Missing python libraries

[paulinefx]

Hello,

Now that I made spladder work, I am trying to run some analysis from these codes. I want to compare tumour and normal data to find cancer specific events.

I am trying to run the code compare_events_anno.gtex_subset.py but it calling python libraries utils, violin_plot, ExoressionData, and TCGA_colors that I cannot find in these github repository.

Thanks,

Pauline

[akahles]

Hi Pauline,

the code in this repository is the documentation of analyses that were carried out in the paper. It is not directly runnable within a new environment. For instance, it is based on an older version of SplAdder. I would recommend that any new anlyses are based on the current version.

Best, Andre

[paulinefx]

Hi Andre,

I ran SplAdder with newest version. But in itself, with a couple of twitching the scripts of the analysis of the paper should be able to run.

In this code pancanatlas_code_public/alt_splice/tumor_vs_normal_stats/compare_events_anno.gtex.py at line 10 till 30

sys.path.append('/cluster/home/akahles/git/projects/2013/PanCancerTCGA/rerun2017')
import utils.utils as utils
import utils.samples as samples
from utils.paths import paths

import matplotlib
matplotlib.use('Agg')
matplotlib.rcParams['lines.linewidth'] = 2
matplotlib.rcParams['axes.linewidth'] = 2
import matplotlib.pyplot as plt
import matplotlib.gridspec as gridspec

sys.path.append('/cluster/home/akahles/git/tools/python/viz') 
from distribution import violin_plot
from axes import *

sys.path.append('/cluster/home/akahles/git/tools/python/oop_libs')
from expression import ExpressionData

sys.path.append('/cluster/home/akahles/git/projects/2013/PanCancerTCGA/colors')
import TCGA_colors as tc

If I understand well, when you sys.path.append is to call some personal libraries ? Is there a new version of this ?

Best, Pauline

[akahles]

I see your point. I will try to make these scripts/tools available soon, if possible. I just have to get into contact with the other authors first.

Cheers, Andre

[mhjiang97]

Hello,

Now that I made spladder work, I am trying to run some analysis from these codes. I want to compare tumour and normal data to find cancer specific events.

I am trying to run the code compare_events_anno.gtex_subset.py but it calling python libraries utils, violin_plot, ExoressionData, and TCGA_colors that I cannot find in these github repository.

Thanks,

Pauline

Hi, Paulinefx. I am confused about how to figure out if an alternative splicing in the spladder output files is an annotated one in user-provided gtf. Do you have any idea about this question? If I cannot directly know which alternative splicing event is already annotated from the spladder output files, what should I do to solve it? Thank you very much! I'm looking forward to your reply~

[mhjiang97]

Hello,

Now that I made spladder work, I am trying to run some analysis from these codes. I want to compare tumour and normal data to find cancer specific events.

I am trying to run the code compare_events_anno.gtex_subset.py but it calling python libraries utils, violin_plot, ExoressionData, and TCGA_colors that I cannot find in these github repository.

Thanks,

Pauline

I'm here again🤣. Could you tell me how to create a file like this using spladder? "merge_graphs_intron_retention_C2.anno_only.pickle" I found it in pancanatlas_code_public/alt_splice/event_stats_sub/plot_event_stats_tcga.py

### load annotation index
is_anno_tcga = cPickle.load(open(os.path.join(paths.basedir_as_sub, 'merge_graphs_%s_C%i.anno_only.pickle' % (event_type, CONF)), 'r'))

Does it mean the file having suffix ".anno_only.pickle" contains the annotated alternative splicing events? Thank you very much!