build the SUGP1 KD signature with splicedice
background, see [[run splicedice on SUGP1 KD signature with splicedice]] for splicedice steps through “pairwise”
raksha called these “reference” SRR12801019 SRR12801023
she called these “sample” SRR12801020 SRR12801024
connect to server
log into prism vpn ssh ubuntu@10.50.100.135
cd /mnt/code/dennisrm_splicedice
git clone https://github.com/dennisrm/splicedice.git
sig=/mnt/code/dennisrm_splicedice/splicedice/code/signature.py
cd /mnt/code/rakshya_RBPSig
git clone https://github.com/codewithrakshya/RBPSig
cd /mnt/code/rakshya_RBPSig/RBPSig
python ./filter_data.py --output-prefix /mnt/output/splicedice_2024.12.19_23.40.49/
iterating
python3 ./filter_data.py --output-prefix /mnt/output/splicedice_2024.12.19_23.40.49/
pip3 install pandas
sudo apt install python3-pandas
sudo apt install python3-argparse
python3 ./filter_data.py --output-prefix /mnt/output/splicedice_2024.12.19_23.40.49/
python3 ./filter_data.hcb.py --output-prefix /mnt/output/splicedice_2024.12.19_23.40.49/
errors addressed
Traceback (most recent call last):
File "/mnt/code/rakshya_RBPSig/RBPSig/./filter_data.py", line 10, in <module>
import pandas as pd
ModuleNotFoundError: No module named 'pandas'
ubuntu@hbeale-mesa:/mnt/code/rakshya_RBPSig/RBPSig$ pip3 install pandas
error: externally-managed-environment
× This environment is externally managed
╰─> To install Python packages system-wide, try apt install
python3-xyz, where xyz is the package you are trying to
install.
cp ./filter_data.py ./filter_data.hcb.py
nano ./filter_data.hcb.py
# changed _pairwiseFisherResults.tsv to pairwise.tsv
copied ./filter_data.py to ./filter_data.hcb.py changed pairwiseFisher to pairwise
ran without error:
ubuntu@hbeale-mesa:/mnt/code/rakshya_RBPSig/RBPSig$ python3 ./filter_data.hcb.py --output-prefix /mnt/output/splicedice_2024.12.19_23.40.49/
Filtered data saved to /mnt/output/splicedice_2024.12.19_23.40.49/_filteredPairwiseResults.tsv
Filtered _allPS data saved to /mnt/output/splicedice_2024.12.19_23.40.49/_filteredAllPS.tsv
signature.py
attempt 1
cd /mnt/output/splicedice_2024.12.19_23.40.49
python3 /mnt/code/dennisrm_splicedice/splicedice/code/signature.py \
fit_beta \
-x significance_threshold=0.05 \
-p /mnt/output/splicedice_2024.12.19_23.40.49/_filteredAllPS.tsv \
-n 10 \
-m /mnt/output/splicedice_2024.12.19_23.40.49/_manifest.txt \
-o test
ModuleNotFoundError: No module named 'statsmodels'
sudo apt install python3-statsmodels
consider also numpy scipy.stats
tools warnings config
attempt 2
cd /mnt/output/splicedice_2024.12.19_23.40.49
python3 /mnt/code/dennisrm_splicedice/splicedice/code/signature.py \
fit_beta \
-x significance_threshold=0.05 \
-p /mnt/output/splicedice_2024.12.19_23.40.49/_filteredAllPS.tsv \
-n 10 \
-m /mnt/output/splicedice_2024.12.19_23.40.49/_manifest.txt \
-o test
error when no sig intervals
ubuntu@hbeale-mesa:/mnt/output/splicedice_2024.12.19_23.40.49$ python3 /mnt/code/dennisrm_splicedice/splicedice/code/signature.py fit_beta -x significance_threshold=0.05 -p /mnt/output/splicedice_2024.12.19_23.40.49/_filteredAllPS.tsv -n 10 -m /mnt/output/splicedice_2024.12.19_23.40.49/_manifest.txt -o test
significance_threshold=0.05
try
Testing for differential splicing...
