BioInf - Delphi Bioinformatics library

Delphi library/package for reading/writing microbiology DNA sample/chromatogram files (ABI, AB, AB1, SCF, FASTA, SEQ, etc).

Has support for:

• SNP (Single Nucleotide Polymorphism)
• QV (base Quality Value)
• Integrated trimming engine (automatic bad-end trimming)
• Recalling of bad (N) peaks using proprietary algorithm
• Automatic sequence direction (F/R)
• Reading and displaying the chromatogram data
• read/write SCF chromatogram files
• read ABI/AB/AB1/AB! chromatogram files
• read/write FASTA chromatogram files
• read/write GeneBank (GBK) chromatogram files.

The import functionality is accessible with a call to a single function: TCubeImport.Import(FileName)

  TCube = class(TCubeAbstractSnp)    
  public     
   {IMPORT}     
   function  Import(CONST FileName: string): Boolean;                                                         { Fasta and GBK files are not supported because they may contain more than one sample! }  
   function  AssignGBK     (CONST Gbk : TGbkObj): Boolean;  
   function  AssignScf     (CONST SCF : TScfObj): boolean;  
   function  AssignAbi     (CONST ABI : TAbiObj; EditedField: boolean= True): Boolean;                      
   {EXPORT}                           
   function  ExportAs      (CONST aFileName: string; Clean: Boolean; OUT BasesLeft: Integer): Boolean;          
   procedure ExportAsFASTA (CONST FileName : string; Clean: Boolean; OUT BasesLeft: Integer); overload;   
   procedure ExportToSCF   (CONST aFileName: string; Clean: Boolean);            overload;                    { This will remove all GAPs }  
   function  ExportToSCF   (CONST                    Clean: Boolean): string;    overload;                    { Returns the name used to save the file }  
   function  AsFasta       (CONST aFileName: string; Clean: Boolean): TFastaObj; overload;                    { Return a TFastaObj object built from this cube }  
  
   procedure SaveChromaAsBmp(CONST Nume: string);  
 end; 

The code was tested on millions of DNA samples over the years and works flawlessly.

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Features:

• TrimEngine
• Assign(TSample)
• Average Quality
• Highest QV
• FindAdaptor
• Clip Left/Right
• Good Bases
• Can work with sequences with length over 65535 bases
• Implements a single SFF read
• NoOfGoodBases
• GoodBases
• Conversion to Fasta
• BuildQVGraph
• etc

Next to come:

• Code to import NextGen DNA sequence files such as SFF. SFQ, FAS.
• DNA sequence assembly
• SNMP / Mutation detection

Requires the LightSaber library.

Details + similar libraries