HMMER file format support for the GHMM library.
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Imported modules
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import StringIO
import re
import string
import sys
from xml.dom import minidom
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Functions
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build_matrix
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build_matrix ( n, m )
builds n x m matrix with lists
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del_mat
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del_mat ( mat, r )
deletes the <r>th columns and row from the matrix
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gotoLine
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gotoLine ( f, res )
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map_entries
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map_entries ( dic, lis )
translates the letters to the number of the columns
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norm_mat
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norm_mat ( mat )
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red_mat_end
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red_mat_end ( mat, r )
delete <r> rows and columns from the end of the matrix
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remove_state
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remove_state ( matrix, index )
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sum_mrows
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sum_mrows ( mat )
sums the rows of a matrix
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toint
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toint ( i )
return integer if i is value or 0
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write_file
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write_file ( strf, strcontent )
writes <strcontent> in file <strf>
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xml_newdatanode
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xml_newdatanode (
doc,
nodename,
attributename,
attribute,
text,
)
returns node with attribute and text
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Classes
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hmmer |
reads hmmer file and converts it to xml
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