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<a href="Bio-module.html">Package Bio</a> ::
<a href="Bio.expressions-module.html">Package expressions</a> ::
<a href="Bio.expressions.blast-module.html">Package blast</a> ::
Module wublast
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<!-- ==================== MODULE DESCRIPTION ==================== -->
<h1 class="epydoc">Module wublast</h1><p class="nomargin-top"><span class="codelink"><a href="Bio.expressions.blast.wublast-pysrc.html">source code</a></span></p>
<!-- ==================== FUNCTIONS ==================== -->
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<td><span class="summary-sig"><a name="main"></a><span class="summary-sig-name">main</span>(<span class="summary-sig-arg">outf</span>)</span></td>
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<span class="codelink"><a href="Bio.expressions.blast.wublast-pysrc.html#main">source code</a></span>
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<!-- ==================== VARIABLES ==================== -->
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<td align="left"><span class="table-header">Variables</span></td>
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<span class="summary-type"> </span>
</td><td class="summary">
<a name="wublast_version"></a><span class="summary-name">wublast_version</span> = <code title="Re("2\.[^-]+-WashU")">Re("2\.[^-]+-WashU")</code>
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<td width="15%" align="right" valign="top" class="summary">
<span class="summary-type"> </span>
</td><td class="summary">
<a href="Bio.expressions.blast.wublast-module.html#blastn_appheader" class="summary-name">blastn_appheader</a> = <code title="replace_groups(ncbiblast.blastn_appheader, [("appversion", wublast_ver\
sion)])">replace_groups(ncbiblast.blastn_appheader, <code class="variable-ellipsis">...</code></code>
</td>
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<td width="15%" align="right" valign="top" class="summary">
<span class="summary-type"> </span>
</td><td class="summary">
<a href="Bio.expressions.blast.wublast-module.html#blastp_appheader" class="summary-name">blastp_appheader</a> = <code title="replace_groups(ncbiblast.blastp_appheader, [("appversion", wublast_ver\
sion)])">replace_groups(ncbiblast.blastp_appheader, <code class="variable-ellipsis">...</code></code>
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<td width="15%" align="right" valign="top" class="summary">
<span class="summary-type"> </span>
</td><td class="summary">
<a href="Bio.expressions.blast.wublast-module.html#blastx_appheader" class="summary-name">blastx_appheader</a> = <code title="replace_groups(ncbiblast.blastx_appheader, [("appversion", wublast_ver\
sion)])">replace_groups(ncbiblast.blastx_appheader, <code class="variable-ellipsis">...</code></code>
</td>
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<td width="15%" align="right" valign="top" class="summary">
<span class="summary-type"> </span>
</td><td class="summary">
<a href="Bio.expressions.blast.wublast-module.html#tblastn_appheader" class="summary-name">tblastn_appheader</a> = <code title="replace_groups(ncbiblast.tblastn_appheader, [("appversion", wublast_ve\
rsion)])">replace_groups(ncbiblast.tblastn_appheader<code class="variable-ellipsis">...</code></code>
</td>
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<td width="15%" align="right" valign="top" class="summary">
<span class="summary-type"> </span>
</td><td class="summary">
<a href="Bio.expressions.blast.wublast-module.html#tblastx_appheader" class="summary-name">tblastx_appheader</a> = <code title="replace_groups(ncbiblast.tblastx_appheader, [("appversion", wublast_ve\
rsion)])">replace_groups(ncbiblast.tblastx_appheader<code class="variable-ellipsis">...</code></code>
</td>
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<td width="15%" align="right" valign="top" class="summary">
<span class="summary-type"> </span>
</td><td class="summary">
<a name="spaces_line"></a><span class="summary-name">spaces_line</span> = <code title="Opt(Spaces())+ AnyEol()">Opt(Spaces())+ AnyEol()</code>
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<td width="15%" align="right" valign="top" class="summary">
<span class="summary-type"> </span>
</td><td class="summary">
<a href="Bio.expressions.blast.wublast-module.html#query_database" class="summary-name">query_database</a> = <code title="Str("Database:")+ Opt(Spaces())+ Std.database_name(UntilEol())+ AnyEol\
()+ Spaces()+ Std.database_num_sequences(Number(), {"bioformat:decode"\
: "int.comma"})+ Str(" sequences;")+ Spaces()+ Std.database_num_letter\
s(Number(), {"bioformat:decode": "int.comma"})+ Spaces()+ Str("total l\
etters.")+ ToEol()">Str("Database:")+ Opt(Spaces())+ Std.database<code class="variable-ellipsis">...</code></code>
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<td width="15%" align="right" valign="top" class="summary">
<span class="summary-type"> </span>
</td><td class="summary">
<a href="Bio.expressions.blast.wublast-module.html#to_table" class="summary-name">to_table</a> = <code title="SkipLinesUntil(Str("Sequences producing High-scoring Segment"))+ ToEol\
()+ AnyEol()">SkipLinesUntil(Str("Sequences producing High-scorin<code class="variable-ellipsis">...</code></code>
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<td width="15%" align="right" valign="top" class="summary">
<span class="summary-type"> </span>
</td><td class="summary">
<a href="Bio.expressions.blast.wublast-module.html#table_entry" class="summary-name">table_entry</a> = <code title="AssertNot(AnyEol())+ Std.search_table_description(Re(r".{60}"))+ Space\
s()+ Std.search_table_value(Float(), {"name": "score", "bioformat:deco\
de": "float"})+ Spaces()+ Std.search_table_value(Float(), {"name": "P"\
, "bioformat:decode": "float"})+ Spaces()+ Std.search_table_value(Digi\
ts(), {"name": "N", "bioformat:decode": "float"})+ AnyEol()">AssertNot(AnyEol())+ Std.search_table_descriptio<code class="variable-ellipsis">...</code></code>
