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@Alexander-Mitrofanov
Alexander-Mitrofanov committed Jul 3, 2023
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18 changes: 16 additions & 2 deletions README.md
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Expand Up @@ -36,14 +36,28 @@ Then Miniconda should be installed. On a linux machine the command is similar to
bash Miniconda3-latest-Linux-x86_64.sh
```

Then we create an environment. The necessary setup is provided in the "environment.yml" file inside the "for_environment" directory
Then we create an environment. The necessary setup is provided in the "environment.yml" file.

In order to install the corresponding environment one can execute the following command from the "for_environment" directory
In order to install the corresponding environment one can execute the following command.

```
conda env create -f environment.yml
```

We recommend to install mamba package manager which is a faster alternative to conda.

```
conda install -c conda-forge mamba
```

Then we can create the environment using mamba.
```
mamba env create -f environment.yml
```

<sub><sub>We want to acknowledge Richard Stöckl @richardstoeckl for his contribution to the environment.yml file.</sub></sub>


### Additional preparations

CRISPRidentify utilizes CRISPRcasIdentifier for the detection of the cas genes.
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42 changes: 21 additions & 21 deletions components/module_non_array_computations.py
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Expand Up @@ -166,29 +166,29 @@ def _group_by_output_separated(allowed_intervals, regular_clusters):

self.cas_results = dict_groups


def _calculate_strand(self):
if self.flags_non_arrays_computations["flag_strand"]:
try:
st = StrandComputationNew(list_of_crisprs=self.list_of_crisprs_bona_fide,
absolute_directory_path=self.absolute_directory_path)
self.strand_results["Bona-fide"] = st.output()
st = StrandComputationNew(list_of_crisprs=self.list_of_crisprs_alternative,
absolute_directory_path=self.absolute_directory_path)
self.strand_results["Alternative"] = st.output()
st = StrandComputationNew(list_of_crisprs=self.list_of_crisprs_possible,
absolute_directory_path=self.absolute_directory_path)
self.strand_results["Possible"] = st.output()
except Exception:
st = StrandComputation(list_of_crisprs=self.list_of_crisprs_bona_fide,
absolute_directory_path=self.absolute_directory_path)
self.strand_results["Bona-fide"] = st.output()
st = StrandComputation(list_of_crisprs=self.list_of_crisprs_alternative,
absolute_directory_path=self.absolute_directory_path)
self.strand_results["Alternative"] = st.output()
st = StrandComputation(list_of_crisprs=self.list_of_crisprs_possible,
absolute_directory_path=self.absolute_directory_path)
self.strand_results["Possible"] = st.output()
st = StrandComputationNew(list_of_crisprs=self.list_of_crisprs_bona_fide,
absolute_directory_path=self.absolute_directory_path)
self.strand_results["Bona-fide"] = st.output()
st = StrandComputationNew(list_of_crisprs=self.list_of_crisprs_alternative,
absolute_directory_path=self.absolute_directory_path)
self.strand_results["Alternative"] = st.output()
st = StrandComputationNew(list_of_crisprs=self.list_of_crisprs_possible,
