gistfile1.txt

import pandas as pd
import synapseclient
import os

def compare2Files(fname, originFiles, newFiles, syn):
    df1 = pd.read_csv(syn.get(originFiles[fname]).path, sep="\t")
    df2 = pd.read_csv(syn.get(newFiles[fname]).path, sep="\t")
    df1 = df1.ix[sort(df1.index), sort(df1.columns)]
    df2 = df2.ix[sort(df2.index), sort(df2.columns)]

original = "syn2812961"
new = "syn3270657"
orginalFolder = "original"
newFolder = "new"

syn=synapseclient.login()

originFiles = {x["file.name"]: x["file.id"] for x in syn.chunkedQuery("select name from file where benefactorId=='%s'"%original)}
newFiles = {x["file.name"]: x["file.id"] for x in syn.chunkedQuery("select name from file where benefactorId=='%s'"%new)}
        
fname = 'unc.edu_GBM_AgilentG4502A_07_2.geneExp.tsv'
df1 = pd.read_csv(syn.get(originFiles[fname]).path, sep="\t", index_col=0)
df2 = pd.read_csv(syn.get(newFiles[fname]).path, sep="\t", index_col=0)
df1 = df1.ix[sorted(df1.index), sorted(df1.columns)]
df2 = df2.ix[sorted(df2.index), sorted(df2.columns)]