vsoch

function xls_to_sql(input,sheet,outfile,database,table)

% This script reads in an excel sheet and converts it into sql insert
% statements.  The first row is expected to be the titles for the tables,
% followed by rows of raw data.
%-------------------------------------------------------------------------
% INPUT
% input    ----- input excel file should be excel file, .xls or .xlsx
% sheet    ----- name of sheet to read from
% outfile  ----- name of output file (without extension)

vsoch

function covcheck_free()
% COVERAGE CHECKING for SPM ANALYSIS (covcheck_free.m)
% Vanessa Sochat
%
% This script takes in a list of subjects processed in SPM, an ROI mask
% that will be used for group analysis, and a user specified coverage 
% percentage.  It will calculate the size of a single subject mask and
% determine if the subject has that percentage coverage.
%__________________________________________________________________________
%

vsoch

%% GRAB TIMESERIES:
% Creates a matrix of average mean timeseries for each VOI in individual subject folders, separating out VOI name and number of subjects included
% This data is then formatted into a csv file to be used to create an interactive chart with Google Charts (Gapminder)


%% GET DATA TIMESERIES
% Get list of all subjects in Analyzed Folder
anadir = 'path/path/path'; cd(anadir); all = dir;

% These are set in advance so we have control over our charts

vsoch

#!/usr/bin/python


import sys
import os.path
import re
import datetime


#-MADLIB---------------------------------------------------------------------

vsoch

function beerrank()
%-------------------------------------------------------------------------
% beerrank(): takes in a list of beers, ranking criteria, and allows the
% user to enter rankings and produce a chart of averages and winners!
% Created on December 14, 2010 for the LoNG annual Tasting Party!
%-------------------------------------------------------------------------
% RUNNING:
% - should be run with no input arguments
% - will take in a number of beers, and output file name
%      if outfile already exists, will append data to next empty row

vsoch

function confirmation_email(contactemail)

% CONFIRMATION_EMAIL
% Vanessa Sochat
%
% This script sends confirmation emails for imaging and battery appointments 
% added to the calendar the previous day.
%
% -------------------------------------------------------------------------
% VARIABLES:

vsoch

# This script will read in individual brain datasets 
# (a MNI coordinate file, and a structure ID file)
# compile into one matrix, and save to both text and Rdata file
# Read in data for each brain, save to matrix

filenames = c("H0351.2002","H0351.2001","H0351.1009","H0351.1012","H0351.1015","H0351.1016")

filey = filenames[1]
MNI = read.csv(paste('data/human_ma_samples_MNI_',filey,'.txt',sep=""),head=FALSE,sep="")
STRUC = read.csv(paste('data/human_ma_samples_region_',filey,'.txt',sep=""),head=FALSE,sep="")

vsoch

# foursquareASD will create a map of ASD locations across the United States
  
library(RJSONIO)
library(RCurl)

options(RCurlOptions = list(cainfo = system.file("CurlSSL", "cacert.pem", package = "RCurl")))

# First, read in file with latitudes and longitudes of major cities
# Obtained from http://notebook.gaslampmedia.com/download-zip-code-latitude-longitude-city-state-county-csv/
ll = read.csv('zip_codes_states.csv',sep=",",head=TRUE)

vsoch

#!/bin/bash

# Key off existence of the "data" mount point to determine whether
# this is the first boot.
if [[ ! -e /mnt/data ]]; then
  # Basic setup - get the JRE installed
  apt-get update
  apt-get install --fix-broken
  mkdir -p /mnt/data
fi

vsoch

# This script will convert a list of gene symbols to kegg (KO) identifiers

# We need libraries to read and parse URL
library(RCurl)
options(RCurlOptions = list(cainfo = system.file("CurlSSL", "cacert.pem", package = "RCurl")))

# Read in file with Gene Symbols
# This is tab separated file with Id, Label, color from Geshi
infile = '/home/vanessa/Desktop/group5[Nodes].csv'
data = read.table(infile,sep="\t",head=TRUE)