[pygr-notify] Issue 103 in pygr: Excessive memory consumption in megatests

[codesite-noreply at google.com]

Comment #2 on issue 103 by deepreds: Excessive memory consumption in  
megatests
http://code.google.com/p/pygr/issues/detail?id=103

This is modified version of annotation_hg18_megatest.py
You need to make .pygrrc in your running directory. Please parepare all  
necessary
files for full megatest.

[deepreds at s137 Megatest]$ cat .pygrrc
[megatests]
expectedRunningTime = 12
logDir = /data4/deepreds/projects/Pygr_Project/Megatest/megatest_logs
mailFrom = deepreds at s137.rna.kr
mailTo_failed = deepreds at yahoo.com
mailTo_ok = deepreds at yahoo.com
runningTimeAllowedDelay = 9
testInputDB = PYGR_MEGATESTS
testInputDir =  
/data4/deepreds/projects/Pygr_Project/Megatest/input_and_results
testOutputBaseDir =  
/data4/deepreds/projects/Pygr_Project/Megatest/megatest_tmp

[megatests_dm2]
#smallSampleKey = chrYh
#smallSampleKey_nlmsa = chr4h
mafDir = /data4/deepreds/projects/Pygr_Project/Megatest/maf_data
msaDir = /data4/deepreds/projects/Pygr_Project/Megatest/maf_test
seqDir = /data4/deepreds/projects/Pygr_Project/Megatest/seq_data

[megatests_hg18]
#smallSampleKey = chrY
axtDir = /data4/deepreds/projects/Pygr_Project/Megatest/axt_data3
mafDir = /data4/deepreds/projects/Pygr_Project/Megatest/maf_data3
msaDir = /data4/deepreds/projects/Pygr_Project/Megatest/maf_test3
seqDir = /data4/deepreds/projects/Pygr_Project/Megatest/seq_data3

Just run this script without nose/protest.py
$ python annotation_hg18_megatest.py megatest_tmp/

You can comment out a test at the bottom of the script.
myBase = PygrBuildNLMSAMegabase()
myTestBase = Build_Test()
myTestBase.test_seqdb()
myTestBase.test_collectionannot() # COMMENT OUT IF YOU DON'T WANT THIS
myTestBase.test_mysqlannot() # COMMENT OUT IF YOU DON'T WANT THIS

Attachments:
	annotation_hg18_megatest.py  52.2 KB

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