Hi,
Whenever I have tried to run jacks i keep getting a key issue error
Here is the error code
[2019-05-23 16:36:55,172] jacks: INFO Loading sample specification
[2019-05-23 16:36:55,172] jacks: INFO Loading gene mappings
[2019-05-23 16:36:55,186] jacks: INFO Loading data and pre-processing
Traceback (most recent call last):
File "/home/alexander/bioTools/JACKS/jacks/run_JACKS.py", line 7, in
runJACKSFromArgs()
File "/home/alexander/bioTools/JACKS/jacks/jacks/jacks_io.py", line 441, in runJACKSFromArgs
args.outprefix, args.reffile, args.n_pseudo, args.count_prior)
File "/home/alexander/bioTools/JACKS/jacks/jacks/jacks_io.py", line 431, in runJACKS
outprefix, apply_w_hp=apply_w_hp, norm_type=norm_type, ctrl_genes=ctrl_genes, fdr=fdr, fdr_thresh_type=fdr_thresh_type, n_pseudo=n_pseudo, count_prior=count_prior )
File "/home/alexander/bioTools/JACKS/jacks/jacks/jacks_io.py", line 383, in load_data_and_run
data, meta, sample_ids, genes, gene_index = loadDataAndPreprocess(sample_spec, gene_spec,ctrl_spec=ctrl_spec,normtype=norm_type, ctrl_geneset=ctrl_geneset, prior=count_prior)
File "/home/alexander/bioTools/JACKS/jacks/jacks/preprocess.py", line 147, in loadDataAndPreprocess
counts.append([np.log2(eval(row[colname])+prior) for sample_id, colname in sample_spec[filename]])
File "/home/alexander/bioTools/JACKS/jacks/jacks/preprocess.py", line 147, in
counts.append([np.log2(eval(row[colname])+prior) for sample_id, colname in sample_spec[filename]])
KeyError: 'd15Cas9k2'
Here is a copy of the input
python ~/bioTools/JACKS/jacks/run_JACKS.py smallCount.tab smallRep.tab guideMapping.tab --ctrl_sample_hdr=Control
Here is what the smallRep.tab looks like
Replicate Sample Control
d15Cas9k1 d15Cas9 d15Wt
d15Cas9k2 d15Cas9 d15Wt
d15WTk1 d15Wt d15Wt
d15WTk2 d15Wt d15Wt
Here is a sample of the smallCount.tab file
sgRNA d15Cas9k1 d15Cas9k2 d15WTk1 d15WTk2
PMVK_NM_006556.3_154936638 3214 3573 4319 4463
PLK2_NM_006622.3_58457530 6003 5871 8658 6865
CHEK1_NM_001114121.2_125627805 3948 2687 5182 5021
MAP4K5_NM_006575.4_50485610 3688 3408 5612 5653
CKS2_NM_001827.2_89311315 6709 7779 9329 8668
AK4_NM_013410.3_65148450 5115 4971 6398 6486
An help would be deeply appreciated.
Thank you.