Pysam VariantFile.fetch() without specifying contig

Question

[ricardoguerreiro2121]

Hello,

I'm using the Pysam module of Python and calling the function:

VF = VariantFile("input_file")

VF.fetch()

seems to retrieve all reads in the file,

while this retrieves reads from positions 0 to 1000 in one specific contig:

VF.fetch(contig="contig_name", start=0, end=1000)

My question is: is it possible to retrieve sequences based on positions without specifying the contig name? Or better, specifying multiple contig names? (gives error, expects one string).

This is because I have a file with multiple contigs, but I would like to get for example all reads in positions 0:1000 in all contigs.

If I do this:

VF.fetch( start=0, end=1000)

It ignores my start and end specification, and retrieves all reads, like if it were no arguments inside fetch.

Answer 1

[finswimmer]

Hello,

you can get all the contig names via VCF.header.contigs. This returns a view you can iterate over (untested):

for name in VCF.header.contigs:
    VF.fetch(contig=name, start=0, end=1000)

This presumes that the contigs are listed in the header.

fin swimmer

[ricardoguerreiro2121]

Brilliant! Sometimes you just have to go around the problems, not force your way through.

Danke schön!

Ricardo