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BioInf
Library for reading microbiology DNA files (ABI, SCF, FASTA, etc)
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README
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.
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.