File Format Compatibility Matrix

[ababaian]

File format and software port compatibility matrix for bioSyntax.

	status
X	Syntax Complete
o	In Development
-	Unavailable
*	Bug Fix Needed

Core Syntaxes

File Format	Description	sublime	vim	gedit	less	vscode
.fasta	Generic nt/aa sequence	X	X	X	X	X
.fastq	Fasta + PHRED quality	X	X	X	X	X
.clustal	Multiple Sequence Alignment	X	X	X	X	X
.bed	Genomic Ranges	X	X	X	X	X
.gtf	Genomic Annotation	X	X	X	X	X
.pdb	Protein Structure	X	X	X	X	X
.vcf	Variant Call Format	X	X	X	X	X
.sam	NGS Sequence Data	X	X	X	X	X

Auxillary Syntaxes

File Format	Description	sublime	vim	gedit	less	vscode
.fasta	fasta alternative AA colors
-	Clustal	X	-	X	-
-	Taylor	X	-	X	-
-	Zappo	X	-	X	-
-	Hydrophobicity	X	-	X	-
.fai	Fasta Index (faidx)	X	X	X	X	X
.flagstat	samtools flag summary	X	X	X	X	X
.cwl	Common Workflow Language	X	X	X	-	X
.wig	Wiggle data	-	-	X	-	X
.pdbx	Protein Structure (large)	-	-	-	-	-
.phylip	Multiple Sequence Alignment	-	-	-	-	-
.newick	Tree Format	-	-	-	-	-
.nexus	Phylogenetics data	-	X	-	-	-
.pml	Pymol Scripts	X	X	-	-	X
.ped	Plink Pedigree Format	-	-	-	-	-
.probam	Protein Bam	-	-	-	-	-
Psi Fasta	(http://www.psidev.info/peff)

See Also: Alternative/User Syntax Definitions

These syntaxes are not part of the unified bioSyntax suite but often serve specialized and useful functions.

Science Syntaxes

File Format	Description	sublime	vim	gedit	less
.gaussian	Gaussian File (chemistry)	-	X	-	-

[Daniel-Mietchen]

Consider adding/ curating metadata about the file formats via Wikidata, e.g. as per https://www.wikidata.org/wiki/Q1111641 for FASTA.
The information gathered this way can then be exposed via a dedicated frontend at http://wikidp.org/ .

[emulatingkat]

I created a Wikidata item for the project: https://www.wikidata.org/wiki/Q52991773. I added info about the majority of file formats. Those not yet represented need to be added to Wikidata. If you would be willing to provide pointers to documentation of the file formats that still need to be added I'd be happy to create new items for them in Wikidata. Also possible that they are listed under a different name in Wikidata.

[emulatingkat]

Here is the current view in WikiDP: http://wikidp.org/Q52991773.