Motif-mark searches for and maps the positions of transcription factor binding motifs along gene sequences in input FASTA files. The Python script in this repo, motif-mark-oop.py, takes in at least one FASTA file (including those where each sequence is split across multiple lines rather than all being on one line) and at least one text file of motifs to be searched for, where each motif is on a new line.
For each input FASTA file, the script outputs a one-line sequence version of the FASTA file, along with a PNG image file depicting relative positions of motifs along each gene sequence in the FASTA file. Each output PNG image depicts genes going left to right from 5'->3' and also denotes intron and exon positions. Moreover, each gene in an output PNG image is preceded by a text label that includes the gene name, the chromosome on which the gene is located (denoted by "chr"), and the start and stop positions of the gene along that chromosome (denoted by "pos:").
For best results, make sure you are using Python 3.9 or higher and are in a Linux- or Unix-based environment.
Create a Conda environment called motif_mark that uses Python 3.9 and install the following packages in it:
pycairo (version 1.19.1)
seaborn (version 0.11.2)
Then, make sure the following packages and versions are also included in the Conda environment:
# Name Version Build Channel
appnope 0.1.2 py39h6e9494a_2 conda-forge
asttokens 2.0.5 pyhd8ed1ab_0 conda-forge
backcall 0.2.0 pyh9f0ad1d_0 conda-forge
backports 1.0 py_2 conda-forge
backports.functools_lru_cache 1.6.4 pyhd8ed1ab_0 conda-forge
black 22.1.0 pyhd8ed1ab_0 conda-forge
blas 1.0 mkl
bottleneck 1.3.2 py39he3068b8_1
brotli 1.0.9 hb1e8313_2
ca-certificates 2022.2.1 hecd8cb5_0
cairo 1.16.0 h8023c5d_1
certifi 2021.10.8 py39hecd8cb5_2
click 8.0.3 py39h6e9494a_1 conda-forge
cycler 0.11.0 pyhd3eb1b0_0
dataclasses 0.8 pyhc8e2a94_3 conda-forge
debugpy 1.5.1 py39h9fcab8e_0 conda-forge
decorator 5.1.1 pyhd8ed1ab_0 conda-forge
entrypoints 0.4 pyhd8ed1ab_0 conda-forge
executing 0.8.2 pyhd8ed1ab_0 conda-forge
fontconfig 2.13.1 ha9ee91d_0
fonttools 4.25.0 pyhd3eb1b0_0
freetype 2.11.0 hd8bbffd_0
gettext 0.21.0 h7535e17_0
giflib 5.2.1 haf1e3a3_0
glib 2.69.1 h8346a28_1
icu 58.2 h0a44026_3
intel-openmp 2021.4.0 hecd8cb5_3538
ipykernel 6.9.0 py39h71a6800_0 conda-forge
ipython 8.0.1 py39h6e9494a_0 conda-forge
jedi 0.18.1 py39h6e9494a_0 conda-forge
jpeg 9d h9ed2024_0
jupyter_client 7.1.2 pyhd8ed1ab_0 conda-forge
jupyter_core 4.9.1 py39h6e9494a_1 conda-forge
kiwisolver 1.3.2 py39he9d5cce_0
lcms2 2.12 hf1fd2bf_0
libcxx 12.0.0 h2f01273_0
libffi 3.3 hb1e8313_2
libgfortran 3.0.1 h93005f0_2
libiconv 1.16 h1de35cc_0
libpng 1.6.37 ha441bb4_0
libsodium 1.0.18 hbcb3906_1 conda-forge
libtiff 4.2.0 h87d7836_0
libwebp 1.2.2 h56c3ce4_0
libwebp-base 1.2.2 hca72f7f_0
libxml2 2.9.12 hcdb78fc_0
llvm-openmp 12.0.0 h0dcd299_1