</td>
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<td width="15%" align="right" valign="top" class="summary">
<span class="summary-type"> </span>
</td><td class="summary">
<a href="Bio.expressions.blast.wublast-module.html#header" class="summary-name">header</a> = <code title="replace_groups(ncbiblast.header, (("query_database", query_database), \
("to_table", to_table), ("table_entry", table_entry)))">replace_groups(ncbiblast.header, (("query_database", <code class="variable-ellipsis">...</code></code>
</td>
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<td width="15%" align="right" valign="top" class="summary">
<span class="summary-type"> </span>
</td><td class="summary">
<a href="Bio.expressions.blast.wublast-module.html#hit_descr" class="summary-name">hit_descr</a> = <code title="Str(">")+ Std.hit_description(UntilEol())+ AnyEol()+ Rep(AssertNot(hit\
_length)+ Std.hit_description(UntilEol())+ AnyEol())">Str(">")+ Std.hit_description(UntilEol())+ AnyEol(<code class="variable-ellipsis">...</code></code>
</td>
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<td width="15%" align="right" valign="top" class="summary">
<span class="summary-type"> </span>
</td><td class="summary">
<a href="Bio.expressions.blast.wublast-module.html#hit_length" class="summary-name">hit_length</a> = <code title="Spaces()+ Str("Length = ")+ Std.hit_length(Digits())+ AnyEol()+ Opt(Sp\
aces())+ AnyEol()">Spaces()+ Str("Length = ")+ Std.hit_length(Digits<code class="variable-ellipsis">...</code></code>
</td>
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<td width="15%" align="right" valign="top" class="summary">
<span class="summary-type"> </span>
</td><td class="summary">
<a href="Bio.expressions.blast.wublast-module.html#blastp_score" class="summary-name">blastp_score</a> = <code title="Re(r" *Score = *")+ Std.hsp_value(Digits(), {"name": "bits", "bioforma\
t:decode": "int",})+ ToSep(sep= "=")+ Spaces()+ Std.hsp_value(Float(),\
{"name": "expect", "bioformat:decode": "float",})+(Str(", P =") | Re(\
r", Sum P\(\d+\) ="))+ Spaces()+ Std.hsp_value(Float(), {"name": "P", \
"bioformat:decode": "float",})+ ToEol()">Re(r" *Score = *")+ Std.hsp_value(Digits(), {"n<code class="variable-ellipsis">...</code></code>
</td>
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<td width="15%" align="right" valign="top" class="summary">
<span class="summary-type"> </span>
</td><td class="summary">
<a href="Bio.expressions.blast.wublast-module.html#identities" class="summary-name">identities</a> = <code title="Re(r" *Identities = ")+ Std.hsp_value(Digits(), {"name": "identical", \
"bioformat:decode": "int",})+ Str("/")+ Std.hsp_value(Digits(), {"name\
": "length", "bioformat:decode": "int",})+ ToSep(sep= ",")+ Str(" Posi\
tives =")+ Spaces()+ Std.hsp_value(Digits(), {"name": "positives", "bi\
oformat:decode": "int",})+ ToEol()">Re(r" *Identities = ")+ Std.hsp_value(Digits(), {<code class="variable-ellipsis">...</code></code>
</td>
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<td width="15%" align="right" valign="top" class="summary">
<span class="summary-type"> </span>
</td><td class="summary">
<a name="blastp_hsp_header"></a><span class="summary-name">blastp_hsp_header</span> = <code title="blastp_score+ identities+ spaces_line">blastp_score+ identities+ spaces_line</code>
</td>
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<td width="15%" align="right" valign="top" class="summary">
<span class="summary-type"> </span>
</td><td class="summary">
<a name="blastn_strand"></a><span class="summary-name">blastn_strand</span> = <code title="Re(r" *(Plus|Minus) Strand HSPs:\R")">Re(r" *(Plus|Minus) Strand HSPs:\R")</code>
</td>
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<td width="15%" align="right" valign="top" class="summary">
<span class="summary-type"> </span>
</td><td class="summary">
<a href="Bio.expressions.blast.wublast-module.html#blastn_score" class="summary-name">blastn_score</a> = <code title="Re(r" *Score = *")+ Std.hsp_value(Digits(), {"name": "bits", "bioforma\
t:decode": "int",})+ ToSep(sep= "=")+ Spaces()+ Std.hsp_value(Float(),\
{"name": "expect", "bioformat:decode": "float",})+(Str(", P =") | Re(\
r", Sum P\(\d+\) ="))+ Spaces()+ Std.hsp_value(Float(), {"name": "P", \
"bioformat:decode": "float",})+ ToEol()">Re(r" *Score = *")+ Std.hsp_value(Digits(), {"n<code class="variable-ellipsis">...</code></code>
</td>
</tr>
<tr>
<td width="15%" align="right" valign="top" class="summary">
<span class="summary-type"> </span>
</td><td class="summary">
<a href="Bio.expressions.blast.wublast-module.html#blastn_identities" class="summary-name">blastn_identities</a> = <code title="Re(r" *Identities = ")+ Std.hsp_value(Digits(), {"name": "identical", \
"bioformat:decode": "int",})+ Str("/")+ Std.hsp_value(Digits(), {"name\
": "length", "bioformat:decode": "int",})+ ToSep(sep= ",")+ Str(" Posi\
tives =")+ Spaces()+ Std.hsp_value(Digits(), {"name": "positives", "bi\
oformat:decode": "int",})+ ToSep(sep= ",")+ Str(" ")+ ncbiblast.strand">Re(r" *Identities = ")+ Std.hsp_value(Digi<code class="variable-ellipsis">...</code></code>
</td>
</tr>
<tr>
<td width="15%" align="right" valign="top" class="summary">
<span class="summary-type"> </span>
</td><td class="summary">
<a href="Bio.expressions.blast.wublast-module.html#blastn_hsp_header" class="summary-name">blastn_hsp_header</a> = <code title="Opt(blastn_strand+ spaces_line)+ blastn_score+ blastn_identities+ spac\
es_line">Opt(blastn_strand+ spaces_line)+ blastn_sc<code class="variable-ellipsis">...</code></code>
</td>
</tr>
<tr>
<td width="15%" align="right" valign="top" class="summary">
<span class="summary-type"> </span>
</td><td class="summary">
<a href="Bio.expressions.blast.wublast-module.html#blastx_table_entry" class="summary-name">blastx_table_entry</a> = <code title="AssertNot(AnyEol())+ Std.search_table_description(Re(r".{57}"))+ Space\
s()+ Std.search_table_value(Integer(), {"name": "frame", "bioformat:de\
code": "int"})+ Spaces()+ Std.search_table_value(Float(), {"name": "sc\
