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File Format Compatibility Matrix #1
Description
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 | - | - |
Activity
Daniel-Mietchen commentedon May 10, 2018
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 commentedon May 10, 2018
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 commentedon May 10, 2018
Here is the current view in WikiDP: http://wikidp.org/Q52991773.