odin_instal_rewriting

First Need to copy cat odin file system on my laptop

mkdir -p ~/Odin/data1/001_exome/diagnosticSamples/EE
cd ~/Odin/data1/001_exome/diagnosticSamples/EE	
mkdir -p Sample1/060_delivery

Then decide where from now i will keep the definition file. For now on it will be in the the same directory then the scripts but will still to give a path to the scripts

Then run the existing scripts from one Results folder (yvans@macus40:~/Odin/data1/001_exome/diagnosticSamples/EE/Sample1/060_delivery)

I should try all the scenarios possible

First call the scripts without options

> python MergeResults.py
usage: MergeResults [-h] -vcf [VCF] [-taq [TAQ]] [-defi [DEFI]]
MergeResults: error: argument -vcf is required

empty vcf option

> python ~/Home/workspace/amg/fingerprinting/testData/MergeResults.py -vcf
Traceback (most recent call last):
File "MergeResults.py", line 21, in <module>
	import SnpsHts
File "SnpsHts.py", line 23, in <module>
	import ReadDefinitionFile
File "ReadDefinitionFile.py", line 10, in <module>
	from SnpsHts import values
ImportError: cannot import name values

Need to check if vcf or definition files exist! Done

> python MergeResults.py -vcf .snpFingerPrintingTest

Please don't forget to add the correct file path to the vcf option

	call the MergeResults script with -h to get more help.

New type of error

how to pass correctly the options to the next script

> python MergeResults.py -vcf snpFingerPrintingTest.vcf -defi snpQC.V1.tab
Traceback (most recent call last):
File "MergeResults.py", line 26, in <module>
	import SnpsHts
File "SnpsHts.py", line 23, in <module>
	import ReadDefinitionFile
File "ReadDefinitionFile.py", line 10, in <module>
	from SnpsHts import values
ImportError: cannot import name values

I need use smaller steps to make this happen, first steps comment out all except the call

import SnpsHts

> python MergeResults.py -vcf snpFingerPrintingTest.vcf -defi snpQC.V1.tab
Traceback (most recent call last):
File "MergeResults.py", line 29, in <module>
	import SnpsHts
File "SnpsHts.py", line 23, in <module>
	import ReadDefinitionFile
File "ReadDefinitionFile.py", line 67, in <module>
	definition_dict = read_definition_file(definition_file)
NameError: name 'definition_file' is not defined

Ok now the definition file is passed via the option from MergeResults script. Still need to correct for the proper directory result lookout.

> python MergeResults.py -vcf snpFingerPrintingTest.vcf -defi snpQC.V1.tab
snpQC.V1.tab
Target //070_QC/
target exists
13000217701
location /Volumes/data1.odin/001_exome//diagnosticSamples/TaqManSNP-ID
Could not find the TaqMan results for Sample_Diag-excap17-13000217701-KIT-AI50Mbv5

Done! Now I need to read the Taqmann file

> python MergeResults.py -vcf SsnpFingerPrintingTest.vcf -defi snpQC.V1.tab
/Users/yvans/Home/workspace/amg/fingerprinting/testData/snpQC.V1.tab
QC_target exists
13000217701
location /Users/yvans/Odin/data1/001_exome/diagnosticSamples/TaqManSNP-ID

Uncomment in MergeResults

> python MergeResults.py -vcf snpFingerPrintingTest.vcf -defi snpQC.V1.tab
Traceback (most recent call last):
  File "MergeResults.py", line 29, in <module>
    import SnpsHts
  File "SnpsHts.py", line 23, in <module>
    import ReadDefinitionFile
  File "ReadDefinitionFile.py", line 11, in <module>
    from MergeResults import args
  File "MergeResults.py", line 33, in <module>
    import snpQCreader
  File "snpQCreader.py", line 18, in <module>
    from ReadDefinitionFile import GetCoordinatesByRs
ImportError: cannot import name GetCoordinatesByRs