ore", "bioformat:decode": "float"})+ Spaces()+ Std.search_table_value(\
Float(), {"name": "P", "bioformat:decode": "float"})+ Spaces()+ Std.se\
arch_table_value(Digits(), {"name": "N", "bioformat:decode": "int"})+ \
AnyEol()">AssertNot(AnyEol())+ Std.search_table_des<code class="variable-ellipsis">...</code></code>
</td>
</tr>
<tr>
<td width="15%" align="right" valign="top" class="summary">
<span class="summary-type"> </span>
</td><td class="summary">
<a href="Bio.expressions.blast.wublast-module.html#blastx_to_database" class="summary-name">blastx_to_database</a> = <code title="Str(" Translating both strands of query sequence in all 6 reading fra\
mes")+ AnyEol()+ AnyEol()">Str(" Translating both strands of query <code class="variable-ellipsis">...</code></code>
</td>
</tr>
<tr>
<td width="15%" align="right" valign="top" class="summary">
<span class="summary-type"> </span>
</td><td class="summary">
<a href="Bio.expressions.blast.wublast-module.html#blastx_identities" class="summary-name">blastx_identities</a> = <code title="Re(r" *Identities = ")+ Std.hsp_value(Digits(), {"name": "identical", \
"bioformat:decode": "int",})+ Str("/")+ Std.hsp_value(Digits(), {"name\
": "length", "bioformat:decode": "int",})+ ToSep(sep= ",")+ Str(" Posi\
tives =")+ Spaces()+ Std.hsp_value(Digits(), {"name": "positives", "bi\
oformat:decode": "int",})+ ToSep(sep= "=")+ Str(" ")+ Std.hsp_frame(In\
teger(), {"which": "query"})+ AnyEol()">Re(r" *Identities = ")+ Std.hsp_value(Digi<code class="variable-ellipsis">...</code></code>
</td>
</tr>
<tr>
<td width="15%" align="right" valign="top" class="summary">
<span class="summary-type"> </span>
</td><td class="summary">
<a href="Bio.expressions.blast.wublast-module.html#blastx_score" class="summary-name">blastx_score</a> = <code title="Re(r" *Score = *")+ Std.hsp_value(Digits(), {"name": "bits", "bioforma\
t:decode": "int",})+ ToSep(sep= "=")+ Spaces()+ Std.hsp_value(Float(),\
{"name": "expect", "bioformat:decode": "float",})+(Str(", P =") | Re(\
r", Sum P\(\d+\) ="))+ Spaces()+ Std.hsp_value(Float(), {"name": "P", \
"bioformat:decode": "float",})+ ToEol()">Re(r" *Score = *")+ Std.hsp_value(Digits(), {"n<code class="variable-ellipsis">...</code></code>
</td>
</tr>
<tr>
<td width="15%" align="right" valign="top" class="summary">
<span class="summary-type"> </span>
</td><td class="summary">
<a name="blastx_strand"></a><span class="summary-name">blastx_strand</span> = <code title="Re(r" *(Plus|Minus) Strand HSPs:\R")">Re(r" *(Plus|Minus) Strand HSPs:\R")</code>
</td>
</tr>
<tr>
<td width="15%" align="right" valign="top" class="summary">
<span class="summary-type"> </span>
</td><td class="summary">
<a href="Bio.expressions.blast.wublast-module.html#blastx_hsp_header" class="summary-name">blastx_hsp_header</a> = <code title="Opt(blastx_strand+ spaces_line)+ blastx_score+ blastx_identities+ spac\
es_line">Opt(blastx_strand+ spaces_line)+ blastx_sc<code class="variable-ellipsis">...</code></code>
</td>
</tr>
<tr>
<td width="15%" align="right" valign="top" class="summary">
<span class="summary-type"> </span>
</td><td class="summary">
<a name="tblastn_strand"></a><span class="summary-name">tblastn_strand</span> = <code title="Re(r" *(Plus|Minus) Strand HSPs:\R")">Re(r" *(Plus|Minus) Strand HSPs:\R")</code>
</td>
</tr>
<tr>
<td width="15%" align="right" valign="top" class="summary">
<span class="summary-type"> </span>
</td><td class="summary">
<a href="Bio.expressions.blast.wublast-module.html#tblastn_score" class="summary-name">tblastn_score</a> = <code title="Re(r" *Score = *")+ Std.hsp_value(Digits(), {"name": "bits", "bioforma\
t:decode": "int",})+ ToSep(sep= "=")+ Spaces()+ Std.hsp_value(Float(),\
{"name": "expect", "bioformat:decode": "float",})+(Str(", P =") | Re(\
r", Sum P\(\d+\) ="))+ Spaces()+ Std.hsp_value(Float(), {"name": "P", \
"bioformat:decode": "float",})+ ToEol()">Re(r" *Score = *")+ Std.hsp_value(Digits(), {"<code class="variable-ellipsis">...</code></code>
</td>
</tr>
<tr>
<td width="15%" align="right" valign="top" class="summary">
<span class="summary-type"> </span>
</td><td class="summary">
<a href="Bio.expressions.blast.wublast-module.html#tblastn_identities" class="summary-name">tblastn_identities</a> = <code title="Re(r" *Identities = ")+ Std.hsp_value(Digits(), {"name": "identical", \
"bioformat:decode": "int",})+ Str("/")+ Std.hsp_value(Digits(), {"name\
": "length", "bioformat:decode": "int",})+ ToSep(sep= ",")+ Str(" Posi\
tives =")+ Spaces()+ Std.hsp_value(Digits(), {"name": "positives", "bi\
oformat:decode": "int",})+ ToSep(sep= ",")+ ncbiblast.frame">Re(r" *Identities = ")+ Std.hsp_value(Dig<code class="variable-ellipsis">...</code></code>
</td>
</tr>
<tr>
<td width="15%" align="right" valign="top" class="summary">
<span class="summary-type"> </span>
</td><td class="summary">
<a href="Bio.expressions.blast.wublast-module.html#tblastn_hsp_header" class="summary-name">tblastn_hsp_header</a> = <code title="Opt(tblastn_strand+ spaces_line)+ tblastn_score+ tblastn_identities+ s\
paces_line">Opt(tblastn_strand+ spaces_line)+ tblastn<code class="variable-ellipsis">...</code></code>
</td>
</tr>
<tr>
<td width="15%" align="right" valign="top" class="summary">
<span class="summary-type"> </span>
</td><td class="summary">
<a href="Bio.expressions.blast.wublast-module.html#ending_start" class="summary-name">ending_start</a> = <code title="Opt(Str("WARNING")+ ToEol()+ Rep(AssertNot(Str(">"))+ AssertNot(Str("P\
arameters"))+ ToEol()))+ Str("Parameters:")+ ToEol()">Opt(Str("WARNING")+ ToEol()+ Rep(AssertNot(Str(<code class="variable-ellipsis">...</code></code>
</td>
</tr>
<tr>
<td width="15%" align="right" valign="top" class="summary">
<span class="summary-type"> </span>
</td><td class="summary">
<a name="parameters"></a><span class="summary-name">parameters</span> = <code title="SkipLinesUntil(Str("Statistics:"))">SkipLinesUntil(Str("Statistics:"))</code>
</td>
</tr>
<tr>
<td width="15%" align="right" valign="top" class="summary">
<span class="summary-type"> </span>
</td><td class="summary">
