#!/home/vanessa/python-lapack-blas/bin/python import sys import neuro2gene SEARCH_TERM = sys.argv[1] THRESHOLD = sys.argv[2] # 0.001 analysisTime = sys.argv[3] #'2-12-2014' dataset = neuro2gene.neurosynthInit() features = neuro2gene.getFeatures(dataset) sids, xyz, colnames, aba = neuro2gene.loadABA() print "Starting analysis for term " + SEARCH_TERM # First query neurosynth for relevant activation # dataset = neuro2gene.neurosynthInit() # Return MNI coordinates where there is FDR corrected, significant activation coords = neuro2gene.neurosynthQuery(SEARCH_TERM, THRESHOLD, dataset) # Read in data file to get specimen IDs and structures to query keepers, colnames = neuro2gene.ReadAllenBrainSample(coords) # Get the analysis time for all output files # Print table to file of matches neuro2gene.printSampleMatches(keepers, SEARCH_TERM, analysisTime, colnames)
#!/usr/bin/python
import neuro2gene
import datetime
# HERE IS RUNNING FOR ONE TERM
SEARCH_TERM = "associative"
THRESHOLD = 0.001
print "Starting analysis for term " + SEARCH_TERM
# First query neurosynth for relevant activation
dataset = neuro2gene.neurosynthInit()
# Return MNI coordinates where there is FDR corrected, significant activation
coords = neuro2gene.neurosynthQuery(SEARCH_TERM,THRESHOLD,dataset)
# Read in data file to get specimen IDs and structures to query
keepers,colnames = neuro2gene.ReadAllenBrainSample(coords)
# Get the analysis time for all output files
#analysisTime = datetime.datetime.now().strftime('%b-%d-%Y-%I-%M-%S')
analysisTime = '_4-4-2014'
# Print table to file of matches
neuro2gene.printSampleMatches(keepers,SEARCH_TERM,analysisTime,colnames)
# Now query to download expression data for our list
# neuro2gene.AllenQuery(keepers,SEARCH_TERM)
# HERE IS RUNNING FOR ALL TERMS
import neuro2gene
dataset = neuro2gene.neurosynthInit('525')
features = neuro2gene.getFeatures(dataset)
THRESHOLD = 0.05
sids,xyz,colnames,aba = neuro2gene.loadABA()
