From b21a7deec5755203ce3d907dfde5cb66fa0fb8ac Mon Sep 17 00:00:00 2001 From: Vyacheslav Brover Date: Tue, 19 Mar 2024 17:11:45 -0400 Subject: [PATCH] Element symbol is _operon, Element name contains operon quality attribute --- stxtyper.cpp | 27 ++++++++++++++------------- version.txt | 2 +- 2 files changed, 15 insertions(+), 14 deletions(-) diff --git a/stxtyper.cpp b/stxtyper.cpp index c007869..3e1b7b1 100644 --- a/stxtyper.cpp +++ b/stxtyper.cpp @@ -32,6 +32,7 @@ * Dependencies: NCBI BLAST, gunzip (optional) * * Release changes: +* 1.0.18 03/19/2024 PD-4910 Element symbol is _operon, Element name is as below Sequence name -> Element name in header Sequence name, now Element name, should be type/subtype and include info when not complete e.g.,: @@ -110,22 +111,22 @@ const string na ("na"); -string stxType_reported_operon2elementSymbol (const string &stxType_reported, - const string &operon) +string stxType_reported_operon2elementName (const string &stxType_reported, + const string &operon) { - string elementSymbol (stxType_reported + " operon"); + string elementName (stxType_reported + " operon"); if (operon == "FRAMESHIFT") - elementSymbol += " with frameshift"; + elementName += " with frameshift"; else if (operon == "INTERNAL_STOP") - elementSymbol += " with internal stop"; + elementName += " with internal stop"; else if (contains (operon, "PARTIAL")) - elementSymbol = "Partial " + elementSymbol; + elementName = "Partial " + elementName; else if (operon == "EXTENDED") - elementSymbol = "Extended " + elementSymbol; + elementName = "Extended " + elementName; else if (contains (operon, "NOVEL")) - elementSymbol = "Novel " + elementSymbol; + elementName = "Novel " + elementName; - return elementSymbol; + return elementName; } @@ -289,8 +290,8 @@ struct BlastAlignment << targetStart + 1 // 3 "Start" << targetEnd // 4 "Stop" << strand // 5 "Strand" - << stxType_reported_operon2elementSymbol (stxType_reported, operon) // 6 "Element symbol" - << "Shiga toxin" // 7 "Sequence name" + << stxType_reported + "_operon" // 6 "Element symbol" + << stxType_reported_operon2elementName (stxType_reported, operon) // 7 "Element name" << "plus" // 8 "Scope" << "VIRULENCE" // 9 "Element type" << "STX_TYPE" //10 "Element subtype" @@ -543,8 +544,8 @@ struct Operon << start // 3 "Start" << stop // 4 "Stop" << strand // 5 "Strand" - << stxType_reported_operon2elementSymbol (stxType_reported, operonType) // 6 "Element symbol" - << "Shiga toxin" // 7 "Sequence name" + << stxType_reported + "_operon" // 6 "Element symbol" + << stxType_reported_operon2elementName (stxType_reported, operonType) // 7 "Element name" << "plus" // 8 "Scope" << "VIRULENCE" // 9 "Element type" << "STX_TYPE" //10 "Element subtype" diff --git a/version.txt b/version.txt index 8fc77d0..f8f3c08 100644 --- a/version.txt +++ b/version.txt @@ -1 +1 @@ -1.0.17 +1.0.18