Goal

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Tasks

• [ ]

Required files

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# Imports
%matplotlib inline
%config InlineBackend.figure_format = 'retina'
from basepair.imports import *
hv.extension('bokeh')

Using TensorFlow backend.

from basepair.models import seq_bpnet_cropped_extra_seqlen

from basepair.layers import *

seq_bpnet_cropped_extra_seqlen(25, n_dil_layers=9, tconv_kernel_size=50, target_seqlen=1000)

3118

len_change_dense_dilated_valid_conv??

Signature: len_change_dense_dilated_valid_conv(conv1_kernel_size=25, n_dil_layers=6)
Source:   
def len_change_dense_dilated_valid_conv(conv1_kernel_size=25, n_dil_layers=6):
    """Compute length change"""
    d = 0

    # conv
    d -= 2 * (conv1_kernel_size // 2)
    for i in range(1, n_dil_layers + 1):
        dillation = 2**i
        d -= 2 * dillation
    return d
File:      ~/workspace/basepair/basepair/layers.py
Type:      function

seq_bpnet_cropped_extra_seqlen??

Signature:
seq_bpnet_cropped_extra_seqlen(
    ['conv1_kernel_size=21', 'n_dil_layers=6', 'tconv_kernel_size=25', 'target_seqlen=0', '**kwargs'],
)
Source:   
@gin.configurable
def seq_bpnet_cropped_extra_seqlen(conv1_kernel_size=21,
                                   n_dil_layers=6,
                                   tconv_kernel_size=25,
                                   target_seqlen=0,
                                   **kwargs):
    """Compute the extra sequence length required
    """
    from basepair.layers import len_change_dense_dilated_valid_conv, len_change_cropped_deconv_1d
    return target_seqlen + (- len_change_dense_dilated_valid_conv(conv1_kernel_size=conv1_kernel_size,
                                                                  n_dil_layers=n_dil_layers)
                            - len_change_cropped_deconv_1d(tconv_kernel_size=tconv_kernel_size))
File:      ~/workspace/basepair/basepair/models.py
Type:      function