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Generate simulated reads¶

In brief¶

Simulate reads as a NanopolishComp like file from a fasta file and an inbuild model.

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Import the package and plotting tools¶

from nanocompore.SimReads import SimReads

# Ploting lib imports
import matplotlib.pyplot as pl
%matplotlib inline

Generate reads without modifications¶

SimReads (
    fasta_fn="./references/simulated/ref.fa",
    ref_list=["ref_0000"],
    outpath="./results/",
    overwrite="True",
    plot=True,
    nreads_per_ref=100)

2020-12-08 11:20:48.610 | INFO     | nanocompore.SimReads:SimReads:90 - Checking and initialising Simreads
2020-12-08 11:20:48.613 | DEBUG    | nanocompore.common:log_init_state:50 -     package_name: nanocompore
2020-12-08 11:20:48.615 | DEBUG    | nanocompore.common:log_init_state:51 -     package_version: 1.0.1.dev0
2020-12-08 11:20:48.619 | DEBUG    | nanocompore.common:log_init_state:52 -     timestamp: 2020-12-08 11:20:48.619541
2020-12-08 11:20:48.620 | DEBUG    | nanocompore.common:log_init_state:55 -     fasta_fn: ./references/simulated/ref.fa
2020-12-08 11:20:48.622 | DEBUG    | nanocompore.common:log_init_state:55 -     outpath: ./results/
2020-12-08 11:20:48.623 | DEBUG    | nanocompore.common:log_init_state:55 -     outprefix: out
2020-12-08 11:20:48.625 | DEBUG    | nanocompore.common:log_init_state:55 -     overwrite: True
2020-12-08 11:20:48.626 | DEBUG    | nanocompore.common:log_init_state:55 -     run_type: RNA
2020-12-08 11:20:48.627 | DEBUG    | nanocompore.common:log_init_state:55 -     ref_list: ['ref_0000']
2020-12-08 11:20:48.628 | DEBUG    | nanocompore.common:log_init_state:55 -     nreads_per_ref: 100
2020-12-08 11:20:48.639 | DEBUG    | nanocompore.common:log_init_state:55 -     plot: True
2020-12-08 11:20:48.641 | DEBUG    | nanocompore.common:log_init_state:55 -     intensity_mod: 0
2020-12-08 11:20:48.642 | DEBUG    | nanocompore.common:log_init_state:55 -     dwell_mod: 0
2020-12-08 11:20:48.644 | DEBUG    | nanocompore.common:log_init_state:55 -     mod_reads_freq: 0
2020-12-08 11:20:48.646 | DEBUG    | nanocompore.common:log_init_state:55 -     mod_bases_freq: 0.25
2020-12-08 11:20:48.647 | DEBUG    | nanocompore.common:log_init_state:55 -     mod_bases_type: A
2020-12-08 11:20:48.649 | DEBUG    | nanocompore.common:log_init_state:55 -     mod_extend_context: 2
2020-12-08 11:20:48.650 | DEBUG    | nanocompore.common:log_init_state:55 -     min_mod_dist: 6
2020-12-08 11:20:48.651 | DEBUG    | nanocompore.common:log_init_state:55 -     pos_rand_seed: 42
2020-12-08 11:20:48.652 | DEBUG    | nanocompore.common:log_init_state:55 -     not_bound: False
2020-12-08 11:20:48.653 | DEBUG    | nanocompore.common:log_init_state:55 -     progress: False
2020-12-08 11:20:48.655 | INFO     | nanocompore.SimReads:SimReads:101 - Importing RNA model file
2020-12-08 11:20:48.682 | INFO     | nanocompore.SimReads:SimReads:108 - Reading Fasta file and simulate corresponding data
2020-12-08 11:20:48.686 | DEBUG    | nanocompore.SimReads:SimReads:126 - Processing reference ref_0000

SimReads (
    fasta_fn="./references/simulated/ref.fa",
    ref_list=["ref_0000"],
    outpath="./results/",
    overwrite="True",
    plot=True,
    mod_extend_context=3,
    nreads_per_ref=100,
    intensity_mod=5,
    dwell_mod=5,
    mod_reads_freq=0.5)

