assembly_finder v0.6.0

Summary

Major release to use ncbi-datasets-cli to fetch genomes, assembly info and taxonomy

What's Changed

• Release 0.6.0 by @farchaab in #11

Full Changelog: v0.4.2...v0.6.0

assembly_finder v0.4.2

Summary

• Small release to fix genbank paths and checksum verification

Changes

• a98eacd Changed default exclude to anomalous
• 25264d8 Use python os.path for rule paths
• f930788 Changed default outdir

Fixes

• fedcb6f fixes absolute paths when downloading from genbank
• 25264d8 fixes #9

assembly_finder v0.4.1

Summary

• Small patch to fix input table parsing

Fixes

• 800f44b Fixed entries and nb conversion to integers

assembly_finder v0.4.0

Summary

• Input table requires column names now
• Auto complete of missing columns when input is a table
• Added a more flexible input search (assembly accessions, names...)
• Added retries in downloads
• Bug fixes
• updated README

Additions

• e38d74e Added input table examples
• 39db04a Added auto complete of missing columns in input table
• d5575c3 Added retries in download rules

Changes

• fbe383a Improved params names
• a1d8ebb d1cacbc Changed input search to support assembly names, accessions and uid
• 3f4f6f0 Renamed extensions param to suffix
• d6a8b96 Use column names in input table
• e9d7e70 Changed params ordering
• 8ed3daa Improved click help message (click choices)
• 43bac2f Snakemake args are now added with "--" (--force intead of force for example)
• 1bfd3c7 Updated documentation in README

Fixes

• 2f76629 Fixed index error when no fasta is downloaded
• 3f4f6f0 Fixed checksum extension bug

assembly_finder v0.3.3

Summary

• Added option to download assembly reports, fasta and more (gff,gtf ...)
• Bug fixes

Details

Additions

• 306278c Added option to download assembly fasta, reports, gff, gtf... #5

Changes

• 7537461 Simplified params names
• f570581 Removed unnecessary dictionary

Fixes

• ab40351 5c98c71 Fixed boolean params
• 9f83793 Fixed assembly level filter #4

assembly_finder v0.3.2

Summary

• Small update to fix the bioconda package

Details

Fixes

• 2ac37e0 Add Snakefile and scripts in bioconda package
• bb9a9e4 Fixed empty assembly method, and sequencing technology columns from assembly report

assembly_finder v0.3.1

Summary

• Small update to use up-to-date aspera-cli from bioconda

Details

Changes

• e4b85d3 Changed path to ascp private key
• 931114f Use updated aspera-cli from bioconda instead of HCC

assembly_finder v0.3.0

Summary

• Simplified assembly_finder cli
• Added checksum verification
• Split summary table into three tables for sequence, assembly and taxonomy summary
• Allow different parameters (assembly status, refseq category ...) for each entry
• Improvements and bugfixes

Details

Additions

• 25e7f05 81efbf6 Added sequencing technology, organism name, Biosource submission types in assembly table
• 81efbf6 Added sequence table to have sequence info (header to taxid correspondance)
• 81efbf6 Added taxonomy table to have linear taxonomy info
• 12dfee4 Allow for different assembly search parameters for each entry
• dbca07a Added sha256 checksum verification
• 5907660 56a0389 Added taxa.sqlite rules and option to avoid saving it in the conda env

Changes

• 81efbf6 Split summary table into three tables for sequence, assembly and taxonomy summary
• 12dfee4 Changed sort priority to refseq category then assembly status, followed by coverage and N50
• a17e3a1 Improved directory structure (moved scripts to bin directory)
• cb1f4af Removed run sub-command for simpler cli
• 25e7f05 Renamed summary table headers (no more CamelCase !)
• 43a8d0e Removed required NCBI email and key
• 2335ea7 Removed wget option
• 8c947f4 Updated dependency versions

Fixes

• 6f43cd7 Fixed number of assembly selection with or without rank filtering

0.2.0: Merge pull request #2 from metagenlab/dev

• added wrapper
• added n_target_rank to retrieve n genomes of each target rank (e.g species) within a taxon (e.g an entire family)

First alpha release

Pipeline that searches and download genomes from NCBI's assembly database.

For this release assembly_finder:

• Takes taxonomy identifiers or taxonomic ranks plus the number of assemblies to download as inputs in a tsv file.

• Outputs a summary table listing information on the downloaded assemblies.

• Has a search term that includes all assemblies except the ones from metagenomes (by default).

• Has a filtering function that prioritizes reference or representative genomes (by default).