<a href="Bio.expressions.blast.wublast-module.html#timestamp" class="summary-name">timestamp</a> = <code title="Time.make_expression("%(Mon) %(Jan) %(day) %(hour):%(minute):%(second)\
%(YYYY)")">Time.make_expression("%(Mon) %(Jan) %(day) %(hour)<code class="variable-ellipsis">...</code></code>
</td>
</tr>
<tr>
<td width="15%" align="right" valign="top" class="summary">
<span class="summary-type"> </span>
</td><td class="summary">
<a href="Bio.expressions.blast.wublast-module.html#statistics" class="summary-name">statistics</a> = <code title="Str("Statistics:")+ AnyEol()+ spaces_line+ _nv(" Database: ", Std.sea\
rch_statistic(UntilEol(), {"name": "database"}))+ _nv(" Title: ", S\
td.search_statistic(UntilEol(), {"name": "database_title"}))+ _nv(" \
Release date: ", Std.search_statistic(UntilEol(), {"name": "release_d\
ate"}))+ _nv(" Posted date: ", Std.search_statistic(UntilEol(), {"n\
ame": "posted_date"}))+ _nv(" Format: ", Std.search_statistic(Until\
Eol(), {"name": "format"}))+ _nv(" # of letters in database: ", int_\
stat("num_letters_in_database", comma= 1))+ _nv(" # of sequences in d\
...">Str("Statistics:")+ AnyEol()+ spaces_line+ _nv(" <code class="variable-ellipsis">...</code></code>
</td>
</tr>
<tr>
<td width="15%" align="right" valign="top" class="summary">
<span class="summary-type"> </span>
</td><td class="summary">
<a name="ending"></a><span class="summary-name">ending</span> = <code title="ending_start+ parameters+ statistics">ending_start+ parameters+ statistics</code>
</td>
</tr>
<tr>
<td width="15%" align="right" valign="top" class="summary">
<span class="summary-type"> </span>
</td><td class="summary">
<a name="blastp_ending"></a><span class="summary-name">blastp_ending</span> = <code title="ending_start+ parameters+ statistics">ending_start+ parameters+ statistics</code>
</td>
</tr>
<tr>
<td width="15%" align="right" valign="top" class="summary">
<span class="summary-type"> </span>
</td><td class="summary">
<a name="blastn_ending"></a><span class="summary-name">blastn_ending</span> = <code title="ending_start+ parameters+ statistics">ending_start+ parameters+ statistics</code>
</td>
</tr>
<tr>
<td width="15%" align="right" valign="top" class="summary">
<span class="summary-type"> </span>
</td><td class="summary">
<a name="blastx_ending"></a><span class="summary-name">blastx_ending</span> = <code title="ending_start+ parameters+ statistics">ending_start+ parameters+ statistics</code>
</td>
</tr>
<tr>
<td width="15%" align="right" valign="top" class="summary">
<span class="summary-type"> </span>
</td><td class="summary">
<a href="Bio.expressions.blast.wublast-module.html#format" class="summary-name">format</a> = <code title="replace_groups(ncbiblast.format, (("to_table", to_table), ("table_entr\
y", table_entry), ("ending", ending)))">replace_groups(ncbiblast.format, (("to_table", to_tab<code class="variable-ellipsis">...</code></code>
</td>
</tr>
<tr>
<td width="15%" align="right" valign="top" class="summary">
<span class="summary-type"> </span>
</td><td class="summary">
<a href="Bio.expressions.blast.wublast-module.html#blastp" class="summary-name">blastp</a> = <code title="replace_groups(format, (("appheader", blastp_appheader), ("hsp_header"\
, blastp_hsp_header)))">replace_groups(format, (("appheader", blastp_appheade<code class="variable-ellipsis">...</code></code>
</td>
</tr>
<tr>
<td width="15%" align="right" valign="top" class="summary">
<span class="summary-type"> </span>
</td><td class="summary">
<a href="Bio.expressions.blast.wublast-module.html#blastn" class="summary-name">blastn</a> = <code title="replace_groups(format, (("appheader", blastn_appheader), ("hsp_header"\
, blastn_hsp_header)))">replace_groups(format, (("appheader", blastn_appheade<code class="variable-ellipsis">...</code></code>
</td>
</tr>
<tr>
<td width="15%" align="right" valign="top" class="summary">
<span class="summary-type"> </span>
</td><td class="summary">
<a href="Bio.expressions.blast.wublast-module.html#blastx" class="summary-name">blastx</a> = <code title="replace_groups(format, (("appheader", blastx_appheader), ("table_entry\
", blastx_table_entry), ("to_database", blastx_to_database), ("hsp_hea\
der", blastx_hsp_header)))">replace_groups(format, (("appheader", blastx_appheade<code class="variable-ellipsis">...</code></code>
</td>
</tr>
<tr>
<td width="15%" align="right" valign="top" class="summary">
<span class="summary-type"> </span>
</td><td class="summary">
<a href="Bio.expressions.blast.wublast-module.html#tblastn" class="summary-name">tblastn</a> = <code title="replace_groups(format, (("appheader", tblastn_appheader), ("table_entr\
y", blastx_table_entry), ("hsp_header", tblastn_hsp_header)))">replace_groups(format, (("appheader", tblastn_apphea<code class="variable-ellipsis">...</code></code>
</td>
</tr>
<tr>
<td width="15%" align="right" valign="top" class="summary">
<span class="summary-type"> </span>
</td><td class="summary">
<a href="Bio.expressions.blast.wublast-module.html#__warningregistry__" class="summary-name">__warningregistry__</a> = <code title="{('Bio.expressions was deprecated, as it does not work with recent ver\
sions of mxTextTools. If you want to continue to use this module, plea\
se get in contact with the Biopython developers at biopython-dev@biopy\
thon.org to avoid permanent removal of this module from Biopython',
<type 'exceptions.DeprecationWarning'>,
2): 1}"><code class="variable-group">{</code><code class="variable-group">(</code><code class="variable-quote">'</code><code class="variable-string">Bio.expressions was deprecated, as it</code><code class="variable-ellipsis">...</code></code>
</td>
</tr>
</table>
<!-- ==================== VARIABLES DETAILS ==================== -->
<a name="section-VariablesDetails"></a>
<table class="details" border="1" cellpadding="3"
cellspacing="0" width="100%" bgcolor="white">
<tr bgcolor="#70b0f0" class="table-header">
<td colspan="2" class="table-header">
<table border="0" cellpadding="0" cellspacing="0" width="100%">
<tr valign="top">
<td align="left"><span class="table-header">Variables Details</span></td>
<td align="right" valign="top"
