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View Code? Open in Web Editor NEWReimplementation of PROmiRNA: miRNA promoter recognition
License: MIT License
Reimplementation of PROmiRNA: miRNA promoter recognition
License: MIT License
When creating the training set, we seed the background to N*10
positions (default N = 1000).
We then proceed to filter out positions which do not fit our requirements:
Per chance, the sample of positions left after filtering may be less than N ... causing the following error:
Traceback (most recent call last):
File "create-training-set.py", line 660, in <module>
main(args.files, args.outdir, args.n , args.l, args.get_id, args.f_config, args.verbose)
File "create-training-set.py", line 578, in main
selectedlines = random.sample(range(1,wc+1), N)
File "/raid2/local/python2.7.3/lib/python2.7/random.py", line 320, in sample
raise ValueError("sample larger than population")
ValueError: sample larger than population
Quick and easy thing to do is to rerun the code. Also make sure the tcnorm.ini
is updated.
custom.py script is generating duplicates
Add verify feature?
Getting way more positions than expected
The error:
Argument "" isn't numeric in multiplication (*) at promi2/code/external/tc_quantify/bin/rle_tpm_transform.pl line 48, <MFILE> line 184828.
Argument "" isn't numeric in multiplication (*) at promi2/code/external/tc_quantify/bin/rle_tpm_transform.pl line 48, <MFILE> line 184829.
...
Traceback (most recent call last):
File "promi2/code/custom.py", line 436, in <module>
main(args.f_config, args.infile, args.outdir, args.has_mirna, args.make_plots)
File "promi2/code/custom.py", line 370, in main
gff_allfeatures = extractFeatures_given_gff(f_config, gff_infile, outdir, has_mirna, is_consider_corr)
File "promi2/code/custom.py", line 249, in extractFeatures_given_gff
_, chrom, start, _, stop, strand = re.split('[r:.,]', l[3])
ValueError: need more than 1 value to unpack
Cause:
chr5 107718031 107718064 chr5:107718031..107718064,- . - 0
0 0 0 0 0 0
0 0 0 0 0 0
lab
needs to be added after aes_string
TODO:
data/miriad_human_labels_v2014.gff
came fromTo find the probability of promoter per TSS position, we can
Current setup is situation 1.
Traceback (most recent call last):
File "create-training-set.py", line 664, in <module>
main(args.files, args.outdir, args.n , args.l, args.get_id, args.f_config, args.verbose)
File "create-training-set.py", line 533, in main
os.path.join(outdir, 'tc-norm_negSet'))
File "/raid2/local/python2.7.3/lib/python2.7/shutil.py", line 289, in move
raise Error, "Destination path '%s' already exists" % real_dst
shutil.Error: Destination path '../Test-tset/tc-norm_negSet/tc-norm_negSet' already exists
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