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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.embl-module.html">Package embl</a> ::
Module embl65
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<!-- ==================== MODULE DESCRIPTION ==================== -->
<h1 class="epydoc">Module embl65</h1><p class="nomargin-top"><span class="codelink"><a href="Bio.expressions.embl.embl65-pysrc.html">source code</a></span></p>
<p>Format from EMBL Nucleotide Sequence Database Release 65, December
2000</p>
<!-- ==================== VARIABLES ==================== -->
<a name="section-Variables"></a>
<table class="summary" 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</span></td>
<td align="right" valign="top"
><span class="options">[<a href="#section-Variables"
class="privatelink" onclick="toggle_private();"
>hide private</a>]</span></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="whitespace"></a><span class="summary-name">whitespace</span> = <code title="Martel.Spaces()">Martel.Spaces()</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.embl.embl65-module.html#divisions" class="summary-name">divisions</a> = <code title="Martel.Re("EST|PHG|FUN|GSS|HTC|HTG|HUM|INV|ORG|MAM|VRT|PLN|"+ "PRO|ROD\
|SYN|STS|UNC|VRL|[A-Z]{3}")">Martel.Re("EST|PHG|FUN|GSS|HTC|HTG|HUM|INV|ORG|MAM<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.embl.embl65-module.html#ID_line" class="summary-name">ID_line</a> = <code title="Martel.Str("ID ")+ Std.dbid(Martel.UntilSep("entry_name", " "), {"ty\
pe": "primary", "dbname": "embl"})+ whitespace+ Martel.ToSep("dataclas\
s", ";")+ whitespace+ Martel.Group("molecule", Std.alphabet(Martel.Str\
("DNA", "circular DNA"), {"alphabet": "iupac-ambiguous-dna"}) | Std.al\
phabet(Martel.Str("RNA", "circular RNA"), {"alphabet": "iupac-ambiguou\
s-rna"}) | Std.alphabet(Martel.Str("XXX"), {"alphabet": "nucleotide"})\
)+ Martel.Str("; ")+ Martel.Group("division", divisions)+ Martel.Str("\
; ")+ Martel.Digits("length")+ Martel.Str(" BP.")+ Martel.AnyEol()">Martel.Str("ID ")+ Std.dbid(Martel.UntilSep("entry<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.embl.embl65-module.html#accession" class="summary-name">accession</a> = <code title="Std.dbid(Martel.UntilSep("accession", ";"), {"type": "accession", "dbn\
ame": "embl"})+ Martel.Str(";")">Std.dbid(Martel.UntilSep("accession", ";"), {"type<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.embl.embl65-module.html#AC_line" class="summary-name">AC_line</a> = <code title="Martel.Str("AC ")+ accession+ Martel.Rep(Martel.Str(" ")+ accession)\
+ Martel.AnyEol()">Martel.Str("AC ")+ accession+ Martel.Rep(Martel.St<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="AC_block"></a><span class="summary-name">AC_block</span> = <code title="Martel.Rep1(AC_line)">Martel.Rep1(AC_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 href="Bio.expressions.embl.embl65-module.html#SV_line" class="summary-name">SV_line</a> = <code title="Martel.Str("SV ")+ Martel.Group("sequence_version", Martel.ToSep("ac\
cession", ".")+ Martel.Digits("version"))+ Martel.AnyEol()">Martel.Str("SV ")+ Martel.Group("sequence_version"<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="date"></a><span class="summary-name">date</span> = <code title="Time.make_expression("%(day)-%(Jan)-%(year)")">Time.make_expression("%(day)-%(Jan)-%(year)")</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.embl.embl65-module.html#DT_created_line" class="summary-name">DT_created_line</a> = <code title="Martel.Str("DT ")+ Martel.Group("date_created", date)+ Martel.Str(" \
(Rel. ")+ Martel.Digits("release_created")+ Martel.Str(", Created)")+ \