><span class="options">[<a href="#section-VariablesDetails"
class="privatelink" onclick="toggle_private();"
>hide private</a>]</span></td>
</tr>
</table>
</td>
</tr>
</table>
<a name="blastn_appheader"></a>
<div>
<table class="details" border="1" cellpadding="3"
cellspacing="0" width="100%" bgcolor="white">
<tr><td>
<h3 class="epydoc">blastn_appheader</h3>
<dl class="fields">
</dl>
<dl class="fields">
<dt>Value:</dt>
<dd><table><tr><td><pre class="variable">
replace_groups(ncbiblast.blastn_appheader, [("appversion", wublast_ver<span class="variable-linewrap"><img src="crarr.png" alt="\" /></span>
sion)])
</pre></td></tr></table>
</dd>
</dl>
</td></tr></table>
</div>
<a name="blastp_appheader"></a>
<div>
<table class="details" border="1" cellpadding="3"
cellspacing="0" width="100%" bgcolor="white">
<tr><td>
<h3 class="epydoc">blastp_appheader</h3>
<dl class="fields">
</dl>
<dl class="fields">
<dt>Value:</dt>
<dd><table><tr><td><pre class="variable">
replace_groups(ncbiblast.blastp_appheader, [("appversion", wublast_ver<span class="variable-linewrap"><img src="crarr.png" alt="\" /></span>
sion)])
</pre></td></tr></table>
</dd>
</dl>
</td></tr></table>
</div>
<a name="blastx_appheader"></a>
<div>
<table class="details" border="1" cellpadding="3"
cellspacing="0" width="100%" bgcolor="white">
<tr><td>
<h3 class="epydoc">blastx_appheader</h3>
<dl class="fields">
</dl>
<dl class="fields">
<dt>Value:</dt>
<dd><table><tr><td><pre class="variable">
replace_groups(ncbiblast.blastx_appheader, [("appversion", wublast_ver<span class="variable-linewrap"><img src="crarr.png" alt="\" /></span>
sion)])
</pre></td></tr></table>
</dd>
</dl>
</td></tr></table>
</div>
<a name="tblastn_appheader"></a>
<div>
<table class="details" border="1" cellpadding="3"
cellspacing="0" width="100%" bgcolor="white">
<tr><td>
<h3 class="epydoc">tblastn_appheader</h3>
<dl class="fields">
</dl>
<dl class="fields">
<dt>Value:</dt>
<dd><table><tr><td><pre class="variable">
replace_groups(ncbiblast.tblastn_appheader, [("appversion", wublast_ve<span class="variable-linewrap"><img src="crarr.png" alt="\" /></span>
rsion)])
</pre></td></tr></table>
</dd>
</dl>
</td></tr></table>
</div>
<a name="tblastx_appheader"></a>
<div>
<table class="details" border="1" cellpadding="3"
cellspacing="0" width="100%" bgcolor="white">
<tr><td>
<h3 class="epydoc">tblastx_appheader</h3>
<dl class="fields">
</dl>
<dl class="fields">
<dt>Value:</dt>
<dd><table><tr><td><pre class="variable">
replace_groups(ncbiblast.tblastx_appheader, [("appversion", wublast_ve<span class="variable-linewrap"><img src="crarr.png" alt="\" /></span>
rsion)])
</pre></td></tr></table>
</dd>
</dl>
</td></tr></table>
</div>
<a name="query_database"></a>
<div>
<table class="details" border="1" cellpadding="3"
cellspacing="0" width="100%" bgcolor="white">
<tr><td>
<h3 class="epydoc">query_database</h3>
<dl class="fields">
</dl>
<dl class="fields">
<dt>Value:</dt>
<dd><table><tr><td><pre class="variable">
Str("Database:")+ Opt(Spaces())+ Std.database_name(UntilEol())+ AnyEol<span class="variable-linewrap"><img src="crarr.png" alt="\" /></span>
()+ Spaces()+ Std.database_num_sequences(Number(), {"bioformat:decode"<span class="variable-linewrap"><img src="crarr.png" alt="\" /></span>
: "int.comma"})+ Str(" sequences;")+ Spaces()+ Std.database_num_letter<span class="variable-linewrap"><img src="crarr.png" alt="\" /></span>
s(Number(), {"bioformat:decode": "int.comma"})+ Spaces()+ Str("total l<span class="variable-linewrap"><img src="crarr.png" alt="\" /></span>
etters.")+ ToEol()
</pre></td></tr></table>
</dd>
</dl>
</td></tr></table>
</div>
<a name="to_table"></a>
<div>
<table class="details" border="1" cellpadding="3"
cellspacing="0" width="100%" bgcolor="white">
<tr><td>
<h3 class="epydoc">to_table</h3>
<dl class="fields">
</dl>
<dl class="fields">
<dt>Value:</dt>
<dd><table><tr><td><pre class="variable">
SkipLinesUntil(Str("Sequences producing High-scoring Segment"))+ ToEol<span class="variable-linewrap"><img src="crarr.png" alt="\" /></span>
()+ AnyEol()
</pre></td></tr></table>
</dd>
</dl>
</td></tr></table>
</div>
<a name="table_entry"></a>
<div>
<table class="details" border="1" cellpadding="3"
cellspacing="0" width="100%" bgcolor="white">
<tr><td>
<h3 class="epydoc">table_entry</h3>
<dl class="fields">
</dl>
<dl class="fields">
<dt>Value:</dt>
<dd><table><tr><td><pre class="variable">
AssertNot(AnyEol())+ Std.search_table_description(Re(r".{60}"))+ Space<span class="variable-linewrap"><img src="crarr.png" alt="\" /></span>
s()+ Std.search_table_value(Float(), {"name": "score", "bioformat:deco<span class="variable-linewrap"><img src="crarr.png" alt="\" /></span>
de": "float"})+ Spaces()+ Std.search_table_value(Float(), {"name": "P"<span class="variable-linewrap"><img src="crarr.png" alt="\" /></span>
, "bioformat:decode": "float"})+ Spaces()+ Std.search_table_value(Digi<span class="variable-linewrap"><img src="crarr.png" alt="\" /></span>
ts(), {"name": "N", "bioformat:decode": "float"})+ AnyEol()
</pre></td></tr></table>
</dd>
</dl>
</td></tr></table>
</div>
<a name="header"></a>
<div>
<table class="details" border="1" cellpadding="3"
cellspacing="0" width="100%" bgcolor="white">
<tr><td>
<h3 class="epydoc">header</h3>
<dl class="fields">
</dl>
<dl class="fields">
<dt>Value:</dt>
<dd><table><tr><td><pre class="variable">
replace_groups(ncbiblast.header, (("query_database", query_database), <span class="variable-linewrap"><img src="crarr.png" alt="\" /></span>
("to_table", to_table), ("table_entry", table_entry)))
</pre></td></tr></table>
</dd>
</dl>
</td></tr></table>
</div>
<a name="hit_descr"></a>
<div>
<table class="details" border="1" cellpadding="3"
cellspacing="0" width="100%" bgcolor="white">
<tr><td>
<h3 class="epydoc">hit_descr</h3>
<dl class="fields">
</dl>
<dl class="fields">
<dt>Value:</dt>
<dd><table><tr><td><pre class="variable">
Str(">")+ Std.hit_description(UntilEol())+ AnyEol()+ Rep(AssertNot(hit<span class="variable-linewrap"><img src="crarr.png" alt="\" /></span>
_length)+ Std.hit_description(UntilEol())+ AnyEol())
