spacr.qt.widgets.sra_picker

Choose which published sequencing runs to fetch, and how much of each.

Map Barcodes offers the paper’s own reads, and lets the user say how many sequencing lines to take from each file.

The read limit sets the download size. The four runs are 20.4 GB in full; a hundred thousand reads from each is about 30 MB, because ENA serves gzipped FASTQ that spacr.sra.fetch_reads() reads as a stream and abandons once it has enough. The estimate is shown before anything starts and is recomputed as the limit changes, so the size is known before the download begins.

Classes

SraPicker

List the published runs, take a read limit, and fetch what is ticked.

Module Contents

class spacr.qt.widgets.sra_picker.SraPicker(destination, parent=None, *, files=None)

Bases: PySide6.QtWidgets.QDialog

List the published runs, take a read limit, and fetch what is ticked.

Offer the published runs and download the ticked ones.

Parameters:

• destination – the folder downloads are written to.

• parent – parent widget.

• files – the runs to offer. None asks the index for them, so a test can supply a list without reaching the network.

chosen_files() → list

Every ticked run file.

max_reads()

The limit, or None for the whole file.

reject() → None

Cancel the picker, leaving whatever was chosen before untouched.