Martel.AnyEol()">Martel.Str("DT ")+ Martel.Group("date_crea<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.embl.embl65-module.html#DT_updated_line" class="summary-name">DT_updated_line</a> = <code title="Martel.Str("DT ")+ Martel.Group("date_updated", date)+ Martel.Str(" \
(Rel. ")+ Martel.Digits("release_updated")+ Martel.Str(", Last updated\
, Version ")+ Martel.Digits("version_number")+ Martel.Str(")")+ Martel\
.AnyEol()">Martel.Str("DT ")+ Martel.Group("date_upda<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="DT_block"></a><span class="summary-name">DT_block</span> = <code title="DT_created_line+ DT_updated_line">DT_created_line+ DT_updated_line</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.embl.embl65-module.html#DE_line" class="summary-name">DE_line</a> = <code title="Martel.Str("DE ")+ Std.description(Martel.UntilEol("description"))+ \
Martel.AnyEol()">Martel.Str("DE ")+ Std.description(Martel.UntilEol<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.embl.embl65-module.html#DE_block" class="summary-name">DE_block</a> = <code title="Std.description_block(Martel.Group("description_block", Martel.Rep1(DE\
_line)))">Std.description_block(Martel.Group("description_blo<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="KW_line"></a><span class="summary-name">KW_line</span> = <code title="Martel.Str("KW ")+ Martel.ToEol("keyword_data")">Martel.Str("KW ")+ Martel.ToEol("keyword_data")</code>
</td>
</tr>
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<td width="15%" align="right" valign="top" class="summary">
<span class="summary-type"> </span>
</td><td class="summary">
<a name="KW_block"></a><span class="summary-name">KW_block</span> = <code title="Martel.Rep1(KW_line)">Martel.Rep1(KW_line)</code>
</td>
</tr>
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<td width="15%" align="right" valign="top" class="summary">
<span class="summary-type"> </span>
</td><td class="summary">
<a name="OS_block"></a><span class="summary-name">OS_block</span> = <code title="sprot38.OS_block">sprot38.OS_block</code>
</td>
</tr>
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<td width="15%" align="right" valign="top" class="summary">
<span class="summary-type"> </span>
</td><td class="summary">
<a name="OC_block"></a><span class="summary-name">OC_block</span> = <code title="sprot38.OC_block">sprot38.OC_block</code>
</td>
</tr>
<tr>
<td width="15%" align="right" valign="top" class="summary">
<span class="summary-type"> </span>
</td><td class="summary">
<a name="OG_block"></a><span class="summary-name">OG_block</span> = <code title="sprot38.OG_block">sprot38.OG_block</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.embl.embl65-module.html#organism" class="summary-name">organism</a> = <code title="Martel.Group("organism", OS_block+ OC_block+ Martel.Opt(OG_block))">Martel.Group("organism", OS_block+ OC_block+ Martel<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="RN_line"></a><span class="summary-name">RN_line</span> = <code title="sprot38.RN">sprot38.RN</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="RC_block"></a><span class="summary-name">RC_block</span> = <code title="sprot38.RC_block">sprot38.RC_block</code>
</td>
</tr>
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<td width="15%" align="right" valign="top" class="summary">
<span class="summary-type"> </span>
</td><td class="summary">
<a name="RP_line"></a><span class="summary-name">RP_line</span> = <code title="sprot38.RP">sprot38.RP</code>
</td>
</tr>
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<td width="15%" align="right" valign="top" class="summary">
<span class="summary-type"> </span>