</pre></td></tr></table>
</dd>
</dl>
</td></tr></table>
</div>
<a name="hit_length"></a>
<div>
<table class="details" border="1" cellpadding="3"
cellspacing="0" width="100%" bgcolor="white">
<tr><td>
<h3 class="epydoc">hit_length</h3>
<dl class="fields">
</dl>
<dl class="fields">
<dt>Value:</dt>
<dd><table><tr><td><pre class="variable">
Spaces()+ Str("Length = ")+ Std.hit_length(Digits())+ AnyEol()+ Opt(Sp<span class="variable-linewrap"><img src="crarr.png" alt="\" /></span>
aces())+ AnyEol()
</pre></td></tr></table>
</dd>
</dl>
</td></tr></table>
</div>
<a name="blastp_score"></a>
<div>
<table class="details" border="1" cellpadding="3"
cellspacing="0" width="100%" bgcolor="white">
<tr><td>
<h3 class="epydoc">blastp_score</h3>
<dl class="fields">
</dl>
<dl class="fields">
<dt>Value:</dt>
<dd><table><tr><td><pre class="variable">
Re(r" *Score = *")+ Std.hsp_value(Digits(), {"name": "bits", "bioforma<span class="variable-linewrap"><img src="crarr.png" alt="\" /></span>
t:decode": "int",})+ ToSep(sep= "=")+ Spaces()+ Std.hsp_value(Float(),<span class="variable-linewrap"><img src="crarr.png" alt="\" /></span>
{"name": "expect", "bioformat:decode": "float",})+(Str(", P =") | Re(<span class="variable-linewrap"><img src="crarr.png" alt="\" /></span>
r", Sum P\(\d+\) ="))+ Spaces()+ Std.hsp_value(Float(), {"name": "P", <span class="variable-linewrap"><img src="crarr.png" alt="\" /></span>
"bioformat:decode": "float",})+ ToEol()
</pre></td></tr></table>
</dd>
</dl>
</td></tr></table>
</div>
<a name="identities"></a>
<div>
<table class="details" border="1" cellpadding="3"
cellspacing="0" width="100%" bgcolor="white">
<tr><td>
<h3 class="epydoc">identities</h3>
<dl class="fields">
</dl>
<dl class="fields">
<dt>Value:</dt>
<dd><table><tr><td><pre class="variable">
Re(r" *Identities = ")+ Std.hsp_value(Digits(), {"name": "identical", <span class="variable-linewrap"><img src="crarr.png" alt="\" /></span>
"bioformat:decode": "int",})+ Str("/")+ Std.hsp_value(Digits(), {"name<span class="variable-linewrap"><img src="crarr.png" alt="\" /></span>
": "length", "bioformat:decode": "int",})+ ToSep(sep= ",")+ Str(" Posi<span class="variable-linewrap"><img src="crarr.png" alt="\" /></span>
tives =")+ Spaces()+ Std.hsp_value(Digits(), {"name": "positives", "bi<span class="variable-linewrap"><img src="crarr.png" alt="\" /></span>
oformat:decode": "int",})+ ToEol()
</pre></td></tr></table>
</dd>
</dl>
</td></tr></table>
</div>
<a name="blastn_score"></a>
<div>
<table class="details" border="1" cellpadding="3"
cellspacing="0" width="100%" bgcolor="white">
<tr><td>
<h3 class="epydoc">blastn_score</h3>
<dl class="fields">
</dl>
<dl class="fields">
<dt>Value:</dt>
<dd><table><tr><td><pre class="variable">
Re(r" *Score = *")+ Std.hsp_value(Digits(), {"name": "bits", "bioforma<span class="variable-linewrap"><img src="crarr.png" alt="\" /></span>
t:decode": "int",})+ ToSep(sep= "=")+ Spaces()+ Std.hsp_value(Float(),<span class="variable-linewrap"><img src="crarr.png" alt="\" /></span>
{"name": "expect", "bioformat:decode": "float",})+(Str(", P =") | Re(<span class="variable-linewrap"><img src="crarr.png" alt="\" /></span>
r", Sum P\(\d+\) ="))+ Spaces()+ Std.hsp_value(Float(), {"name": "P", <span class="variable-linewrap"><img src="crarr.png" alt="\" /></span>
"bioformat:decode": "float",})+ ToEol()
</pre></td></tr></table>
</dd>
</dl>
</td></tr></table>
</div>
<a name="blastn_identities"></a>
<div>
<table class="details" border="1" cellpadding="3"
cellspacing="0" width="100%" bgcolor="white">
<tr><td>
<h3 class="epydoc">blastn_identities</h3>
<dl class="fields">
</dl>
<dl class="fields">
<dt>Value:</dt>
<dd><table><tr><td><pre class="variable">
Re(r" *Identities = ")+ Std.hsp_value(Digits(), {"name": "identical", <span class="variable-linewrap"><img src="crarr.png" alt="\" /></span>
"bioformat:decode": "int",})+ Str("/")+ Std.hsp_value(Digits(), {"name<span class="variable-linewrap"><img src="crarr.png" alt="\" /></span>
": "length", "bioformat:decode": "int",})+ ToSep(sep= ",")+ Str(" Posi<span class="variable-linewrap"><img src="crarr.png" alt="\" /></span>
tives =")+ Spaces()+ Std.hsp_value(Digits(), {"name": "positives", "bi<span class="variable-linewrap"><img src="crarr.png" alt="\" /></span>
oformat:decode": "int",})+ ToSep(sep= ",")+ Str(" ")+ ncbiblast.strand
</pre></td></tr></table>
</dd>
</dl>
</td></tr></table>
</div>
<a name="blastn_hsp_header"></a>
<div>
<table class="details" border="1" cellpadding="3"
cellspacing="0" width="100%" bgcolor="white">
<tr><td>
<h3 class="epydoc">blastn_hsp_header</h3>
<dl class="fields">
</dl>
<dl class="fields">
<dt>Value:</dt>
<dd><table><tr><td><pre class="variable">
Opt(blastn_strand+ spaces_line)+ blastn_score+ blastn_identities+ spac<span class="variable-linewrap"><img src="crarr.png" alt="\" /></span>
es_line
</pre></td></tr></table>
</dd>
</dl>
</td></tr></table>
</div>
<a name="blastx_table_entry"></a>
<div>
<table class="details" border="1" cellpadding="3"
cellspacing="0" width="100%" bgcolor="white">
<tr><td>
<h3 class="epydoc">blastx_table_entry</h3>
<dl class="fields">
</dl>
<dl class="fields">
<dt>Value:</dt>
<dd><table><tr><td><pre class="variable">
AssertNot(AnyEol())+ Std.search_table_description(Re(r".{57}"))+ Space<span class="variable-linewrap"><img src="crarr.png" alt="\" /></span>
s()+ Std.search_table_value(Integer(), {"name": "frame", "bioformat:de<span class="variable-linewrap"><img src="crarr.png" alt="\" /></span>
code": "int"})+ Spaces()+ Std.search_table_value(Float(), {"name": "sc<span class="variable-linewrap"><img src="crarr.png" alt="\" /></span>
ore", "bioformat:decode": "float"})+ Spaces()+ Std.search_table_value(<span class="variable-linewrap"><img src="crarr.png" alt="\" /></span>
Float(), {"name": "P", "bioformat:decode": "float"})+ Spaces()+ Std.se<span class="variable-linewrap"><img src="crarr.png" alt="\" /></span>
arch_table_value(Digits(), {"name": "N", "bioformat:decode": "int"})+ <span class="variable-linewrap"><img src="crarr.png" alt="\" /></span>
AnyEol()
</pre></td></tr></table>
</dd>
