usage: expression_transform.py [-h] (--ufile UFILE | --ustring USTRING)
                               (--sfile SFILE | --sstring SSTRING)

optional arguments:
  -h, --help         show this help message and exit
  --ufile UFILE      json file from user input
  --ustring USTRING  json string from user input
  --sfile SFILE      server setup JSON file
  --sstring SSTRING  server setup JSON string



#Input
#1. metadata in json with the following:

"""
{xfile:"comparisons file",
xformat:"csv || tsv || xls ||  xlsx",
xsetup:"gene_matrix || gene_list",
source_id_type:"refseq_locus_tag || alt_locus_tag || feature_id",
data_type: "Transcriptomics || Proteomics || Phenomics",
title: "User input",
description: "User input",
organism: "user input",
pmid: "user_input",
output_path: "path",
"metadata_template":"file",
"metadata_format":"csv || tsv || xls ||  xlsx"}
"""
#2. server info for the data api
"""
{"data_api":"url"}
"""

#Sample Output
#experiment.json
#{"origFileName":"filename","geneMapped":4886,"samples":8,"geneTotal":4985,"cdate":"2013-01-28 13:40:47","desc":"user input","organism":"some org","owner":"user name","title":"user input","pmid":"user input","expid":"whatever","collectionType":"ExpressionExperiment","genesMissed":99,"mdate":"2013-01-28 13:40:47"}

#expression.json
#{"expression":[{"log_ratio":"0.912","na_feature_id":"36731006","exp_locus_tag":"VBISalEnt101322_0001","pid":"8f2e7338-9f04-4ba5-9fe2-5365c857d57fS0","z_score":"-0.23331085637221843"}]

#mapping.json
#{"mapping":{"unmapped_list":[{"exp_locus_tag":"VBISalEnt101322_pg001"}],"unmapped_ids":99,"mapped_list":[{"na_feature_id":"36731006","exp_locus_tag":"VBISalEnt101322_0001"}],"mapped_ids":4886}}

#sample.json
#{"sample":[{"sig_log_ratio":2675,"expmean":"1.258","sampleUserGivenId":"LB_stat_AerobicM9_stat_aerobic","expname":"LB_stat_AerobicM9_stat_aerobic","pid":"8f2e7338-9f04-4ba5-9fe2-5365c857d57fS0","genes":4429,"sig_z_score":139,"expstddev":"1.483"}]}