</td><td class="summary">
<a name="RX_line"></a><span class="summary-name">RX_line</span> = <code title="sprot38.RX">sprot38.RX</code>
</td>
</tr>
<tr>
<td width="15%" align="right" valign="top" class="summary">
<span class="summary-type"> </span>
</td><td class="summary">
<a name="RX_block"></a><span class="summary-name">RX_block</span> = <code title="Martel.Group("RX_block", Martel.Rep1(RX_line))">Martel.Group("RX_block", Martel.Rep1(RX_line))</code>
</td>
</tr>
<tr>
<td width="15%" align="right" valign="top" class="summary">
<span class="summary-type"> </span>
</td><td class="summary">
<a name="RA_block"></a><span class="summary-name">RA_block</span> = <code title="sprot38.RA_block">sprot38.RA_block</code>
</td>
</tr>
<tr>
<td width="15%" align="right" valign="top" class="summary">
<span class="summary-type"> </span>
</td><td class="summary">
<a name="RT_block"></a><span class="summary-name">RT_block</span> = <code title="sprot38.RT_block">sprot38.RT_block</code>
</td>
</tr>
<tr>
<td width="15%" align="right" valign="top" class="summary">
<span class="summary-type"> </span>
</td><td class="summary">
<a name="RL_block"></a><span class="summary-name">RL_block</span> = <code title="sprot38.RL_block">sprot38.RL_block</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.embl.embl65-module.html#reference" class="summary-name">reference</a> = <code title="Martel.Group("reference", RN_line+ Martel.Opt(RC_block)+ Martel.Opt(RP\
_line)+ Martel.Opt(RX_block)+ RA_block+ RT_block+ RL_block)">Martel.Group("reference", RN_line+ Martel.Opt(RC_b<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="DR_block"></a><span class="summary-name">DR_block</span> = <code title="sprot38.DR_block">sprot38.DR_block</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.embl.embl65-module.html#FH_block" class="summary-name">FH_block</a> = <code title="Martel.Str("FH Key Location/Qualifiers")+ Martel.AnyEol(\
)+ Martel.Str("FH")+ Martel.AnyEol()">Martel.Str("FH Key Location/Qualifier<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.embl.embl65-module.html#fq_dbxref" class="summary-name">fq_dbxref</a> = <code title="Std.feature_qualifier_name(Martel.Str("db_xref"))+ Martel.Str('=')+ St\
d.feature_qualifier_description(Martel.Str('"')+ Std.dbxref(Std.dbxref\
_dbname(Martel.UntilSep(None, ":"))+ Martel.Str(":")+ Std.dbxref_dbid(\
Martel.UntilSep(None, '"')))+ Martel.Str('"'))+ Martel.AnyEol()">Std.feature_qualifier_name(Martel.Str("db_xref"))+<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.embl.embl65-module.html#fq_generic" class="summary-name">fq_generic</a> = <code title="Martel.Assert(Martel.Word()+ Martel.Str("="))+ Std.feature_qualifier_n\
ame(Martel.Word())+ Martel.Str("=")+ Std.feature_qualifier_description\
(Martel.UntilEol())+ Martel.AnyEol()+ Martel.Rep(Martel.Str("FT \
")+(Martel.AssertNot(Martel.Str("/")) | Martel.AssertNot(M\
artel.Re(r"/\w+=")))+ Std.feature_qualifier_description(Martel.UntilEo\
l())+ Martel.AnyEol())">Martel.Assert(Martel.Word()+ Martel.Str("="))+ St<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.embl.embl65-module.html#feature_qualifier" class="summary-name">feature_qualifier</a> = <code title="Std.feature_qualifier(Martel.Str("FT /")+(fq_dbxref \
| fq_generic))">Std.feature_qualifier(Martel.Str("FT <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.embl.embl65-module.html#feature" class="summary-name">feature</a> = <code title="Std.feature(Martel.Str("FT ")+ Std.feature_name(Martel.UntilSep(sep=\
" "))+ whitespace+ Std.feature_location(Martel.UntilEol())+ Martel.An\
yEol()+ Martel.Rep(Martel.Str("FT ")+ Martel.AssertN\
ot(Martel.Str("/"))+ Std.feature_location(Martel.UntilEol())+ Martel.A\
nyEol())+ Martel.Rep(feature_qualifier))">Std.feature(Martel.Str("FT ")+ Std.feature_name(Ma<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.embl.embl65-module.html#FT_block" class="summary-name">FT_block</a> = <code title="Std.feature_block(Martel.Rep(feature), {"location-style": "genbank"})">Std.feature_block(Martel.Rep(feature), {"location-s<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="CC_line"></a><span class="summary-name">CC_line</span> = <code title="Martel.Str("CC ")+ Martel.ToEol("comment")">Martel.Str("CC ")+ Martel.ToEol("comment")</code>
</td>
</tr>
<tr>
<td width="15%" align="right" valign="top" class="summary">
<span class="summary-type"> </span>
</td><td class="summary">
<a name="CC_block"></a><span class="summary-name">CC_block</span> = <code title="Martel.Rep1(CC_line)">Martel.Rep1(CC_line)</code>
</td>
</tr>
<tr>
<td width="15%" align="right" valign="top" class="summary">
<span class="summary-type"> </span>
</td><td class="summary">
<a name="XX"></a><span class="summary-name">XX</span> = <code title="Martel.Str("XX")+ Martel.AnyEol()">Martel.Str("XX")+ Martel.AnyEol()</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.embl.embl65-module.html#SQ_line" class="summary-name">SQ_line</a> = <code title="Martel.Str("SQ Sequence ")+ Martel.Digits("num_BP")+ Martel.Str(" BP\
; ")+ Martel.Digits("num_A")+ Martel.Str(" A; ")+ Martel.Digits("num_C\
")+ Martel.Str(" C; ")+ Martel.Digits("num_G")+ Martel.Str(" G; ")+ Ma\
rtel.Digits("num_T")+ Martel.Str(" T; ")+ Martel.Digits("num_other")+ \
Martel.Str(" other;")+ Martel.AnyEol()">Martel.Str("SQ Sequence ")+ Martel.Digits("num_BP"<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.embl.embl65-module.html#SQ_data" class="summary-name">SQ_data</a> = <code title="Martel.Str(" ")+ Std.sequence(Martel.Re(".{65}"))+ whitespace+ Mar\
tel.Digits("end_position")+ Martel.AnyEol()">Martel.Str(" ")+ Std.sequence(Martel.Re(".{65}")<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="SQ_block"></a><span class="summary-name">SQ_block</span> = <code title="Std.sequence_block(SQ_line+ Martel.Rep1(SQ_data))">Std.sequence_block(SQ_line+ Martel.Rep1(SQ_data))</code>
</td>
</tr>
<tr>
<td width="15%" align="right" valign="top" class="summary">
<span class="summary-type"> </span>
</td><td class="summary">
<a name="end"></a><span class="summary-name">end</span> = <code title="Martel.Str("//")+ Martel.AnyEol()">Martel.Str("//")+ Martel.AnyEol()</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.embl.embl65-module.html#record" class="summary-name">record</a> = <code title="Martel.Group("record", ID_line+ Martel.Opt(XX)+ AC_block+ Martel.Opt(X\
X)+ SV_line+ Martel.Opt(XX)+ DT_block+ Martel.Opt(XX)+ DE_block+ Marte\
l.Opt(XX)+ KW_block+ Martel.Opt(XX)+ Martel.Rep1(organism+ Martel.Opt(\
XX))+ Martel.Rep(reference+ Martel.Opt(XX))+ Martel.Opt(DR_block+ Mart\
el.Opt(XX))+ Martel.Rep(CC_block+ Martel.Opt(XX))+ FH_block+ FT_block+\
Martel.Opt(XX)+ SQ_block+ end, {"format": "embl/65"})">Martel.Group("record", ID_line+ Martel.Opt(XX)+ AC_bl<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.embl.embl65-module.html#format_expression" class="summary-name">format_expression</a> = <code title="Martel.Group("dataset", Martel.Rep1(record), {"format": "embl/65"})">Martel.Group("dataset", Martel.Rep1(record<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.embl.embl65-module.html#format" class="summary-name">format</a> = <code title="Martel.ParseRecords("dataset", {"format": "embl/65"}, record, RecordRe\
ader.EndsWith, ("//\n",))">Martel.ParseRecords("dataset", {"format": "embl/65"},<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.embl.embl65-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'>,
6): 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="divisions"></a>
<div>
<table class="details" border="1" cellpadding="3"
cellspacing="0" width="100%" bgcolor="white">
<tr><td>
<h3 class="epydoc">divisions</h3>
<dl class="fields">
</dl>
<dl class="fields">
<dt>Value:</dt>
<dd><table><tr><td><pre class="variable">
Martel.Re("EST|PHG|FUN|GSS|HTC|HTG|HUM|INV|ORG|MAM|VRT|PLN|"+ "PRO|ROD<span class="variable-linewrap"><img src="crarr.png" alt="\" /></span>
|SYN|STS|UNC|VRL|[A-Z]{3}")
</pre></td></tr></table>
</dd>
</dl>
</td></tr></table>
</div>
<a name="ID_line"></a>
<div>
<table class="details" border="1" cellpadding="3"
cellspacing="0" width="100%" bgcolor="white">
<tr><td>
<h3 class="epydoc">ID_line</h3>
<dl class="fields">
</dl>
<dl class="fields">
<dt>Value:</dt>
<dd><table><tr><td><pre class="variable">
Martel.Str("ID ")+ Std.dbid(Martel.UntilSep("entry_name", " "), {"ty<span class="variable-linewrap"><img src="crarr.png" alt="\" /></span>
pe": "primary", "dbname": "embl"})+ whitespace+ Martel.ToSep("dataclas<span class="variable-linewrap"><img src="crarr.png" alt="\" /></span>
s", ";")+ whitespace+ Martel.Group("molecule", Std.alphabet(Martel.Str<span class="variable-linewrap"><img src="crarr.png" alt="\" /></span>
("DNA", "circular DNA"), {"alphabet": "iupac-ambiguous-dna"}) | Std.al<span class="variable-linewrap"><img src="crarr.png" alt="\" /></span>
phabet(Martel.Str("RNA", "circular RNA"), {"alphabet": "iupac-ambiguou<span class="variable-linewrap"><img src="crarr.png" alt="\" /></span>
s-rna"}) | Std.alphabet(Martel.Str("XXX"), {"alphabet": "nucleotide"})<span class="variable-linewrap"><img src="crarr.png" alt="\" /></span>
)+ Martel.Str("; ")+ Martel.Group("division", divisions)+ Martel.Str("<span class="variable-linewrap"><img src="crarr.png" alt="\" /></span>
; ")+ Martel.Digits("length")+ Martel.Str(" BP.")+ Martel.AnyEol()
</pre></td></tr></table>
</dd>
</dl>
</td></tr></table>
</div>
<a name="accession"></a>
<div>
<table class="details" border="1" cellpadding="3"
cellspacing="0" width="100%" bgcolor="white">
<tr><td>
<h3 class="epydoc">accession</h3>
<dl class="fields">
</dl>
<dl class="fields">
<dt>Value:</dt>
<dd><table><tr><td><pre class="variable">
Std.dbid(Martel.UntilSep("accession", ";"), {"type": "accession", "dbn<span class="variable-linewrap"><img src="crarr.png" alt="\" /></span>
ame": "embl"})+ Martel.Str(";")
</pre></td></tr></table>
</dd>
</dl>
</td></tr></table>
</div>
<a name="AC_line"></a>
<div>
<table class="details" border="1" cellpadding="3"
cellspacing="0" width="100%" bgcolor="white">
<tr><td>
<h3 class="epydoc">AC_line</h3>
<dl class="fields">
</dl>
<dl class="fields">
<dt>Value:</dt>
<dd><table><tr><td><pre class="variable">
Martel.Str("AC ")+ accession+ Martel.Rep(Martel.Str(" ")+ accession)<span class="variable-linewrap"><img src="crarr.png" alt="\" /></span>
+ Martel.AnyEol()
</pre></td></tr></table>
</dd>
</dl>
</td></tr></table>
</div>
<a name="SV_line"></a>
<div>
<table class="details" border="1" cellpadding="3"
cellspacing="0" width="100%" bgcolor="white">
<tr><td>
<h3 class="epydoc">SV_line</h3>
<dl class="fields">
</dl>
<dl class="fields">
<dt>Value:</dt>
<dd><table><tr><td><pre class="variable">
Martel.Str("SV ")+ Martel.Group("sequence_version", Martel.ToSep("ac<span class="variable-linewrap"><img src="crarr.png" alt="\" /></span>
cession", ".")+ Martel.Digits("version"))+ Martel.AnyEol()
</pre></td></tr></table>
</dd>
</dl>
</td></tr></table>
</div>
<a name="DT_created_line"></a>
<div>
<table class="details" border="1" cellpadding="3"
