at the Train HMM step I am getting the following warnings/errors:
**Use global TMM approach
Compute HMM's training set
Train HMM**
mambaforge/envs/rgts/lib/python3.7/site-packages/rgt/THOR/neg_bin_rep_hmm.py:295: PendingDeprecationWarning: the matrix subclass is not the recommended way to represent matrices or deal with linear algebra (see https://docs.scipy.org/doc/numpy/user/numpy-for-matlab-users.html). Please adjust your code to use regular ndarray.
self.alpha = np.matrix([[self.get_alpha(m) for m in np.asarray(self.mu[i])[0]] for i in range(self.n_features)])
mambaforge/envs/rgts/lib/python3.7/site-packages/rgt/THOR/neg_bin_rep_hmm.py:159: PendingDeprecationWarning: the matrix subclass is not the recommended way to represent matrices or deal with linear algebra (see https://docs.scipy.org/doc/numpy/user/numpy-for-matlab-users.html). Please adjust your code to use regular ndarray.
self.neg_distr = np.matrix([raw1, raw2]) #matrix of all Neg. Bin. Distributions, columns=HMM's state (3), row=#samples (2)
Compute HMM's posterior probabilities and Viterbi path to call differential peaks
- taking into account chr1
mambaforge/envs/rgts/lib/python3.7/site-packages/rgt/THOR/MultiCoverageSet.py:164: PendingDeprecationWarning: the matrix subclass is not the recommended way to represent matrices or deal with linear algebra (see https://docs.scipy.org/doc/numpy/user/numpy-for-matlab-users.html). Please adjust your code to use regular ndarray.
overall_coverage_strand = [[np.matrix(tmp2[0][0]), np.matrix(tmp2[0][1])],
mambaforge/envs/rgts/lib/python3.7/site-packages/rgt/THOR/MultiCoverageSet.py:165: PendingDeprecationWarning: the matrix subclass is not the recommended way to represent matrices or deal with linear algebra (see https://docs.scipy.org/doc/numpy/user/numpy-for-matlab-users.html). Please adjust your code to use regular ndarray.
[np.matrix(tmp2[1][0]), np.matrix(tmp2[0][1])]]
mambaforge/envs/rgts/lib/python3.7/site-packages/rgt/THOR/MultiCoverageSet.py:167: PendingDeprecationWarning: the matrix subclass is not the recommended way to represent matrices or deal with linear algebra (see https://docs.scipy.org/doc/numpy/user/numpy-for-matlab-users.html). Please adjust your code to use regular ndarray.
overall_coverage = [np.matrix(tmp[0]), np.matrix(tmp[1])]
**Compute HMM's posterior probabilities and Viterbi path to call differential peaks**
the following seem to be related to the bigwig as in #270
**wigToBigWig v 4** - Convert ascii format wig file (in fixedStep, variableStep
or bedGraph format) to binary big wig format.
usage:
wigToBigWig in.wig chrom.sizes out.bw
Where in.wig is in one of the ascii wiggle formats, but not including track lines
and chrom.sizes is two column: <chromosome name> <size in bases>
and out.bw is the output indexed big wig file.
Use the script: fetchChromSizes to obtain the actual chrom.sizes information
from UCSC, please do not make up a chrom sizes from your own information.
options:
-blockSize=N - Number of items to bundle in r-tree. Default 256
-itemsPerSlot=N - Number of data points bundled at lowest level. Default 1024
-clip - If set just issue warning messages rather than dying if wig
file contains items off end of chromosome.
-unc - If set, do not use compression.
-fixedSummaries - If set, use a predefined sequence of summary levels.
-keepAllChromosomes - If set, store all chromosomes in b-tree.
wigToBigWig v 4 - Convert ascii format wig file (in fixedStep, variableStep
or bedGraph format) to binary big wig format.
usage:
wigToBigWig in.wig chrom.sizes out.bw
Where in.wig is in one of the ascii wiggle formats, but not including track lines
and chrom.sizes is two column: <chromosome name> <size in bases>
and out.bw is the output indexed big wig file.
Use the script: fetchChromSizes to obtain the actual chrom.sizes information
from UCSC, please do not make up a chrom sizes from your own information.
options:
-blockSize=N - Number of items to bundle in r-tree. Default 256
-itemsPerSlot=N - Number of data points bundled at lowest level. Default 1024
-clip - If set just issue warning messages rather than dying if wig
file contains items off end of chromosome.
-unc - If set, do not use compression.
-fixedSummaries - If set, use a predefined sequence of summary levels.
-keepAllChromosomes - If set, store all chromosomes in b-tree.
wigToBigWig v 4 - Convert ascii format wig file (in fixedStep, variableStep
or bedGraph format) to binary big wig format.
usage:
wigToBigWig in.wig chrom.sizes out.bw
Where in.wig is in one of the ascii wiggle formats, but not including track lines
and chrom.sizes is two column: <chromosome name> <size in bases>
and out.bw is the output indexed big wig file.
Use the script: fetchChromSizes to obtain the actual chrom.sizes information
from UCSC, please do not make up a chrom sizes from your own information.
options:
-blockSize=N - Number of items to bundle in r-tree. Default 256
-itemsPerSlot=N - Number of data points bundled at lowest level. Default 1024
-clip - If set just issue warning messages rather than dying if wig
file contains items off end of chromosome.
