File Format / Syntax Compatibility Matrix

[ababaian]

File format and software compatibility matrix for bioSyntax.

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

Core Syntaxes

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

Auxillary Syntaxes

File Format	Description	sublime	vim	gedit	less
.fasta	fasta alternative AA colors
-	Clustal	X	o	X	-
-	Taylor	X	o	X	-
-	Zappo	X	o	X	-
-	Hydrophobicity	X	o	X	-
.fai	Fasta Index (faidx)	X	X	X	X
.flagstat	samtools flag summary	X	-	-	X
.wig	Wiggle data	o	-	X	-
.newick	Tree Format	-	-	-	-
.pdbx	Protein Structure (large)	-	-	-	-
.phylip	Multiple Sequence Alignment	-	-	-	-
.cwl	Common Workflow Language	-	-	-	-

[alyeffy]

Might I suggest including compatibility for Atom as well?

[ababaian]

I've heard a few people mention Atom; 1) What kind of syntax highlighting is required, which language is it written in? i.e. if it's textMarkup then the sublime files may be easily converted.

I also would like to get the core set of highly polished syntaxes done for the publication and then look at expanding compatibility.

[alyeffy]

Atom is GitHub's own open-source text editor that's cross-platform (Linux, Mac, Windows). A quick google search shows quite a few tutorials on creating your own syntax highlighting. Seems like it's also based on the one in TextMate (i.e. it should be fairly easy to convert the Sublime Text ones to be compatible with Atom).