[pygr-notify] [pygr commit] r168 - Edited wiki page through web user interface.

[codesite-noreply at google.com]

Author: kmdaily
Date: Tue Mar 31 16:49:01 2009
New Revision: 168

Modified:
    wiki/NlmsaFromAxtPairwise.wiki

Log:
Edited wiki page through web user interface.

Modified: wiki/NlmsaFromAxtPairwise.wiki
==============================================================================
--- wiki/NlmsaFromAxtPairwise.wiki	(original)
+++ wiki/NlmsaFromAxtPairwise.wiki	Tue Mar 31 16:49:01 2009
@@ -2,13 +2,11 @@
  #labels Phase-Implementation,Featured

  = Introduction =
-
  This page explains how to build an NLMSA from the UCSC pairwise alignment  
format [http://genome.ucsc.edu/goldenPath/help/axt.html AXT].

  See  
[http://www.doe-mbi.ucla.edu/~leec/newpygrdocs/reference/cnestedlist.html#module-cnestedlist]  
for full module documentation.

-= Details =
-
+= Requirements =
  In this example, the following are needed:
    # Genomic sequences
      * [http://hgdownload.cse.ucsc.edu/goldenPath/hg18/bigZips/chromFa.zip  
hg18]
@@ -23,6 +21,7 @@
      * [http://hgdownload.cse.ucsc.edu/goldenPath/hg18/vsRn4/axtNet/  
hg18_rn4]
      * [http://hgdownload.cse.ucsc.edu/goldenPath/hg18/vsCanFam2/axtNet/  
hg18_canFam2]

+= Details =
  The steps are as follows:
    # Download the axtNet alignments from UCSC website (for example, those  
listed above) and uncompress gzip archives. To easily get the pairwise  
alignment files, a script like the following is useful:
  {{{
@@ -32,12 +31,12 @@

  tar xvzf *.axt.gz
  }}}
-  # Create a seqdb.BlastDB for all of the genome assemblies. The sequence  
name should be same as assembly name (i.e., save hg18 genome sequence  
as "hg18"). Most of the genomic sequences come split per chromosome. The  
files need to be concatenated into one file. For example:
+  # The sequence name should be same as assembly name (i.e., save hg18  
genome sequence as "hg18"). Most of the genomic sequences come split per  
chromosome. The files need to be concatenated into one file. For example:
  {{{
  unzip chromFa.zip
  cat chr*.fa > hg18
  }}}
-Then, to build them in pygr:
+  # Then, to build them in pygr create a seqdb.SequenceFileDB for all of  
the genome assemblies:
  {{{
  from pygr import seqdb

@@ -48,7 +47,7 @@
  for orgstr in seqlist:
      genomes[orgstr] = seqdb.SequenceFileDB(v)

-# Create the union of these SequenceFileDBs
+  # Create the union of these SequenceFileDBs
  genomeUnion = seqdb.PrefixUnionDict(genomes)
  }}}
    # Then, to build the alignment: