isolateR 1.0.6

• Fixed get_db function stemming from same underlying taxonomy string parsing issue as #19. Custom database creation with "add_taxonomy=TRUE" will now output taxonomic ranks in the correct order in FASTA headers as follows: >Accession_no;d__Domain;p__Phylum;c__Class;o__Order;f__Family;g__Genus;s__Species (e.g., >NR_042817.1;d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiia;o__Verrucomicrobiales;f__Akkermansiaceae;g__Akkermansia;s__Akkermansia_muciniphila).
• Patched sanger_assembly version error related to Issue #20 resulting in the following output: "Error in .call_fun_in_pwalign("pairwiseAlignment", ...) : pairwiseAlignment() has moved from Biostrings to the pwalign package, and is formally defunct in Biostrings >= 2.77.1. Please call pwalign::pairwiseAlignment() to get rid of this error." Function code updated to call pwalign instead of Biostrings where relevant.

isolateR 1.0.5

• Resolved persistent taxonomy-shifting in isoTAX (Issue #19). The underlying problem was only partially fixed in v1.0.4. In certain cases, higher-rank taxonomy did not align with species-level assignments due to subtle row-sorting differences introduced during internal calls to entrez_link and entrez_fetch (via the rentrez package). Row ordering is now explicitly controlled, and all taxonomy outputs appear stable and correct across test cases.
• Addressed isoQC warning: “unimplemented legacy type found in file". This warning was triggered inconsistently depending on the Sanger sequencing instrument used. Some .ab1 files produced it while others from different instruments did not. Since the warning did not affect isoQC performance or outputs, it has now been silenced internally to avoid confusion. The message will no longer appear for users.

isolateR 1.0.4

• Fixed issue related to #19 (taxonomy shifted in isoTAX output columns)
  • Improved taxonomy string calls by implementing entrez_link and entrez_fetch functions from the rentrez package, and then parsing of XML outputs to explicity extract each taxonomy rank by name (phylum, class, order, family, genus, and species).

isolateR 1.0.3

• Fixed issue related to #18 (Error: object 'TreeLine' is not exported by 'namespace:DECIPHER') with internal dependency on the deprecated TreeLine function in later versions of the DECIPHER package.
  • Changes made: TreeLine -> Treeline (Line 164 and Line 234) replacement in "isoLIB_function.R"
• Fixed issue related to #16 causing working directory to be reset and isoQC/isoTAX/isoLIB requiring absolute paths.
  • Changes made: Added normalizePath() functions to isoQC/isoTAX/isoLIB functions, allowing both absolute and relative paths to be speicifed as input.

isolateR 1.0.1

Update: 2024-08-11 (isolateR 1.0.1)

• Updated sanger_assembly function (aka "sanger_consensus" prior to v1.0.1) to allow assembly of paired Sanger sequences
  • This function loads in the CSV results table from isoQC and merges related sequences based on user input.
  • Original file names before isoQC step need to have a common prefix and differentiating suffixes. (e.g. SAMPLE_01_F.ab1, SAMPLE_01_R.ab1).
  • After aligning paired sequences, the consensus sequence is extracted and priority is given to the read with higher quality. Phred quality scores are reassigned in the final output table in a basic way by taking the mean of both input sequences.
  • Note: This function is designed to be used after the isoQC step and before the isoTAX step.
• Fixed warning issue during isoTAX step caused by usage of girafe function from ggiraph package.

isolateR 1.0.0

isolateR 1.0.0

Initializing official release version following publication:

Daisley et al. (2024). isolateR: an R package for generating microbial libraries from Sanger sequencing data. Bioinformatics 40(7):btae448. (https://doi.org/10.1093/bioinformatics/btae448)

Update: 2024-07-21 (isolateR 1.0.0)

• Added feature to isoTAX function to allow input of FASTA format files (relevant to addressing Issue #9).
  • FASTA file type is automatically detected if first character of file is ">".
  • File extension (.fasta/.fa/.fna) does not impact processing.
  • Can handle single- or multi-line FASTA format.
  • If input is a FASTA file, the sequence(s) will be converted and saved as an isoQC-formatted output file in the current working directory ("isolateR_output/01_isoQC_mock_table.csv"). Sequence date, name, length, and number of ambiguous bases (Ns) will be calculated from the input file and used to populate the relevant columns. Phred quality scores (phred_trim) will be set to the maximum value (60) and the remaining columns will be populated with mock data to allow compatibility with the isoTAX function. The main purpose of this output file is for flexibility and to allow users to edit/modify the sequence metadata before continuing with subsequent steps.
• Fixed error with isoLIB function not producing an HTML output file when only one group exists due to all sequences in a given run being identical or very similar in terms of pairwise nucleotide identity.