mkanai/magentapy

Experimental port of MAGENTA software to Python.

magentapy's Issues

0 genes with example file- issues

Hi,
I have prepared data input files as per the instructions given in the readme file. Please give me suggestions if I need to make any changes in the config file or Run_magenta.py file. I had input OR file with 3 columns(no headers), SNP file (1 column and no header), and score file(3 columns chr, pos and Pval).

/MAGENTApy-master/MAGENTA/stepwisefit.py:173: RuntimeWarning: invalid value encountered in divide
MSexplained = np.divide(SStotal - SSresid, df0)
/Python/versions/2.7.15/lib/python2.7/site-packages/scipy/stats/_distn_infrastructure.py:877: RuntimeWarning: invalid value encountered in greater
return (self.a < x) & (x < self.b)
/Python/versions/2.7.15/lib/python2.7/site-packages/scipy/stats/_distn_infrastructure.py:877: RuntimeWarning: invalid value encountered in less
return (self.a < x) & (x < self.b)
/Python/versions/2.7.15/lib/python2.7/site-packages/scipy/stats/_distn_infrastructure.py:1748: RuntimeWarning: invalid value encountered in greater_equal
cond2 = (x >= self.b) & cond0
It took 0.2156 seconds or 0.0036 minutes to correct gene scores with stepwise regression.
Traceback (most recent call last):
File "/MAGENTApy-master/Run_MAGENTA.py", line 650, in
magenta(args)
File "/MAGENTApy-master/Run_MAGENTA.py", line 244, in magenta
gs_GeneIDs_cellarray, num_genes_gs = multi_list2cell_GeneSetDB(GeneSet_db_file_name)
File "/MAGENTApy-master/MAGENTA/multi_list2cell_GeneSetDB.py", line 17, in multi_list2cell_GeneSetDB
geneset[:num_genes_per_gene_set[counter]] = map(lambda x: int(x), genes)
TypeError: slice indices must be integers or None or have an index method

Please give me suggestions.

getting nan values for scores with example data

Hi,
I have been getting the following error even with example data,
Scores_X
[[nan nan nan nan]
[nan nan nan nan]
[nan nan nan nan]
...
[nan nan nan nan]
[nan nan nan nan]
[nan nan nan nan]]
[0 0 0 ... 0 0 0]
['' '' '' ... '' '' '']
There are 0 genes with SNPs in their target region that were not assigned an association score (NaN).

Traceback (most recent call last):
File "Run_MAGENTA.py", line 658, in
magenta(args)
File "Run_MAGENTA.py", line 183, in magenta
AllSNP_rs_num)
File "/GWAMA_input_output/MAGENTApy-master/MAGENTA/ExtractGeneScoreBestSNP_PvalZscore_NumSNPsPerGene.py", line 84, in ExtractGeneScoreBestSNP_PvalZscore_NumSNPsPerGene
print 'num_SNPS_per_gene='.num_SNPs_per_gene
AttributeError: 'str' object has no attribute 'num_SNPs_per_gene'
thanks and regards
Mano