fasta2bed

[yoann-dufresne]

This converter should transform a fasta file representing a scaffold (ordered contigs) into a genome annotation following this specifications:

Fasta:

>contig_1 my first contig
ACT
>contig_2 my second contig
GTGT

Bed:

contig_1 0 2
contig_2 3 6

[cokelaer]

at some point we should define precisely what BED means. We have some BED with 3,6,12 columns.
Here, the BED file has 3 columns. What are the second and third column meaning here. should be in the class documentation. thanks

[blaiseli]

BED has optional columns, but the first 3 should always be present and are well defined.

The first three required BED fields are:

1. chrom - The name of the chromosome (e.g. chr3, chrY, chr2_random) or scaffold (e.g. scaffold10671).
2. chromStart - The starting position of the feature in the chromosome or scaffold. The first base in a chromosome is numbered 0.
3. chromEnd - The ending position of the feature in the chromosome or scaffold. The chromEnd base is not included in the display of the feature. For example, the first 100 bases of a chromosome are defined as chromStart=0, chromEnd=100, and span the bases numbered 0-99.

(see https://genome.ucsc.edu/FAQ/FAQformat.html#format1)