absolute_directory_path=self.absolute_directory_path)
self.strand_results["Possible"] = st.output()


#except Exception:
# st = StrandComputation(list_of_crisprs=self.list_of_crisprs_bona_fide,
# absolute_directory_path=self.absolute_directory_path)
# self.strand_results["Bona-fide"] = st.output()
# st = StrandComputation(list_of_crisprs=self.list_of_crisprs_alternative,
# absolute_directory_path=self.absolute_directory_path)
# self.strand_results["Alternative"] = st.output()
# st = StrandComputation(list_of_crisprs=self.list_of_crisprs_possible,
# absolute_directory_path=self.absolute_directory_path)
# self.strand_results["Possible"] = st.output()
else:
self.strand_results["Bona-fide"] = {index: "Forward (Orientation was not computed)"
for index in range(len(self.list_of_crisprs_bona_fide))}
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194 changes: 45 additions & 149 deletions environment.yml
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@@ -1,155 +1,51 @@
name: crispr_identify_env
channels:
- bioconda
- biobuilds
- bioconda/label/cf201901
- anaconda
- conda-forge
- bioconda
- defaults
- biobuilds
- bioconda/label/cf201901
- r
dependencies:
- _libgcc_mutex=0.1=conda_forge
- _openmp_mutex=4.5=1_gnu
- _py-xgboost-mutex=2.0=cpu_0
- _tflow_select=2.3.0=eigen
- absl-py=0.11.0=py37h06a4308_0
- aiohttp=3.6.3=py37h7b6447c_0
- astunparse=1.6.3=py_0
- async-timeout=3.0.1=py37_0
- attrs=20.3.0=pyhd3eb1b0_0
- biopython=1.76=py37h516909a_0
- blast=2.5.0=hc0b0e79_3
- blinker=1.4=py37_0
- boost=1.73.0=py37h06a4308_11
- brotlipy=0.7.0=py37hb5d75c8_1001
- bzip2=1.0.8=h7b6447c_0
- c-ares=1.17.1=h27cfd23_0
- ca-certificates=2021.5.25=h06a4308_1
- cachetools=4.1.1=py_0
- certifi=2021.5.30=py37h06a4308_0
- cffi=1.14.4=py37hc58025e_1
- chardet=3.0.4=py37he5f6b98_1008
- click=7.1.2=py_0
- clustalo=1.2.3=0
- cryptography=3.1=py37hb09aad4_0
- cycler=0.10.0=py_2
- dbus=1.13.6=he372182_0
- decorator=4.4.2=py_0
- dill=0.3.3=pyhd8ed1ab_0
- expat=2.2.9=he1b5a44_2
- fasta=36.3.8e=1
- fontconfig=2.13.1=he4413a7_1000
- freetype=2.10.2=he06d7ca_0
- gast=0.3.3=py_0
- glib=2.65.0=h3eb4bd4_0
- google-auth=1.23.0=pyhd3eb1b0_0
- google-auth-oauthlib=0.4.2=pyhd3eb1b0_2
- google-pasta=0.2.0=py_0
- grpcio=1.31.0=py37hf8bcb03_0
- gst-plugins-base=1.14.0=hbbd80ab_1
- gstreamer=1.14.0=hb31296c_0
- h5py=2.10.0=py37hd6299e0_1
- hdf5=1.10.6=hb1b8bf9_0
- hmmer=3.3.2=h1b792b2_1
- icu=58.2=hf484d3e_1000
- idna=2.10=pyh9f0ad1d_0
- importlib-metadata=2.0.0=py_1
- joblib=0.14.1=pyh9f0ad1d_0
- jpeg=9d=h516909a_0
- keras=2.4.3=0
- keras-base=2.4.3=py_0
- keras-preprocessing=1.1.0=py_1
- kiwisolver=1.2.0=py37h99015e2_0
- ld_impl_linux-64=2.34=hc38a660_9
- libblas=3.8.0=17_openblas
- libboost=1.73.0=h3ff78a5_11
- libcblas=3.8.0=17_openblas
- libffi=3.3=he6710b0_2
- libgcc=7.2.0=h69d50b8_2
- libgcc-ng=9.3.0=h24d8f2e_15
- libgfortran-ng=7.5.0=hdf63c60_15
- libgomp=9.3.0=h24d8f2e_15
- libiconv=1.15=h516909a_1006
- liblapack=3.8.0=17_openblas
- libopenblas=0.3.10=pthreads_hb3c22a3_4
- libpng=1.6.37=hed695b0_2
- libprotobuf=3.13.0.1=hd408876_0
- libstdcxx-ng=9.3.0=hdf63c60_15
- libuuid=2.32.1=h14c3975_1000
- libxcb=1.13=h14c3975_1002
- libxgboost=1.2.0=he1b5a44_0
- libxml2=2.9.9=h13577e0_2
- lz4-c=1.9.3=h2531618_0
