[pygr-notify] [pygr commit] r75 - wiki

[codesite-noreply at google.com]

Author: ramccreary
Date: Sun Jul 13 19:47:24 2008
New Revision: 75

Modified:
   wiki/GenomeCalculationsUsingpygr.wiki

Log:
Edited wiki page through web user interface.

Modified: wiki/GenomeCalculationsUsingpygr.wiki
==============================================================================
--- wiki/GenomeCalculationsUsingpygr.wiki	(original)
+++ wiki/GenomeCalculationsUsingpygr.wiki	Sun Jul 13 19:47:24 2008
@@ -52,7 +52,7 @@

  The ecoli genome (ecoli_fna_filename) is stored in a BlastDB. The 
BlastDB unpacks the FASTA id and potentially several other ids 
potentially contained in the NCBI genome.

-DictReader (from the csv module) opens the .gff file and reads the 
tab-seperated entries, assigning each a string name. Since the entries 
are seperatedby tabs, the delimiter used to differentiate the fields is 
clearly a tab.
+DictReader (from the csv module) opens the .gff file and reads the 
tab-separated entries, assigning each a string name. Since the entries 
are separated by tabs, the delimiter used to differentiate the fields 
is clearly a tab.

 {{{
 parser = OptionParser()
@@ -80,7 +80,7 @@

  The annots dictionary and E. coli genome are then both stored in 
seqDB, which, as mentioned earlier, is finicky about the sequence ID 
given, so ensure the field assigned to the id in the .gff file is 
actually the desired field that stores the id.

-Next, another dictionary is created, this time to store the counts of 
each nucleotide per gene (ex: In the gene '1364', there are 226 As). 
iteritems() came in handy because it iterated over the dictionary, and 
returned the value for each genome sequence. nucs was the key for the 
ec_count, and each nucleotide base was a value (A, T, G, C,).
+Next, another dictionary is created, this time to store the counts of 
each nucleotide per gene (ex: In the gene '1364', there are 226 As). 
iteritems() came in handy because it iterated over the dictionary, and 
returned the value for each gene. nucs was the key for the ec_count, 
and each nucleotide base was a value (A, T, G, C,).

 {{{
 annots = {}