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Recent Releases of cblaster

cblaster - cblaster v1.3.20

What's Changed

  • fix(remote): accommodated change in NCBI API by @FriederikeBiermann in https://github.com/gamcil/cblaster/pull/115

New Contributors

  • @FriederikeBiermann made their first contribution in https://github.com/gamcil/cblaster/pull/115

Full Changelog: https://github.com/gamcil/cblaster/compare/v1.3.19...v1.3.20

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Published by gamcil about 1 year ago

cblaster - cblaster v1.3.19

What's Changed

  • Checks for mistranslations in CDS annotations and truncated regions, other minor changes by @malanjary-wur in https://github.com/gamcil/cblaster/pull/94
  • Update CITATION.cff with paper DOI by @althonos in https://github.com/gamcil/cblaster/pull/106

New Contributors

  • @althonos made their first contribution in https://github.com/gamcil/cblaster/pull/106

Full Changelog: https://github.com/gamcil/cblaster/compare/v1.3.18...v1.3.19

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Published by gamcil almost 2 years ago

cblaster - cblaster v1.3.18

  • Fix NoneType error during result formatting (#90)
  • Some bug fixes for stability (#87)

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Published by gamcil about 3 years ago

cblaster - cblaster v1.3.17

  • Fix off-by-one issues in extract_clusters module with intermediate genes (#83)
  • Check for empty fields in IPG table (#85)

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Published by gamcil about 3 years ago

cblaster - cblaster v1.3.16

  • Fixes broken identical protein groups efetch request by setting db=ipg instead of db=protein (https://github.com/gamcil/cblaster/issues/84)
  • Convert coordinates from IPG table to zero-based

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Published by gamcil over 3 years ago

cblaster - cblaster v1.3.15

  • Catch ValueError when parsing GFF sequence-region directive without coordinates
  • Do not install genomicsqlite if installing cblaster on arm64

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Published by gamcil over 3 years ago

cblaster - cblaster v1.3.14

  • Fall back to built-in sqlite3 module when importing genomicsqlite fails

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Published by gamcil over 3 years ago

cblaster - cblaster v1.3.13

Thanks to @brymerr921:

Bug fixes: - By default, diamond blastp only saves a maximum of 25 hits per query, severely limiting the number of blast hits reported. Large databases are especially impacted. To solve this, the --hitlist_size is now passed on diamond inside cblaster search -m local. (1c16caa) (See issue #75) - Added an option to cblaster makedb allowing users to provide a single txt file containing a list of input files. This solves the issue where the operating system limits the length of wildcard expansion on the command line. (bb9085c) - Fixed error that arose when specifying sum or max for -bkey (fee315e) (see issue #76, thanks to @chasemc)

Enhancements: - diamond makedb now uses the number of CPUs requested by the user (instead of all available CPUs) (0db55cc)

File compression: - Use genomcsqlite3 to reduce the size of the final sqlite3 database by 40-60% (bae6b31) - cblaster makedb accepts gzipped input files (241894d) - cblaster makedb now writes a fasta.gz output file (241894d) and informs users they will need to decompress first if running hmmsearch (4c63fa5)

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Published by gamcil almost 4 years ago

cblaster - cblaster v1.3.12

  • Fix extract_clusters module not working for HMM searches (https://github.com/gamcil/cblaster/commit/2dcae875ba8bf170c1bba7d55fe13305317a2859)

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Published by gamcil over 4 years ago

cblaster - cblaster v1.3.11

  • Explicitly check for decode method on HTTPResponse objects (as well as status code 200) from IPG Efetch to prevent AttributeError (#62)

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Published by gamcil over 4 years ago

cblaster - cblaster v1.3.10

  • Change default value for --percent argument to 0 from 50 to prevent confusion when no results
  • Fix parsed GFF records not being correctly converted to SQL insertion tuples, should address #63

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Published by gamcil over 4 years ago

cblaster - cblaster v1.3.9

  • Adds the ability to load local profile HMM files instead of just Pfam domains
  • Can now look up Pfams by family name, e.g. --query_profiles AMP-binding
  • Add local profile HMM support to GUI
  • Add example search output and small README on how to generate it
  • Change default font family of generated plot

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Published by gamcil over 4 years ago

cblaster - cblaster v1.3.8

  • Fix bug in preventing use of config module

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Published by gamcil over 4 years ago

cblaster - cblaster v1.3.7

  • Fix manually translated sequences not being cast to str, causing crash when inserting into database
  • Check feature is pseudogene before translation