- markdown=3.3.3=py37h06a4308_0
- matplotlib=3.1.3=py37_0
- matplotlib-base=3.1.3=py37hef1b27d_0
- multidict=4.7.6=py37h7b6447c_1
- ncurses=6.2=he1b5a44_1
- networkx=2.5=py_0
- numpy=1.18.1=py37h8960a57_1
- oauthlib=3.1.0=py_0
- openjdk=8.0.152=h7b6447c_3
- openssl=1.1.1k=h27cfd23_0
- opt_einsum=3.1.0=py_0
- pandas=1.0.3=py37h0da4684_1
- pcre=8.44=he1b5a44_0
- perl=5.26.2=h14c3975_0
- perl-bioperl=1.6.924=4
- perl-biox-seq=0.006007=pl526_1
- perl-compress-bgzf=0.005=pl526_0
- perl-file-which=1.23=pl526_0
- perl-threaded=5.26.0=0
- perl-yaml=1.29=pl526_0
- pip=20.2.2=py_0
- prodigal=2.6.3=1
- protobuf=3.13.0.1=py37he6710b0_1
- pthread-stubs=0.4=h14c3975_1001
- py-boost=1.73.0=py37ha9443f7_11
- py-xgboost=1.2.0=py37hc8dfbb8_0
- pyasn1=0.4.8=py_0
- pyasn1-modules=0.2.8=py_0
- pycparser=2.20=pyh9f0ad1d_2
- pyjwt=1.7.1=py37_0
- pyopenssl=19.1.0=py_1
- pyparsing=2.4.7=pyh9f0ad1d_0
- pyqt=5.9.2=py37hcca6a23_4
- pysocks=1.7.1=py37he5f6b98_2
- python=3.7.7=hcff3b4d_5
- python-dateutil=2.8.1=py_0
- python_abi=3.7=1_cp37m
- pytz=2020.1=pyh9f0ad1d_0
- pyyaml=5.3.1=py37h7b6447c_1
- qt=5.9.7=h5867ecd_1
- readline=8.0=he28a2e2_2
- regex=2019.03.09=py37h14c3975_0
- requests=2.25.0=pyhd3deb0d_0
- requests-oauthlib=1.3.0=py_0
- rsa=4.6=py_0
- scikit-learn=0.22.1=py37hcdab131_1
- scipy=1.4.1=py37ha3d9a3c_3
- setuptools=49.6.0=py37hc8dfbb8_0
- sip=4.19.8=py37hf484d3e_1000
- six=1.15.0=pyh9f0ad1d_0
- sqlite=3.32.3=h4cf870e_1
- tensorboard=2.3.0=pyh4dce500_0
- tensorboard-plugin-wit=1.6.0=py_0
- tensorflow=2.3.0=eigen_py37h189e6a2_0
- tensorflow-base=2.3.0=eigen_py37h3b305d7_0
- tensorflow-estimator=2.3.0=pyheb71bc4_0
- termcolor=1.1.0=py37_1
- tk=8.6.10=hed695b0_0
- tornado=6.0.4=py37h8f50634_1
- urllib3=1.25.11=py_0
- viennarna=2.4.18=py37hfecc14a_0
- vmatch=2.3.0=h779adbc_3
- werkzeug=1.0.1=py_0
- wheel=0.35.1=pyh9f0ad1d_0
- wrapt=1.12.1=py37h7b6447c_1
- xgboost=1.2.0=py37h3340039_0
- xorg-libxau=1.0.9=h14c3975_0
- xorg-libxdmcp=1.1.3=h516909a_0
- xz=5.2.5=h516909a_1
- yaml=0.2.5=h7b6447c_0
- yarl=1.6.2=py37h7b6447c_0
- zipp=3.4.0=pyhd3eb1b0_0
- zlib=1.2.11=h516909a_1007
- zstd=1.4.9=haebb681_0
- anaconda::_tflow_select=2.3.0
- biopython=1.76
- h5py=2.10.0
- hdf5=1.10.6
- hmmer=3.3
- numpy=1.18.1
- pandas=1.0.3
- matplotlib=3.1.3
- perl=5.26.2
- perl-compress-bgzf=0.005
- perl-threaded=5.26.0
- perl-yaml=1.29
- prodigal=2.6.3
- dill=0.3.3
- protobuf=3.13.0.1
- regex=2019.03.09
- pyasn1=0.4.8
- pycparser=2.20
- networkx=2.5
- pyjwt=1.7.1
- pyparsing=2.4.7
- pyqt=5.9.2
- pysocks=1.7.1
- python-dateutil=2.8.1
- python_abi=3.7
- pytz=2020.1
- pyyaml=5.3.1
- scikit-learn=0.22.1
- scipy=1.4.1
- anaconda::tensorboard=2.3.0
- anaconda::tensorboard-plugin-wit=1.6.0
- viennarna=2.4.15
- pyopenssl=22.0.0
- certifi=2022.12.7
- vmatch=2.3.0
- clustalo=1.2.3
- blast=2.5.0
- numpy=1.18.1
- keras=2.4.3
- anaconda::tensorflow=2.3.0
- libffi=3.3
2 changes: 1 addition & 1 deletion tools/strand_prediction/CRISPRstrand/utils.py
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@@ -1,5 +1,5 @@
import numpy as np
import matplotlib.pyplot as plt
#import matplotlib.pyplot as plt
from keras.models import load_model as lm

# =============================================================================
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