lz4-c 1.9.3 h23ab428_1
matplotlib 3.5.1 py39hecd8cb5_0
matplotlib-base 3.5.1 py39hfb0c5b7_0
matplotlib-inline 0.1.3 pyhd8ed1ab_0 conda-forge
mkl 2021.4.0 hecd8cb5_637
mkl-service 2.4.0 py39h9ed2024_0
mkl_fft 1.3.1 py39h4ab4a9b_0
mkl_random 1.2.2 py39hb2f4e1b_0
munkres 1.1.4 py_0
mypy_extensions 0.4.3 py39h6e9494a_4 conda-forge
ncurses 6.3 hca72f7f_2
nest-asyncio 1.5.4 pyhd8ed1ab_0 conda-forge
numexpr 2.8.1 py39h2e5f0a9_0
numpy 1.21.2 py39h4b4dc7a_0
numpy-base 1.21.2 py39he0bd621_0
olefile 0.46 pyhd3eb1b0_0
openssl 1.1.1m hca72f7f_0
packaging 21.3 pyhd3eb1b0_0
pandas 1.4.1 py39he9d5cce_0
parso 0.8.3 pyhd8ed1ab_0 conda-forge
pathspec 0.9.0 pyhd8ed1ab_0 conda-forge
pcre 8.45 h23ab428_0
pexpect 4.8.0 pyh9f0ad1d_2 conda-forge
pickleshare 0.7.5 py_1003 conda-forge
pillow 8.4.0 py39h98e4679_0
pip 21.2.4 py39hecd8cb5_0
pixman 0.40.0 h9ed2024_1
platformdirs 2.5.0 pyhd8ed1ab_0 conda-forge
prompt-toolkit 3.0.27 pyha770c72_0 conda-forge
ptyprocess 0.7.0 pyhd3deb0d_0 conda-forge
pure_eval 0.2.2 pyhd8ed1ab_0 conda-forge
pycairo 1.19.1 py39h06c6e95_0
pygments 2.11.2 pyhd8ed1ab_0 conda-forge
pyparsing 3.0.4 pyhd3eb1b0_0
python 3.9.7 h88f2d9e_1
python-dateutil 2.8.2 pyhd8ed1ab_0 conda-forge
python_abi 3.9 2_cp39 conda-forge
pytz 2021.3 pyhd3eb1b0_0
pyzmq 22.3.0 py39h7fec2f1_1 conda-forge
readline 8.1.2 hca72f7f_1
scipy 1.7.3 py39h8c7af03_0
seaborn 0.11.2 pyhd3eb1b0_0
setuptools 58.0.4 py39hecd8cb5_0
six 1.16.0 pyh6c4a22f_0 conda-forge
sqlite 3.37.2 h707629a_0
stack_data 0.2.0 pyhd8ed1ab_0 conda-forge
tk 8.6.11 h7bc2e8c_0
tomli 2.0.1 pyhd8ed1ab_0 conda-forge
tornado 6.1 py39h89e85a6_2 conda-forge
traitlets 5.1.1 pyhd8ed1ab_0 conda-forge
typed-ast 1.5.2 py39h89e85a6_0 conda-forge
typing_extensions 4.1.1 pyha770c72_0 conda-forge
tzdata 2021e hda174b7_0
wcwidth 0.2.5 pyh9f0ad1d_2 conda-forge
wheel 0.37.1 pyhd3eb1b0_0
xz 5.2.5 h1de35cc_0
zeromq 4.3.4 he49afe7_1 conda-forge
zlib 1.2.11 h4dc903c_4
zstd 1.4.9 h322a384_0
For convenience, a wrapper shell script (motif-mark_wrapper.sh) is included in this repo. The shell script includes information about what Conda environment to activate, as well as information about filepaths and filenames of desired input files. The input file info in this shell script can be changed according to the files you would like to input into the motif-mark-oop.py script. Once the desired input filepaths and filenames are specified, run the wrapper script on the command line with the following command:
bash motif-mark_wrapper.sh
Alternatively, if you would like to run the motif-mark-oop.py script directly without a wrapper, you can also manually specify input filepaths on the command line when executing the Python script:
#activate the motif_mark Conda environment
conda activate motif_mark
#execute the python script
python motif-mark-oop.py -f $input_fasta_filepath -m $input_motif_filepath