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Published by gamcil over 4 years ago

cblaster - cblaster v1.3.6

  • Fix bug when retrieving protein translations from genomes for makedb

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Published by gamcil over 4 years ago

cblaster - cblaster v1.3.5

  • Fix sequences not being saved when searching with query IDs

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Published by gamcil over 4 years ago

cblaster - cblaster v1.3.4

  • Update extract module help
  • Use trusted cutoffs for local HMM searches

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Published by gamcil over 4 years ago

cblaster - cblaster v1.3.3

  • Fix bug when creating local databases from bad method call
  • Lower default values for remote search API call, E-value 0.1 and hitlist size 500
  • Fix bug when parsing translations from genomes

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Published by gamcil over 4 years ago

cblaster - cblaster v1.3.2

  • Fixed issue with gene strandedness when fetching intermediate genes
  • Check for configuration values in extract_clusters module

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Published by gamcil over 4 years ago

cblaster - cblaster v1.3.1.6

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Published by gamcil over 4 years ago

cblaster - cblaster v1.3.1.5

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Published by gamcil almost 5 years ago

cblaster - cblaster v1.3.1.4

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Published by gamcil almost 5 years ago

cblaster - cblaster v1.3.1.3

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Published by gamcil almost 5 years ago

cblaster - cblaster v1.3.1.2

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Published by gamcil almost 5 years ago

cblaster - cblaster v1.3.1.1

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Published by gamcil almost 5 years ago

cblaster - cblaster v1.3.1

  • Fixed bug with scaffolds containing only one hit
  • Fixed bug in databases used during 'combi' mode searches

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Published by gamcil almost 5 years ago

cblaster - cblaster v1.3.0

  • All query sequence information now stored in Sessions, so plot_clusters doesn't require original query file/IDs to work (#48)
  • Added -per/--percentage option for filtering clusters by % of query sequences required (#45)
  • Bug fixes

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Published by gamcil almost 5 years ago

cblaster - cblaster v1.2.9

  • Check for pseudogenes when generating GenBank files in extract_clusters
  • Add fallback for plotting query cluster without a query_file parameter in plot_clusters

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Published by gamcil almost 5 years ago

cblaster - cblaster v1.2.8

  • Revert change to file finding (https://github.com/gamcil/cblaster/issues/40)
  • Fix parsing of protein_id qualifiers from feature tables in intermediate genes module

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Published by gamcil almost 5 years ago

cblaster - cblaster v1.2.7

  • Fix feature table parsing for eukaryotic genomes
  • Fix error message when opening GUI due to color buttons being a list instead of tuple

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Published by gamcil almost 5 years ago

cblaster - cblaster v1.2.6

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Published by gamcil almost 5 years ago

cblaster - cblaster v1.2.5

  • add gffutils to requirements

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Published by gamcil about 5 years ago

cblaster - cblaster v1.2.2

  • Fixed a bug when resuming remote searches from BLAST RID
  • Added extract module to GUI
  • Changed default values for gne module

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Published by gamcil over 5 years ago

cblaster - cblaster v1.2.1

  • Fixed bug when performing local searches on Windows due to issues with temporary files

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Published by gamcil over 5 years ago

cblaster - cblaster v1.2.0

  • Added extra options in plots to adjust size/position/visibility of plot elements
  • Cell borders are now drawn when cells contain shared hit sequences (indicated by same colour border), not just because cell contains >1 hit
  • Sequence names (and optionally sequences via NCBI) can now be extracted from search session files using the extract module
  • Added GFF3 parsing for creating cblaster local databases via genome2json

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Published by gamcil over 5 years ago

cblaster - cblaster v1.1.1

  • Add ability to save raw BLAST and IPG tables
  • Move filtering of IPG table to later stage to avoid missing potential homologues when BLAST hit is e.g. a SwissProt entry
  • Raise hitlist_size from 500 to 5000 to avoid missing potential hits in widespread sequences
  • Updates to the command line interface, example usages, new options
  • Add ability to load and merge multiple session files from the CLI

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Published by gamcil over 5 years ago

cblaster - cblaster v1.1.0

  • Complete rework of plot; remove matplotlib, use D3 JavaScript library instead

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Published by gamcil over 5 years ago