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Release V2.0.0#94

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kbessonov1984 merged 71 commits intomasterphac-nml/ecoli_serotyping:masterfrom v2.0.0phac-nml/ecoli_serotyping:v2.0.0Copy head branch name to clipboardDec 12, 2024

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Commits

Commits on Nov 28, 2023

• towards v2.0.0 species ID wit new mash gtdb+enterobase+refseq sketch implemented

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  11d7c6c

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Commits on Feb 7, 2024

• pathotyping module first release

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Commits on Feb 8, 2024

• updated EPEC rules

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• added ND (not detected) flag for pathotype

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• soreted pathotype outputs

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Commits on Feb 9, 2024

• added new outputs to the report, %id, %cov, top gene hits and other

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Commits on Feb 11, 2024

• added gene length ratio field to output.tsv

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Commits on Feb 12, 2024

• fixed bug on additional fields for non-E.coli genomes. Made species ID to be run always, before only was possible with --verify key

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Commits on Feb 13, 2024

• f-string issue resolved

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• duplicated filenames in batch mode error plus removed tempfile dependency due to delete param not being present only starting python 3.12

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Commits on Feb 16, 2024

• updated patho database with aggA gene

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• added options to specify thresholds for pathotype blastn results

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• small fixes

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  1e6e08d

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Commits on Feb 18, 2024

• fixed local variable 'predictions_pathotype_dict' where it is not associated with a value

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• fixed db missing id field

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Commits on Feb 20, 2024

• Shiga toxin typing module implemented and improved datbase of pathotypes covering EAEC and DAEC

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Commits on Feb 21, 2024

• added hemolysin exhA, hlyA and hlyE typing and accessions field

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Commits on Feb 22, 2024

• ehxA mislabelled

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Commits on Feb 24, 2024

• ehxA gene name correction in DB

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Commits on Feb 26, 2024

• fixed non-typable files being counted as non-E.coli genomes

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Commits on Mar 2, 2024

• Added Dockerfile with Species ID DB init

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• Added Dockerfile with Species ID DB init

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Commits on Mar 8, 2024

• fixed empty fasta or non-fasta file with pathotype flag edge case

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Commits on Mar 22, 2024

• Updated species ID sketch download and added ectyper_init

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• init.py added

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• updated speciesID download link

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• fixed speciesID dbpath reduntant variable

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Commits on Mar 23, 2024

• Added Singularity.def file

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Commits on Apr 18, 2024

• Fixed empty O- and H- antigen BLAST output file found in metagenomic samples and added full length STX1 and STX2 sequences to database, homogenized gene names

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Commits on Apr 20, 2024

• Fixed empty or invalid FASTA file error generated from FASTQ and improved multicore performance on single sample

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Commits on May 11, 2024

• big update for Shiga toxin module typing supporting reporting of multiple stx subtypes including mixed truncated cases with smart hit parsing. Improved shiga toxin database complete sequences cover…

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Commits on May 28, 2024

• shiga toxin module several improvements and application of a threshold

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Commits on May 29, 2024

• Fixed contig naming reporting for FASTA headers with | symbol replaced by _ as it conflicts with contig name extraction

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Commits on Jun 6, 2024

• stx2l sequence for AM904726.1 corrected based on https://doi.org/10.3390/microorganisms10061245

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Commits on Jun 19, 2024

• fixed --verify bug when pathotyping is run on non-E.coli species but should not

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Commits on Jul 17, 2024

• added gunzip compression support, added pathotype gene count, sorting of O and H antigens ascending order by #, add dashes when no stx genes found

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• Report EHEC as EHEC-STEC, add number of genes linked to pathotype(s)

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• renamed ectyper_pathotyping_database_v2.json pathotype database to ectyper_patho_stx_toxin_typing_database.json

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Commits on Jul 19, 2024

• added PMID to pathotype rules in the database

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Commits on Jul 22, 2024

• github actions pytest CI feature added

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• github actions pytest CI feature added

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• github actions pytest CI feature added

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• github actions pytest CI feature added

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• github actions pytest CI feature added

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  33eac5d

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• Added STEC O157:H7 GCA_000181775.1 gzip compressed for testing

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Commits on Jul 29, 2024

• fixed multiprocess Pool freeze on subprocess error and added better messages when file list is provided listing missing files

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• added wildcard characters in path specification and also multiple directories are allowed now to be specified

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Commits on Jul 30, 2024

• Making tool and its module more robust to errors

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  22b6a98

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• Fixed pytest small error with test_emtpy_BLAST_antigen_hits

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  4ef8526

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• Fixing small pytest errors

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Commits on Jul 31, 2024

• fixed batch mode error when one of the files fails FASTA test causing other files in a pool not being analyzed.

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• fixed pytest issues

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Commits on Aug 1, 2024

• Fixed bugs related to batch mode output files displaying only last sample results instead of results from All samples. Also added automatic clceaner for the main output files to prevent excesive fi…

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• Fixed bugs related to batch mode output files displaying only last sample results instead of results from All samples. Also added automatic clceaner for the main output files to prevent excesive fi…

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Commits on Sep 12, 2024

• Updated README.md to follow DAAD format and also updated url to Species ID MASH database now hosted in Zenodo.org

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Commits on Sep 18, 2024

• Updated README.md with species ID module description

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• Updated documentation on Shiga toxin and pathotyping, also fixed bug with the stx_contigs_num field

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Commits on Sep 20, 2024

• updated stx database STX subunit A and B sequences. Only kept STX complete sequences

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Commits on Oct 3, 2024

• Updated pathotyping and toxin typing database by adding protein sequences to each record and adding subunit coordinates and intergenic region of shiga toxin records

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• Updated pathotyping and toxin typing database by adding protein sequences to each record and adding subunit coordinates and intergenic region of shiga toxin records

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• Added test of no directory specified and testing for multiple files inputs. Added solution to issue #87

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Commits on Oct 28, 2024

• added new species ID fields that provide info on species hashes to ref and top reference accession id

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• added Shigella_sonnei test sample

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Commits on Nov 7, 2024

• Updated bowtie2 setting to be compatible with long reads

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• sorted for O mixed antigen is working

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• --longreads option added for FASTQ long reads inputs such as PacBio, ONT, etc. Gives better mapping results

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• --longreads option added for FASTQ long reads inputs such as PacBio, ONT, etc. Gives better mapping results

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• --longreads option added for FASTQ long reads inputs such as PacBio, ONT, etc. Gives better mapping results

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Commits on Dec 12, 2024

• release v2.0.0

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• updated README.md

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• Merge branch 'master' into v2.0.0

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