GFF3 (BioFSharp) | BioFSharp

GFF3 Module

Namespace: BioFSharp.IO
Assembly: BioFSharp.IO.dll

Contains functions for reading and writing GFF3 files

Types and nested modules

Type/Module	Description
FastAHeaderParser	Parse FastA to GFF3
GFFEntry	represents fields of one GFF3 entry line
GFFLine<'a>	represents all kinds of lines which can be present in a GFF3 file

Functions and values

Function or value	Description
`createGFFEntry seqid source feature startPos endPos score strand phase attributes supplement` Full Usage: `createGFFEntry seqid source feature startPos endPos score strand phase attributes supplement` Parameters: seqid : `string` source : `string` feature : `string` startPos : `string` endPos : `string` score : `string` strand : `string` phase : `string` attributes : `string` supplement : `string` Returns: `GFFEntry`	Takes strings of each field and creates a GFFEntry type thereby converting the strings into desired types. seqid : `string` source : `string` feature : `string` startPos : `string` endPos : `string` score : `string` strand : `string` phase : `string` attributes : `string` supplement : `string` Returns: `GFFEntry`
`fromFile fastAconverter filepath` Full Usage: `fromFile fastAconverter filepath` Parameters: fastAconverter : `char seq -> 'a` filepath : `string` Returns: `GFFLine<'a> seq`	reads in a file and gives a GFFLine<'a> list. If file contains a FastA sequence it is converted to FastA.FastaItem with given converter. (Use 'id' as converter if no FastA is required). fastAconverter : `char seq -> 'a` filepath : `string` Returns: `GFFLine<'a> seq`
`fromFileWithoutFasta filepath` Full Usage: `fromFileWithoutFasta filepath` Parameters: filepath : `string` Returns: `GFFLine<char seq> seq`	if no information about Sequence is required or no Fasta is included you can use this function filepath : `string` Returns: `GFFLine<char seq> seq`
`gFFEntrytoString g` Full Usage: `gFFEntrytoString g` Parameters: g : `GFFEntry` Returns: `string`	converts a single GFF entry to a line (string) of a GFF file g : `GFFEntry` Returns: `string`
`getSequence cDSfeature gFFFile` Full Usage: `getSequence cDSfeature gFFFile` Parameters: cDSfeature : `GFFEntry` gFFFile : `GFFLine<'a> seq` Returns: `'a0 seq`	if a FastA sequence is included this function searches the features corresponding sequence cDSfeature : `GFFEntry` gFFFile : `GFFLine<'a> seq` Returns: `'a0 seq`
`parseStrToGFFEntry str` Full Usage: `parseStrToGFFEntry str` Parameters: str : `string` Returns: `GFFEntry`	Converts a string into a GFFEntry type. If there are more than 9 fields an additional "supplement" field gets filled. If there are less than 9 only the supplement field gets filled with the whole line. str : `string` Returns: `GFFEntry`
`relationshipSearch gffList searchterm` Full Usage: `relationshipSearch gffList searchterm` Parameters: gffList : `GFFLine<'a> seq` searchterm : `string` Returns: `GFFEntry seq`	Searches for a term and gives a list of all features of which the searchterm is the mainfeature (ID) or a child of it (Parent). gffList : `GFFLine<'a> seq` searchterm : `string` Returns: `GFFEntry seq`
`sanityCheck filepath` Full Usage: `sanityCheck filepath` Parameters: filepath : `string`	filepath : `string`
`sanityCheckWithSOTerm so_TermsPath filepath` Full Usage: `sanityCheckWithSOTerm so_TermsPath filepath` Parameters: so_TermsPath : `string` filepath : `string`	Validates GFF3 file. Prints all appearances of errors with line index. If no (SO)FA check is needed set "" as so_TermsPath. so_TermsPath : `string` filepath : `string`
`toString converter input` Full Usage: `toString converter input` Parameters: converter : `'a -> char` input : `GFFLine<'a0> seq` Returns: `string seq`	converts GFF lines to string sequence. Hint: Use id as converter if no FASTA sequence is included. converter : `'a -> char` input : `GFFLine<'a0> seq` Returns: `string seq`
`write converter path input` Full Usage: `write converter path input` Parameters: converter : `'a -> char` path : `string` input : `GFFLine<'a0> seq`	writes GFF lines to file. Hint: Use id as converter if no FASTA sequence is included. converter : `'a -> char` path : `string` input : `GFFLine<'a0> seq`
`writeOrAppend converter path input` Full Usage: `writeOrAppend converter path input` Parameters: converter : `'a -> char` path : `string` input : `GFFLine<'a0> seq`	writesOrAppends GFF lines to file. Hint: Use id as converter if no FASTA sequence is included. converter : `'a -> char` path : `string` input : `GFFLine<'a0> seq`