Groups: /mnt/output/splicedice_2024.12.19_23.40.49/_junction_beds/SRR12801019_Aligned.sortedByCoord.out.junc.bed (1), /mnt/output/splicedice_2024.12.19_23.40.49/_junction_beds/SRR12801020_Aligned.sortedByCoord.out.junc.bed (1), /mnt/output/splicedice_2024.12.19_23.40.49/_junction_beds/SRR12801023_Aligned.sortedByCoord.out.junc.bed (1), /mnt/output/splicedice_2024.12.19_23.40.49/_junction_beds/SRR12801024_Aligned.sortedByCoord.out.junc.bed (1)
Fitting beta distributions...
Traceback (most recent call last):
File "/mnt/code/dennisrm_splicedice/splicedice/code/signature.py", line 425, in <module>
main()
File "/mnt/code/dennisrm_splicedice/splicedice/code/signature.py", line 87, in main
beta_stats = manifest.fit_betas(ps_table,compare_stats)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/mnt/code/dennisrm_splicedice/splicedice/code/signature.py", line 328, in fit_betas
interval_set = self.significant_intervals(compare_stats)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/mnt/code/dennisrm_splicedice/splicedice/code/signature.py", line 303, in significant_intervals
for i in range(m): # error when no sig intervals
^
UnboundLocalError: cannot access local variable 'm' where it is not associated with a value
ubuntu@hbeale-mesa:/mnt/output/splicedice_2024.12.19_23.40.49$
review input
/mnt/output/splicedice_2024.12.19_23.40.49/_filteredAllPS.tsv - looks fine; there are differences
16:16317777-16317895:+ 0.726 0.432 0.736 0.408
16:16317777-16318922:+ 0.024 0.145 0.011 0.16
16:16317777-16358956:+ 0.0 0.003 0.0 0.003
fix manifest
i think the problem is the manifest. it should be a new one something like this SRR12801019 Reference SRR12801023 Reference SRR12801020 Sample SRR12801024 Sample
help="TSV file with list of samples (first column) and group labels (second column).")
A19 A20 A23 A24
cd /mnt/output/splicedice_2024.12.19_23.40.49
cp /mnt/code/rakshya_RBPSig/RBPSig/manifest.txt signature_manifest.txt
nano signature_manifest.txt
A19 control
A23 control
A20 SUGP1_knockdown
A24 SUGP1_knockdown
attempt 3
cd /mnt/output/splicedice_2024.12.19_23.40.49
python3 /mnt/code/dennisrm_splicedice/splicedice/code/signature.py \
fit_beta \
-x significance_threshold=0.05 \
-p /mnt/output/splicedice_2024.12.19_23.40.49/_filteredAllPS.tsv \
-n 10 \
-m /mnt/output/splicedice_2024.12.19_23.40.49/signature_manifest.txt \
-o test
ubuntu@hbeale-mesa:/mnt/output/splicedice_2024.12.19_23.40.49$ cd /mnt/output/splicedice_2024.12.19_23.40.49
python3 /mnt/code/dennisrm_splicedice/splicedice/code/signature.py \
fit_beta \
-x significance_threshold=0.05 \
-p /mnt/output/splicedice_2024.12.19_23.40.49/_filteredAllPS.tsv \
-n 10 \
-m /mnt/output/splicedice_2024.12.19_23.40.49/signature_manifest.txt \
-o test
significance_threshold=0.05
try
Testing for differential splicing...
Groups: control (2), SUGP1_knockdown (2)
Fitting beta distributions...
Traceback (most recent call last):
File "/mnt/code/dennisrm_splicedice/splicedice/code/signature.py", line 425, in <module>
main()
File "/mnt/code/dennisrm_splicedice/splicedice/code/signature.py", line 87, in main
beta_stats = manifest.fit_betas(ps_table,compare_stats)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/mnt/code/dennisrm_splicedice/splicedice/code/signature.py", line 328, in fit_betas
interval_set = self.significant_intervals(compare_stats)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/mnt/code/dennisrm_splicedice/splicedice/code/signature.py", line 303, in significant_intervals
for i in range(m): # error when no sig intervals
^
UnboundLocalError: cannot access local variable 'm' where it is not associated with a value
ubuntu@hbeale-mesa:/mnt/output/splicedice_2024.12.19_23.40.49$