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nanoporetech / scrappie

Scrappie is a technology demonstrator for the Oxford Nanopore Research Algorithms group
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Is the scrappy.sequence_to_squiggle in python package serve the same purpose with scrappie squiggle? #32

Closed youyupei closed 5 years ago

youyupei commented 5 years ago

Hi, I am trying to use scrappie squiggle in python, so I install the python package. And I use the function scrappy.sequence_to_squiggle and try to get the same kind of result as scrappie squiggle. This is an example how I use the function:

from scrappy import sequence_to_squiggle test = sequence_to_squiggle("AGGCTAGCTAGCT") test.data(as_numpy=True)

here is the output:

array([[ 0.4144024 , -0.15585916, -1.04943931], [-0.53396642, -0.86973035, -1.28983688], [-1.26228642, -0.67319959, -1.52632558], [-1.71305275, 0.49441418, -2.06113482], [-1.91647649, 0.90141028, -1.77614355], [-1.98690426, -0.42909694, -1.97921693], [-2.25099683, -0.52559912, -2.09264708], [-1.9385221 , 0.68139863, -2.02308011], [-2.29804611, 0.95261008, -1.67299831], [-2.39523888, -0.42203459, -1.7581104 ], [-2.39827061, -0.62816602, -1.52443683], [-2.74950981, 0.41811785, -1.10415864], [-2.69527769, 0.20119289, -0.65440667]], dtype=float32)

It doesn't look like a same output that scrappie squiggle provides. May I ask what is the correct way to simulate a sequence inside python?

cjw85 commented 5 years ago

A example of using these data to create a squiggle can be found here: https://github.com/nanoporetech/pomoxis/blob/master/pomoxis/common/simulate_calls.py#L15

That code will also immediately basecall the simulated squiggle.

Note that there is an updated implementation of squiggle simulation in taiyaki.

youyupei commented 5 years ago

Thanks very much, problem solved. A small question about the squiggle simulation in taiyaki. It is more recommended over scrappie squiggle? Thanks again for your help!!

cjw85 commented 5 years ago

The taiyaki code is certainly more actively maintained, and in at least that sense preferred.

cmar0027 commented 2 years ago

1.04943931

I'm facing the same problem as @youyupei, but unfortunately this link https://github.com/nanoporetech/pomoxis/blob/master/pomoxis/common/simulate_calls.py#L15 is dead and I couldn't find simulate_calls.py neither in https://github.com/nanoporetech/pomoxis nor in its commit history. Would it it be possible to have a new working link?

youyupei commented 2 years ago

1.04943931

I'm facing the same problem as @youyupei, but unfortunately this link https://github.com/nanoporetech/pomoxis/blob/master/pomoxis/common/simulate_calls.py#L15 is dead and I couldn't find simulate_calls.py neither in https://github.com/nanoporetech/pomoxis nor in its commit history. Would it it be possible to have a new working link?

I guess the script has been moved to the dev branch: https://github.com/nanoporetech/pomoxis/blob/dev/pomoxis/common/simulate_calls.py#L15