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<a href="Bio-module.html">Package Bio</a> ::
<a href="Bio.Saf-module.html">Package Saf</a> ::
Module saf_format
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<h1 class="epydoc">Module saf_format</h1><p class="nomargin-top"><span class="codelink"><a href="Bio.Saf.saf_format-pysrc.html">source code</a></span></p>
<pre class="literalblock">
Martel based parser to read SAF formatted files.
This is a huge regular regular expression for SAF, built using
the 'regular expressiona on steroids' capabilities of Martel.
http://www.embl-heidelberg.de/predictprotein/Dexa/optin_safDes.html
Notes:
Just so I remember -- the new end of line syntax is:
New regexp syntax - \R
\R means "
|
?"
[\R] means "[
]"
This helps us have endlines be consistent across platforms.
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<a name="digits"></a><span class="summary-name">digits</span> = <code title="'0123456789'"><code class="variable-quote">'</code><code class="variable-string">0123456789</code><code class="variable-quote">'</code></code>
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<a href="Bio.Saf.saf_format-module.html#valid_sequence_characters" class="summary-name">valid_sequence_characters</a> = <code title="'abcdefghijklmnopqrstuvwxyzABCDEFGHIJKLMNOPQRSTUVWXYZ-. \t'"><code class="variable-quote">'</code><code class="variable-string">abcdefghijklmnopqrstuvwxyzABCDEFG</code><code class="variable-ellipsis">...</code></code>
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<a name="white_space"></a><span class="summary-name">white_space</span> = <code title="'\t '"><code class="variable-quote">'</code><code class="variable-string">\t </code><code class="variable-quote">'</code></code>
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<a name="valid_residue_characters"></a><span class="summary-name">valid_residue_characters</span> = <code title="'0123456789\t .'"><code class="variable-quote">'</code><code class="variable-string">0123456789\t .</code><code class="variable-quote">'</code></code>
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<a href="Bio.Saf.saf_format-module.html#residue_number_line" class="summary-name">residue_number_line</a> = <code title="Group("residue_number_line", Rep1(Any(valid_residue_characters))+ AnyE\
ol())">Group("residue_number_line", Rep1(Any(va<code class="variable-ellipsis">...</code></code>
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<a name="comment_line"></a><span class="summary-name">comment_line</span> = <code title="Group("comment_line", Str("#")+ ToEol())">Group("comment_line", Str("#")+ ToEol())</code>
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<a href="Bio.Saf.saf_format-module.html#ignored_line" class="summary-name">ignored_line</a> = <code title="Group("ignored_line", Alt(comment_line, residue_number_line))">Group("ignored_line", Alt(comment_line, residue<code class="variable-ellipsis">...</code></code>
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<a href="Bio.Saf.saf_format-module.html#candidate_line" class="summary-name">candidate_line</a> = <code title="Group("candidate_line", Assert(Str("#"), 1)+ Assert(Any(valid_residue_\
characters), 1)+ ToSep(sep= ' ')+ Rep(Any(valid_sequence_characters))+\
ToEol())">Group("candidate_line", Assert(Str("#"), 1)+ <code class="variable-ellipsis">...</code></code>
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<a href="Bio.Saf.saf_format-module.html#saf_record" class="summary-name">saf_record</a> = <code title="Group("saf_record", candidate_line+ Rep(Alt(candidate_line, ignored_li\
ne))+ Opt(Str("#")))">Group("saf_record", candidate_line+ Rep(Alt(candi<code class="variable-ellipsis">...</code></code>
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<h3 class="epydoc">valid_sequence_characters</h3>
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<dt>Value:</dt>
<dd><table><tr><td><pre class="variable">
<code class="variable-quote">'</code><code class="variable-string">abcdefghijklmnopqrstuvwxyzABCDEFGHIJKLMNOPQRSTUVWXYZ-. \t</code><code class="variable-quote">'</code>
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<dt>Value:</dt>
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Group("residue_number_line", Rep1(Any(valid_residue_characters))+ AnyE<span class="variable-linewrap"><img src="crarr.png" alt="\" /></span>
ol())
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<h3 class="epydoc">ignored_line</h3>
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<dt>Value:</dt>
<dd><table><tr><td><pre class="variable">
Group("ignored_line", Alt(comment_line, residue_number_line))
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<dt>Value:</dt>
<dd><table><tr><td><pre class="variable">
Group("candidate_line", Assert(Str("#"), 1)+ Assert(Any(valid_residue_<span class="variable-linewrap"><img src="crarr.png" alt="\" /></span>
characters), 1)+ ToSep(sep= ' ')+ Rep(Any(valid_sequence_characters))+<span class="variable-linewrap"><img src="crarr.png" alt="\" /></span>
ToEol())
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<dt>Value:</dt>
<dd><table><tr><td><pre class="variable">
Group("saf_record", candidate_line+ Rep(Alt(candidate_line, ignored_li<span class="variable-linewrap"><img src="crarr.png" alt="\" /></span>
ne))+ Opt(Str("#")))
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