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Write log messages to stderr rather than stdout #5

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30 changes: 15 additions & 15 deletions eigenMT.py
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Original file line number Diff line number Diff line change
Expand Up @@ -86,7 +86,7 @@ def make_gen_dict(GEN_fh, pos_dict):
def make_test_dict(QTL_fh, gen_dict, genpos_dict, phepos_dict, cis_dist):
'''
Function to make dict of SNP-gene tests. Also returns the header of the file.
Keys are gene IDs. Values are dict giving list of tested SNPs and the best SNP and it's p-value.
Keys are gene IDs. Values are dict giving list of tested SNPs and the best SNP and its p-value.
SNPs are identified by their positions.
Assumes the first column of the input file is the SNP ID and the second column is the GENE.
The column with the p-value is determined by the function, which allows for a more flexible input format.
Expand Down Expand Up @@ -204,8 +204,8 @@ def bf_eigen_windows(test_dict, gen_dict, phepos_dict, OUT_fh, input_header, var
for gene in genes:
perc = (100 * counter / numgenes)
if (counter % 100) == 0:
print str(counter) + ' out of ' + str(numgenes) + ' completed ' + '(' + str(round(perc, 3)) + '%)'
sys.stdout.flush()
print >>sys.stderr, str(counter) + ' out of ' + str(numgenes) + ' completed ' + '(' + str(round(perc, 3)) + '%)'
sys.stderr.flush()
counter += 1
snps = np.sort(test_dict[gene]['snps'])
start = 0
Expand Down Expand Up @@ -308,33 +308,33 @@ def find_num_eigs(eigenvalues, variance, var_thresh):
external = args.external

##Make SNP position dict
print 'Processing genotype position file.'
sys.stdout.flush()
print >>sys.stderr, 'Processing genotype position file.'
sys.stderr.flush()
genpos_dict = make_genpos_dict(GENPOS_fh, CHROM)

##Make phenotype position dict
print 'Processing phenotype position file.'
sys.stdout.flush()
print >>sys.stderr, 'Processing phenotype position file.'
sys.stderr.flush()
phepos_dict = make_phepos_dict(PHEPOS_fh, CHROM)

##Make genotype dict
print 'Processing genotype matrix.'
sys.stdout.flush()
print >>sys.stderr, 'Processing genotype matrix.'
sys.stderr.flush()
gen_dict = make_gen_dict(GEN_fh, genpos_dict)

##Make SNP-gene test dict
if not external:
print 'Processing Matrix-eQTL tests file.'
sys.stdout.flush()
print >>sys.stderr, 'Processing Matrix-eQTL tests file.'
sys.stderr.flush()
test_dict, input_header = make_test_dict(QTL_fh, gen_dict, genpos_dict, phepos_dict, cis_dist)
else:
print 'Processing Matrix-eQTL tests file. External genotype matrix and position file assumed.'
sys.stdout.flush()
print >>sys.stderr, 'Processing Matrix-eQTL tests file. External genotype matrix and position file assumed.'
sys.stderr.flush()
test_dict, input_header = make_test_dict_external(QTL_fh, gen_dict, genpos_dict, phepos_dict, cis_dist)

##Perform BF correction using eigenvalue decomposition of the correlation matrix
print 'Performing eigenMT correction.'
sys.stdout.flush()
print >>sys.stderr, 'Performing eigenMT correction.'
sys.stderr.flush()
bf_eigen_windows(test_dict, gen_dict, phepos_dict, OUT_fh, input_header, var_thresh, window)


Expand Down