2020-12-08 11:20:55.001 | INFO     | nanocompore.SimReads:SimReads:90 - Checking and initialising Simreads
2020-12-08 11:20:55.005 | DEBUG    | nanocompore.common:log_init_state:50 -     package_name: nanocompore
2020-12-08 11:20:55.006 | DEBUG    | nanocompore.common:log_init_state:51 -     package_version: 1.0.1.dev0
2020-12-08 11:20:55.008 | DEBUG    | nanocompore.common:log_init_state:52 -     timestamp: 2020-12-08 11:20:55.008532
2020-12-08 11:20:55.009 | DEBUG    | nanocompore.common:log_init_state:55 -     fasta_fn: ./references/simulated/ref.fa
2020-12-08 11:20:55.010 | DEBUG    | nanocompore.common:log_init_state:55 -     outpath: ./results/
2020-12-08 11:20:55.011 | DEBUG    | nanocompore.common:log_init_state:55 -     outprefix: out
2020-12-08 11:20:55.012 | DEBUG    | nanocompore.common:log_init_state:55 -     overwrite: True
2020-12-08 11:20:55.013 | DEBUG    | nanocompore.common:log_init_state:55 -     run_type: RNA
2020-12-08 11:20:55.013 | DEBUG    | nanocompore.common:log_init_state:55 -     ref_list: ['ref_0000']
2020-12-08 11:20:55.014 | DEBUG    | nanocompore.common:log_init_state:55 -     nreads_per_ref: 100
2020-12-08 11:20:55.015 | DEBUG    | nanocompore.common:log_init_state:55 -     plot: True
2020-12-08 11:20:55.017 | DEBUG    | nanocompore.common:log_init_state:55 -     intensity_mod: 5
2020-12-08 11:20:55.018 | DEBUG    | nanocompore.common:log_init_state:55 -     dwell_mod: 5
2020-12-08 11:20:55.020 | DEBUG    | nanocompore.common:log_init_state:55 -     mod_reads_freq: 0.5
2020-12-08 11:20:55.021 | DEBUG    | nanocompore.common:log_init_state:55 -     mod_bases_freq: 0.25
2020-12-08 11:20:55.023 | DEBUG    | nanocompore.common:log_init_state:55 -     mod_bases_type: A
2020-12-08 11:20:55.025 | DEBUG    | nanocompore.common:log_init_state:55 -     mod_extend_context: 3
2020-12-08 11:20:55.026 | DEBUG    | nanocompore.common:log_init_state:55 -     min_mod_dist: 6
2020-12-08 11:20:55.027 | DEBUG    | nanocompore.common:log_init_state:55 -     pos_rand_seed: 42
2020-12-08 11:20:55.028 | DEBUG    | nanocompore.common:log_init_state:55 -     not_bound: False
2020-12-08 11:20:55.029 | DEBUG    | nanocompore.common:log_init_state:55 -     progress: False
2020-12-08 11:20:55.030 | INFO     | nanocompore.SimReads:SimReads:101 - Importing RNA model file
2020-12-08 11:20:55.051 | INFO     | nanocompore.SimReads:SimReads:108 - Reading Fasta file and simulate corresponding data
2020-12-08 11:20:55.053 | DEBUG    | nanocompore.SimReads:SimReads:126 - Processing reference ref_0000
2020-12-08 11:20:55.383 | DEBUG    | nanocompore.SimReads:find_valid_pos_list:293 -     Try to find 15 kmers to modify
2020-12-08 11:20:55.415 | DEBUG    | nanocompore.SimReads:find_valid_pos_list:301 -     Found valid combination for 15 kmers
2020-12-08 11:20:55.416 | DEBUG    | nanocompore.SimReads:find_valid_pos_list:302 -     modified positions: [  0  11  20  31  71  88 103 110 122 128 150 169 176 184 194]