-unc - If set, do not use compression.
-fixedSummaries - If set, use a predefined sequence of summary levels.
-keepAllChromosomes - If set, store all chromosomes in b-tree.
wigToBigWig v 4 - Convert ascii format wig file (in fixedStep, variableStep
or bedGraph format) to binary big wig format.
usage:
wigToBigWig in.wig chrom.sizes out.bw
Where in.wig is in one of the ascii wiggle formats, but not including track lines
and chrom.sizes is two column: <chromosome name> <size in bases>
and out.bw is the output indexed big wig file.
Use the script: fetchChromSizes to obtain the actual chrom.sizes information
from UCSC, please do not make up a chrom sizes from your own information.
options:
-blockSize=N - Number of items to bundle in r-tree. Default 256
-itemsPerSlot=N - Number of data points bundled at lowest level. Default 1024
-clip - If set just issue warning messages rather than dying if wig
file contains items off end of chromosome.
-unc - If set, do not use compression.
-fixedSummaries - If set, use a predefined sequence of summary levels.
-keepAllChromosomes - If set, store all chromosomes in b-tree.
wigToBigWig v 4 - Convert ascii format wig file (in fixedStep, variableStep
or bedGraph format) to binary big wig format.
usage:
wigToBigWig in.wig chrom.sizes out.bw
Where in.wig is in one of the ascii wiggle formats, but not including track lines
and chrom.sizes is two column: <chromosome name> <size in bases>
and out.bw is the output indexed big wig file.
Use the script: fetchChromSizes to obtain the actual chrom.sizes information
from UCSC, please do not make up a chrom sizes from your own information.
options:
-blockSize=N - Number of items to bundle in r-tree. Default 256
-itemsPerSlot=N - Number of data points bundled at lowest level. Default 1024
-clip - If set just issue warning messages rather than dying if wig
file contains items off end of chromosome.
-unc - If set, do not use compression.
-fixedSummaries - If set, use a predefined sequence of summary levels.
-keepAllChromosomes - If set, store all chromosomes in b-tree.
wigToBigWig v 4 - Convert ascii format wig file (in fixedStep, variableStep
or bedGraph format) to binary big wig format.
usage:
wigToBigWig in.wig chrom.sizes out.bw
Where in.wig is in one of the ascii wiggle formats, but not including track lines
and chrom.sizes is two column: <chromosome name> <size in bases>
and out.bw is the output indexed big wig file.
Use the script: fetchChromSizes to obtain the actual chrom.sizes information
from UCSC, please do not make up a chrom sizes from your own information.
options:
-blockSize=N - Number of items to bundle in r-tree. Default 256
-itemsPerSlot=N - Number of data points bundled at lowest level. Default 1024
-clip - If set just issue warning messages rather than dying if wig
file contains items off end of chromosome.
-unc - If set, do not use compression.
-fixedSummaries - If set, use a predefined sequence of summary levels.
-keepAllChromosomes - If set, store all chromosomes in b-tree.
wigToBigWig v 4 - Convert ascii format wig file (in fixedStep, variableStep
or bedGraph format) to binary big wig format.
usage:
wigToBigWig in.wig chrom.sizes out.bw
Where in.wig is in one of the ascii wiggle formats, but not including track lines
and chrom.sizes is two column: <chromosome name> <size in bases>
and out.bw is the output indexed big wig file.
Use the script: fetchChromSizes to obtain the actual chrom.sizes information
from UCSC, please do not make up a chrom sizes from your own information.
options:
-blockSize=N - Number of items to bundle in r-tree. Default 256
-itemsPerSlot=N - Number of data points bundled at lowest level. Default 1024
-clip - If set just issue warning messages rather than dying if wig
file contains items off end of chromosome.
-unc - If set, do not use compression.
-fixedSummaries - If set, use a predefined sequence of summary levels.
-keepAllChromosomes - If set, store all chromosomes in b-tree.
wigToBigWig v 4 - Convert ascii format wig file (in fixedStep, variableStep
or bedGraph format) to binary big wig format.
usage:
wigToBigWig in.wig chrom.sizes out.bw
Where in.wig is in one of the ascii wiggle formats, but not including track lines
and chrom.sizes is two column: <chromosome name> <size in bases>
and out.bw is the output indexed big wig file.
Use the script: fetchChromSizes to obtain the actual chrom.sizes information
from UCSC, please do not make up a chrom sizes from your own information.
options:
-blockSize=N - Number of items to bundle in r-tree. Default 256
-itemsPerSlot=N - Number of data points bundled at lowest level. Default 1024
-clip - If set just issue warning messages rather than dying if wig
file contains items off end of chromosome.
-unc - If set, do not use compression.
-fixedSummaries - If set, use a predefined sequence of summary levels.
-keepAllChromosomes - If set, store all chromosomes in b-tree.
Hi all, as with #270 I created a mamba/conda environment as follows:
the python version is 3.7.12:
I am running rgt-THOR with the folloing command:
at the Train HMM step I am getting the following warnings/errors:
the following seem to be related to the bigwig as in #270
And this goes on for all chromosomes checked.