From c0f7904e2631a17725793969a65cde1ae6217e02 Mon Sep 17 00:00:00 2001 From: Vyacheslav Brover Date: Mon, 16 Oct 2023 11:44:43 -0400 Subject: [PATCH] PD-4772 Remove prodigal GFF format from AMRFinderPlus --- amrfinder.cpp | 10 +++++++--- version.txt | 2 +- 2 files changed, 8 insertions(+), 4 deletions(-) diff --git a/amrfinder.cpp b/amrfinder.cpp index 10ff311..b4d4a30 100644 --- a/amrfinder.cpp +++ b/amrfinder.cpp @@ -33,9 +33,10 @@ * gunzip (optional) * * Release changes: -* 3.11.25 10/13/2023 PD-4771 Revert removing '*' from Prodigal output to ensure ALLELEP and EXCATP matches ?? +* 3.11.26 10/16/2023 PD-4772 Remove prodigal GFF format from AMRFinderPlus +* 3.11.25 10/13/2023 PD-4771 Revert removing '*' from Prodigal output to ensure ALLELEP and EXACTP matches ?? * 3.11.24 10/12/2023 PD-4769 --print_node prints FAM.id replaced by FAM.parent for non-exact allele matches -* 3.11.23 10/06/2023 PD-4764 Remove '*' from Prodigal output to ensure ALLELEP and EXCATP matches +* 3.11.23 10/06/2023 PD-4764 Remove '*' from Prodigal output to ensure ALLELEP and EXACTP matches * 10/05/2023 PD-4761 Remove protein sequences with >= 20 Xs * 3.11.22 10/05/2023 PD-4754 Prodigal GFF * 3.11.21 10/02/2023 PD-4755 bug: calling fusion2geneSymbols() for a mutation protein @@ -317,7 +318,10 @@ struct ThisApplication : ShellApplication addKey ("protein", "Input protein FASTA file (can be gzipped)", "", 'p', "PROT_FASTA"); addKey ("nucleotide", "Input nucleotide FASTA file (can be gzipped)", "", 'n', "NUC_FASTA"); addKey ("gff", "GFF file for protein locations (can be gzipped). Protein id should be in the attribute 'Name=' (9th field) of the rows with type 'CDS' or 'gene' (3rd field).", "", 'g', "GFF_FILE"); - addKey ("annotation_format", "Type of GFF file: " + Gff::names. toString (", "), "genbank", 'a', "ANNOTATION_FORMAT"); + + string annots (Gff::names. toString (", ")); + replaceStr (annots, ", prodigal", ""); // PD-4772 ?? + addKey ("annotation_format", "Type of GFF file: " + annots, "genbank", 'a', "ANNOTATION_FORMAT"); addKey ("database", "Alternative directory with AMRFinder database. Default: $AMRFINDER_DB", "", 'd', "DATABASE_DIR"); addFlag ("database_version", "Print database version", 'V'); diff --git a/version.txt b/version.txt index 63592a6..ab49651 100644 --- a/version.txt +++ b/version.txt @@ -1 +1 @@ -3.11.25 +3.11.26