</dl>
</td></tr></table>
</div>
<a name="blastx_to_database"></a>
<div>
<table class="details" border="1" cellpadding="3"
cellspacing="0" width="100%" bgcolor="white">
<tr><td>
<h3 class="epydoc">blastx_to_database</h3>
<dl class="fields">
</dl>
<dl class="fields">
<dt>Value:</dt>
<dd><table><tr><td><pre class="variable">
Str(" Translating both strands of query sequence in all 6 reading fra<span class="variable-linewrap"><img src="crarr.png" alt="\" /></span>
mes")+ AnyEol()+ AnyEol()
</pre></td></tr></table>
</dd>
</dl>
</td></tr></table>
</div>
<a name="blastx_identities"></a>
<div>
<table class="details" border="1" cellpadding="3"
cellspacing="0" width="100%" bgcolor="white">
<tr><td>
<h3 class="epydoc">blastx_identities</h3>
<dl class="fields">
</dl>
<dl class="fields">
<dt>Value:</dt>
<dd><table><tr><td><pre class="variable">
Re(r" *Identities = ")+ Std.hsp_value(Digits(), {"name": "identical", <span class="variable-linewrap"><img src="crarr.png" alt="\" /></span>
"bioformat:decode": "int",})+ Str("/")+ Std.hsp_value(Digits(), {"name<span class="variable-linewrap"><img src="crarr.png" alt="\" /></span>
": "length", "bioformat:decode": "int",})+ ToSep(sep= ",")+ Str(" Posi<span class="variable-linewrap"><img src="crarr.png" alt="\" /></span>
tives =")+ Spaces()+ Std.hsp_value(Digits(), {"name": "positives", "bi<span class="variable-linewrap"><img src="crarr.png" alt="\" /></span>
oformat:decode": "int",})+ ToSep(sep= "=")+ Str(" ")+ Std.hsp_frame(In<span class="variable-linewrap"><img src="crarr.png" alt="\" /></span>
teger(), {"which": "query"})+ AnyEol()
</pre></td></tr></table>
</dd>
</dl>
</td></tr></table>
</div>
<a name="blastx_score"></a>
<div>
<table class="details" border="1" cellpadding="3"
cellspacing="0" width="100%" bgcolor="white">
<tr><td>
<h3 class="epydoc">blastx_score</h3>
<dl class="fields">
</dl>
<dl class="fields">
<dt>Value:</dt>
<dd><table><tr><td><pre class="variable">
Re(r" *Score = *")+ Std.hsp_value(Digits(), {"name": "bits", "bioforma<span class="variable-linewrap"><img src="crarr.png" alt="\" /></span>
t:decode": "int",})+ ToSep(sep= "=")+ Spaces()+ Std.hsp_value(Float(),<span class="variable-linewrap"><img src="crarr.png" alt="\" /></span>
{"name": "expect", "bioformat:decode": "float",})+(Str(", P =") | Re(<span class="variable-linewrap"><img src="crarr.png" alt="\" /></span>
r", Sum P\(\d+\) ="))+ Spaces()+ Std.hsp_value(Float(), {"name": "P", <span class="variable-linewrap"><img src="crarr.png" alt="\" /></span>
"bioformat:decode": "float",})+ ToEol()
</pre></td></tr></table>
</dd>
</dl>
</td></tr></table>
</div>
<a name="blastx_hsp_header"></a>
<div>
<table class="details" border="1" cellpadding="3"
cellspacing="0" width="100%" bgcolor="white">
<tr><td>
<h3 class="epydoc">blastx_hsp_header</h3>
<dl class="fields">
</dl>
<dl class="fields">
<dt>Value:</dt>
<dd><table><tr><td><pre class="variable">
Opt(blastx_strand+ spaces_line)+ blastx_score+ blastx_identities+ spac<span class="variable-linewrap"><img src="crarr.png" alt="\" /></span>
es_line
</pre></td></tr></table>
</dd>
</dl>
</td></tr></table>
</div>
<a name="tblastn_score"></a>
<div>
<table class="details" border="1" cellpadding="3"
cellspacing="0" width="100%" bgcolor="white">
<tr><td>
<h3 class="epydoc">tblastn_score</h3>
<dl class="fields">
</dl>
<dl class="fields">
<dt>Value:</dt>
<dd><table><tr><td><pre class="variable">
Re(r" *Score = *")+ Std.hsp_value(Digits(), {"name": "bits", "bioforma<span class="variable-linewrap"><img src="crarr.png" alt="\" /></span>
t:decode": "int",})+ ToSep(sep= "=")+ Spaces()+ Std.hsp_value(Float(),<span class="variable-linewrap"><img src="crarr.png" alt="\" /></span>
{"name": "expect", "bioformat:decode": "float",})+(Str(", P =") | Re(<span class="variable-linewrap"><img src="crarr.png" alt="\" /></span>
r", Sum P\(\d+\) ="))+ Spaces()+ Std.hsp_value(Float(), {"name": "P", <span class="variable-linewrap"><img src="crarr.png" alt="\" /></span>
"bioformat:decode": "float",})+ ToEol()
</pre></td></tr></table>
</dd>
</dl>
</td></tr></table>
</div>
<a name="tblastn_identities"></a>
<div>
<table class="details" border="1" cellpadding="3"
cellspacing="0" width="100%" bgcolor="white">
<tr><td>
<h3 class="epydoc">tblastn_identities</h3>
<dl class="fields">
</dl>
<dl class="fields">
<dt>Value:</dt>
<dd><table><tr><td><pre class="variable">
Re(r" *Identities = ")+ Std.hsp_value(Digits(), {"name": "identical", <span class="variable-linewrap"><img src="crarr.png" alt="\" /></span>
"bioformat:decode": "int",})+ Str("/")+ Std.hsp_value(Digits(), {"name<span class="variable-linewrap"><img src="crarr.png" alt="\" /></span>
": "length", "bioformat:decode": "int",})+ ToSep(sep= ",")+ Str(" Posi<span class="variable-linewrap"><img src="crarr.png" alt="\" /></span>
tives =")+ Spaces()+ Std.hsp_value(Digits(), {"name": "positives", "bi<span class="variable-linewrap"><img src="crarr.png" alt="\" /></span>
oformat:decode": "int",})+ ToSep(sep= ",")+ ncbiblast.frame
</pre></td></tr></table>
</dd>
</dl>
</td></tr></table>
</div>
<a name="tblastn_hsp_header"></a>
<div>
<table class="details" border="1" cellpadding="3"
cellspacing="0" width="100%" bgcolor="white">
<tr><td>
<h3 class="epydoc">tblastn_hsp_header</h3>
<dl class="fields">
</dl>
<dl class="fields">
<dt>Value:</dt>
<dd><table><tr><td><pre class="variable">
Opt(tblastn_strand+ spaces_line)+ tblastn_score+ tblastn_identities+ s<span class="variable-linewrap"><img src="crarr.png" alt="\" /></span>
paces_line
</pre></td></tr></table>
</dd>
</dl>
</td></tr></table>
</div>
<a name="ending_start"></a>
<div>
<table class="details" border="1" cellpadding="3"
cellspacing="0" width="100%" bgcolor="white">
<tr><td>
<h3 class="epydoc">ending_start</h3>
<dl class="fields">
</dl>
<dl class="fields">
<dt>Value:</dt>
<dd><table><tr><td><pre class="variable">
Opt(Str("WARNING")+ ToEol()+ Rep(AssertNot(Str(">"))+ AssertNot(Str("P<span class="variable-linewrap"><img src="crarr.png" alt="\" /></span>
arameters"))+ ToEol()))+ Str("Parameters:")+ ToEol()
</pre></td></tr></table>
</dd>
</dl>
</td></tr></table>
</div>
