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

#To run locally likely need __init__.py in the lib folder. Currently missing to avoid conflicts on server.

#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"}]}