[pygr-notify] [pygr commit] r115 - wiki

[codesite-noreply at google.com]

Author: marecki
Date: Fri Dec 19 18:38:30 2008
New Revision: 115

Modified:
    wiki/MegatestSetup.wiki

Log:
Added information from Namshin's second e-mail.

Modified: wiki/MegatestSetup.wiki
==============================================================================
--- wiki/MegatestSetup.wiki	(original)
+++ wiki/MegatestSetup.wiki	Fri Dec 19 18:38:30 2008
@@ -26,7 +26,7 @@

   os.environ['PYGRDATADOWNLOAD'] = '/my/seqdb/path'

-At the top of each dm2/hg18 megatest files in tests directory, you can see  
following lines. You may need to change following lines to  
_PYGRDATADOWNLOAD_ path. If you want to maintain original *megatest.py*  
files intact, you may need to create following directory in your megatest  
machine.
+At the top of each dm2/hg18 megatest files in tests directory, you can see  
following lines. You may need to change following lines to  
_PYGRDATADOWNLOAD_ path. If you want to maintain original *megatest.py*  
files intact, you may need to create following directories on your megatest  
machine.

   seqDir = '/result/pygr_megatest/seq_data'

@@ -41,6 +41,101 @@
   msaDir = '/result/pygr_megatest/maf_test3' # maf_test3.tar in biodb  
MEGATEST URL.

  All the test results and NLMSA will be saved subdirectory of  
_/usr/tmp/deepreds_. You can find _/usr/tmp/deepreds_ path in all of  
*megatest.py*. You may need to change this directory or create one for  
megatest.
+
+----
+
+For mutigenome NLMSA megatest, download the archives
+
+ http://biodb.bioinformatics.ucla.edu/MEGATEST/maf_data.tar
+
+ http://biodb.bioinformatics.ucla.edu/MEGATEST/maf_data3.tar
+
+then extract them to the following two directories on your machine,  
respectively:
+
+ nlmsa_dm2_megatest.py:mafDir = '/result/pygr_megatest/maf_data'
+
+ nlmsa_hg18_megatest.py:mafDir = '/result/pygr_megatest/maf_data3'
+
+
+For pairwise NLMSA megatest, you need to extract files from
+
+  http://biodb.bioinformatics.ucla.edu/MEGATEST/axt_data.tar
+
+to
+
+ pairwise_hg18_megatest.py:axtDir = '/result/pygr_megatest/axt_data'
+
+
+The final archive to download is
+
+ http://biodb.bioinformatics.ucla.edu/MEGATEST/input_and_results.tar
+
+On leelab2, all megatest is running /result/pygr_megatest directory. Thus,
+input_and_results.tar should be extracted in /result/pygr_megatest  
directory
+or create one for your machine.
+
+input_and_results.tar contains the following files:
+
+ * Annotation_ConservedElement_Exons_chrYh_dm2.txt
+ * Annotation_ConservedElement_Exons_chrY_hg18.txt
+ * Annotation_ConservedElement_Exons_dm2.txt
+ * Annotation_ConservedElement_Exons_hg18.txt
+ * Annotation_ConservedElement_Introns_chrYh_dm2.txt
+ * Annotation_ConservedElement_Introns_chrY_hg18.txt
+ * Annotation_ConservedElement_Introns_dm2.txt
+ * Annotation_ConservedElement_Introns_hg18.txt
+ * Annotation_ConservedElement_Stop_chrY_hg18.txt
+ * Annotation_ConservedElement_Stop_hg18.txt
+ * phastConsElements15way_chrYh_dm2.txt
+ * phastConsElements15way_dm2.txt
+ * phastConsElements28way_chrY_hg18.txt
+ * phastConsElements28way_hg18.txt
+ * refGene_cdsAnnot_chrY_hg18.txt
+ * refGene_cdsAnnot_hg18.txt
+ * refGene_exonAnnot_chrYh_dm2.txt
+ * refGene_exonAnnot_chrY_hg18.txt
+ * refGene_exonAnnot_dm2.txt
+ * refGene_exonAnnot_hg18.txt
+ * refGene_spliceAnnot_chrYh_dm2.txt
+ * refGene_spliceAnnot_chrY_hg18.txt
+ * refGene_spliceAnnot_dm2.txt
+ * refGene_spliceAnnot_hg18.txt
+ * snp126_chrY_hg18.txt
+ * snp126_hg18.txt
+ * splicesite_dm2_chr4h_multiz15way.txt
+ * splicesite_dm2_chr4h.txt
+ * splicesite_dm2_multiz15way.txt
+ * splicesite_dm2.txt
+ * splicesite_hg18_chrY_multiz28way.txt
+ * splicesite_hg18_chrY_pairwise5way.txt
+ * splicesite_hg18_chrY.txt
+ * splicesite_hg18_multiz28way.txt
+ * splicesite_hg18_pairwise5way.txt
+ * splicesite_hg18.txt
+
+As you can see, there are full versions and _chrY(hg18)_ and _chrYh(dm2)_  
versions. Current version of pygr megatest uses only short _(chrY for hg18  
and chrYh for dm2)_ versions in order to reduce overload. But, if you want  
to test full version, you need to change *megatest.py* files, i.e. remove  
all _chrY_/_chrYh_ for full megatests.
+
+Comparison between new results and pre-built result will be done by
+md5.digest().
+
+
+== Setting up the Database ==
+
+Next step is to prepare MySQL database in which all above txt input files  
are saved. First, you need to make the _.my.cnf_ file in your HOME  
directory.
+{{
+ [client]
+ port=3306
+ host=your_database_server
+ user=your_account
+ password=your_password
+}}
+Pygr will automatically try to load ~/.my.cnf to connect MySQL database.
+
+Then create a database named PYGRDB_JAN06. Files created by _mysqldump_  
are available at http://biodb.bioinformatics.ucla.edu/MEGATEST/ . You can  
import all these .sql files by _mysql_ command. MySQL version 5 or higher  
is recommended for compatability.
+
+Same NLMSA building Megatest will run twice, one for file-saving version  
and
+the other for MySQL version. In each step, text <-> binary conversion test
+is included.