<a name="timestamp"></a>
<div>
<table class="details" border="1" cellpadding="3"
cellspacing="0" width="100%" bgcolor="white">
<tr><td>
<h3 class="epydoc">timestamp</h3>
<dl class="fields">
</dl>
<dl class="fields">
<dt>Value:</dt>
<dd><table><tr><td><pre class="variable">
Time.make_expression("%(Mon) %(Jan) %(day) %(hour):%(minute):%(second)<span class="variable-linewrap"><img src="crarr.png" alt="\" /></span>
%(YYYY)")
</pre></td></tr></table>
</dd>
</dl>
</td></tr></table>
</div>
<a name="statistics"></a>
<div>
<table class="details" border="1" cellpadding="3"
cellspacing="0" width="100%" bgcolor="white">
<tr><td>
<h3 class="epydoc">statistics</h3>
<dl class="fields">
</dl>
<dl class="fields">
<dt>Value:</dt>
<dd><table><tr><td><pre class="variable">
Str("Statistics:")+ AnyEol()+ spaces_line+ _nv(" Database: ", Std.sea<span class="variable-linewrap"><img src="crarr.png" alt="\" /></span>
rch_statistic(UntilEol(), {"name": "database"}))+ _nv(" Title: ", S<span class="variable-linewrap"><img src="crarr.png" alt="\" /></span>
td.search_statistic(UntilEol(), {"name": "database_title"}))+ _nv(" <span class="variable-linewrap"><img src="crarr.png" alt="\" /></span>
Release date: ", Std.search_statistic(UntilEol(), {"name": "release_d<span class="variable-linewrap"><img src="crarr.png" alt="\" /></span>
ate"}))+ _nv(" Posted date: ", Std.search_statistic(UntilEol(), {"n<span class="variable-linewrap"><img src="crarr.png" alt="\" /></span>
ame": "posted_date"}))+ _nv(" Format: ", Std.search_statistic(Until<span class="variable-linewrap"><img src="crarr.png" alt="\" /></span>
Eol(), {"name": "format"}))+ _nv(" # of letters in database: ", int_<span class="variable-linewrap"><img src="crarr.png" alt="\" /></span>
stat("num_letters_in_database", comma= 1))+ _nv(" # of sequences in d<span class="variable-linewrap"><img src="crarr.png" alt="\" /></span>
<code class="variable-ellipsis">...</code>
</pre></td></tr></table>
</dd>
</dl>
</td></tr></table>
</div>
<a name="format"></a>
<div>
<table class="details" border="1" cellpadding="3"
cellspacing="0" width="100%" bgcolor="white">
<tr><td>
<h3 class="epydoc">format</h3>
<dl class="fields">
</dl>
<dl class="fields">
<dt>Value:</dt>
<dd><table><tr><td><pre class="variable">
replace_groups(ncbiblast.format, (("to_table", to_table), ("table_entr<span class="variable-linewrap"><img src="crarr.png" alt="\" /></span>
y", table_entry), ("ending", ending)))
</pre></td></tr></table>
</dd>
</dl>
</td></tr></table>
</div>
<a name="blastp"></a>
<div>
<table class="details" border="1" cellpadding="3"
cellspacing="0" width="100%" bgcolor="white">
<tr><td>
<h3 class="epydoc">blastp</h3>
<dl class="fields">
</dl>
<dl class="fields">
<dt>Value:</dt>
<dd><table><tr><td><pre class="variable">
replace_groups(format, (("appheader", blastp_appheader), ("hsp_header"<span class="variable-linewrap"><img src="crarr.png" alt="\" /></span>
, blastp_hsp_header)))
</pre></td></tr></table>
</dd>
</dl>
</td></tr></table>
</div>
<a name="blastn"></a>
<div>
<table class="details" border="1" cellpadding="3"
cellspacing="0" width="100%" bgcolor="white">
<tr><td>
<h3 class="epydoc">blastn</h3>
<dl class="fields">
</dl>
<dl class="fields">
<dt>Value:</dt>
<dd><table><tr><td><pre class="variable">
replace_groups(format, (("appheader", blastn_appheader), ("hsp_header"<span class="variable-linewrap"><img src="crarr.png" alt="\" /></span>
, blastn_hsp_header)))
</pre></td></tr></table>
</dd>
</dl>
</td></tr></table>
</div>
<a name="blastx"></a>
<div>
<table class="details" border="1" cellpadding="3"
cellspacing="0" width="100%" bgcolor="white">
<tr><td>
<h3 class="epydoc">blastx</h3>
<dl class="fields">
</dl>
<dl class="fields">
<dt>Value:</dt>
<dd><table><tr><td><pre class="variable">
replace_groups(format, (("appheader", blastx_appheader), ("table_entry<span class="variable-linewrap"><img src="crarr.png" alt="\" /></span>
", blastx_table_entry), ("to_database", blastx_to_database), ("hsp_hea<span class="variable-linewrap"><img src="crarr.png" alt="\" /></span>
der", blastx_hsp_header)))
</pre></td></tr></table>
</dd>
</dl>
</td></tr></table>
</div>
<a name="tblastn"></a>
<div>
<table class="details" border="1" cellpadding="3"
cellspacing="0" width="100%" bgcolor="white">
<tr><td>
<h3 class="epydoc">tblastn</h3>
<dl class="fields">
</dl>
<dl class="fields">
<dt>Value:</dt>
<dd><table><tr><td><pre class="variable">
replace_groups(format, (("appheader", tblastn_appheader), ("table_entr<span class="variable-linewrap"><img src="crarr.png" alt="\" /></span>
y", blastx_table_entry), ("hsp_header", tblastn_hsp_header)))
</pre></td></tr></table>
</dd>
</dl>
</td></tr></table>
</div>
<a name="__warningregistry__"></a>
<div>
<table class="details" border="1" cellpadding="3"
cellspacing="0" width="100%" bgcolor="white">
<tr><td>
<h3 class="epydoc">__warningregistry__</h3>
<dl class="fields">
</dl>
<dl class="fields">
<dt>Value:</dt>
<dd><table><tr><td><pre class="variable">
<code class="variable-group">{</code><code class="variable-group">(</code><code class="variable-quote">'</code><code class="variable-string">Bio.expressions was deprecated, as it does not work with recent ver</code><span class="variable-linewrap"><img src="crarr.png" alt="\" /></span>
<code class="variable-string">sions of mxTextTools. If you want to continue to use this module, plea</code><span class="variable-linewrap"><img src="crarr.png" alt="\" /></span>
<code class="variable-string">se get in contact with the Biopython developers at biopython-dev@biopy</code><span class="variable-linewrap"><img src="crarr.png" alt="\" /></span>
<code class="variable-string">thon.org to avoid permanent removal of this module from Biopython</code><code class="variable-quote">'</code><code class="variable-op">,</code>
<type 'exceptions.DeprecationWarning'><code class="variable-op">,</code>
2<code class="variable-group">)</code><code class="variable-op">: </code>1<code class="variable-group">}</code>
</pre></td></tr></table>
</dd>
</dl>
</td></tr></table>
</div>
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