available tax_ids in data/rank_thresholds.csv (GH 32)
  • exchanged target_rank with condensed_rank (GH 31)
  • status messages now go to 100% (GH 26)
  • fixed bug when no blast hits (GH 34)

1.9.1

  • bioy reverse_complement can take a raw dna string now. Fasta file input is specified using --is-file.
  • new csvjoin, csvconvert and csvdeduplicate that improve on some csvkit commands
  • new subcommand ncbi_fetch fetches sequences from NCBI, given sequence id

1.9

  • classify is now deprecated for the new faster classifier with test cases. See bioy classifier --help for details.
  • classifier summary details now selects the largest clusters grouped by assignment_threshold to more closely align with the assignment pct_id range
  • Known bugs: Tax_ids of valid Blast hits (hits that meet their rank thresholds) may be assigned
    tax_ids of a higher threshold that could represent invalid tax_ids (tax_ids that may not have passed the rank threshold). Travis tests are failing even though they pass locally. The Travis test environment is a work in progress.

1.8.3

  • bioy ssearch checks for empty files before calling ssearch, circumventing a race condition bug

1.8.2

  • hdf5 support

1.8.0

  • remove scipy dependency
  • add pandas dependency
  • dev/bootstrap.sh creates a development environment
  • further simplification of classify --details - only the top pident hit per assignment tax_id is reported
  • tests of subcommands use bioy_pkg.scrips.main as entry point

1.7.7

  • bioy classify details output includes rows unique by sseqid,pident and coverage
  • new coverage column to blast output which is calculated in bioy blast
  • coverage filtering is done in bioy blast
  • bioy primer_trim has new option --keep-all-seqs which keeps sequences who's primers did not pass thresholds
  • bioy map_clusters takes a fasta file as an optional argument. Optional arguments have been renamed and reorganized.
  • bugfix: formatting error in bioy map_clusters