cellspacing="0" width="100%" bgcolor="white">
<tr><td>
<h3 class="epydoc">DT_created_line</h3>
<dl class="fields">
</dl>
<dl class="fields">
<dt>Value:</dt>
<dd><table><tr><td><pre class="variable">
Martel.Str("DT ")+ Martel.Group("date_created", date)+ Martel.Str(" <span class="variable-linewrap"><img src="crarr.png" alt="\" /></span>
(Rel. ")+ Martel.Digits("release_created")+ Martel.Str(", Created)")+ <span class="variable-linewrap"><img src="crarr.png" alt="\" /></span>
Martel.AnyEol()
</pre></td></tr></table>
</dd>
</dl>
</td></tr></table>
</div>
<a name="DT_updated_line"></a>
<div>
<table class="details" border="1" cellpadding="3"
cellspacing="0" width="100%" bgcolor="white">
<tr><td>
<h3 class="epydoc">DT_updated_line</h3>
<dl class="fields">
</dl>
<dl class="fields">
<dt>Value:</dt>
<dd><table><tr><td><pre class="variable">
Martel.Str("DT ")+ Martel.Group("date_updated", date)+ Martel.Str(" <span class="variable-linewrap"><img src="crarr.png" alt="\" /></span>
(Rel. ")+ Martel.Digits("release_updated")+ Martel.Str(", Last updated<span class="variable-linewrap"><img src="crarr.png" alt="\" /></span>
, Version ")+ Martel.Digits("version_number")+ Martel.Str(")")+ Martel<span class="variable-linewrap"><img src="crarr.png" alt="\" /></span>
.AnyEol()
</pre></td></tr></table>
</dd>
</dl>
</td></tr></table>
</div>
<a name="DE_line"></a>
<div>
<table class="details" border="1" cellpadding="3"
cellspacing="0" width="100%" bgcolor="white">
<tr><td>
<h3 class="epydoc">DE_line</h3>
<dl class="fields">
</dl>
<dl class="fields">
<dt>Value:</dt>
<dd><table><tr><td><pre class="variable">
Martel.Str("DE ")+ Std.description(Martel.UntilEol("description"))+ <span class="variable-linewrap"><img src="crarr.png" alt="\" /></span>
Martel.AnyEol()
</pre></td></tr></table>
</dd>
</dl>
</td></tr></table>
</div>
<a name="DE_block"></a>
<div>
<table class="details" border="1" cellpadding="3"
cellspacing="0" width="100%" bgcolor="white">
<tr><td>
<h3 class="epydoc">DE_block</h3>
<dl class="fields">
</dl>
<dl class="fields">
<dt>Value:</dt>
<dd><table><tr><td><pre class="variable">
Std.description_block(Martel.Group("description_block", Martel.Rep1(DE<span class="variable-linewrap"><img src="crarr.png" alt="\" /></span>
_line)))
</pre></td></tr></table>
</dd>
</dl>
</td></tr></table>
</div>
<a name="organism"></a>
<div>
<table class="details" border="1" cellpadding="3"
cellspacing="0" width="100%" bgcolor="white">
<tr><td>
<h3 class="epydoc">organism</h3>
<dl class="fields">
</dl>
<dl class="fields">
<dt>Value:</dt>
<dd><table><tr><td><pre class="variable">
Martel.Group("organism", OS_block+ OC_block+ Martel.Opt(OG_block))
</pre></td></tr></table>
</dd>
</dl>
</td></tr></table>
</div>
<a name="reference"></a>
<div>
<table class="details" border="1" cellpadding="3"
cellspacing="0" width="100%" bgcolor="white">
<tr><td>
<h3 class="epydoc">reference</h3>
<dl class="fields">
</dl>
<dl class="fields">
<dt>Value:</dt>
<dd><table><tr><td><pre class="variable">
Martel.Group("reference", RN_line+ Martel.Opt(RC_block)+ Martel.Opt(RP<span class="variable-linewrap"><img src="crarr.png" alt="\" /></span>
_line)+ Martel.Opt(RX_block)+ RA_block+ RT_block+ RL_block)
</pre></td></tr></table>
</dd>
</dl>
</td></tr></table>
</div>
<a name="FH_block"></a>
<div>
<table class="details" border="1" cellpadding="3"
cellspacing="0" width="100%" bgcolor="white">
<tr><td>
<h3 class="epydoc">FH_block</h3>
<dl class="fields">
</dl>
<dl class="fields">
<dt>Value:</dt>
<dd><table><tr><td><pre class="variable">
Martel.Str("FH Key Location/Qualifiers")+ Martel.AnyEol(<span class="variable-linewrap"><img src="crarr.png" alt="\" /></span>
)+ Martel.Str("FH")+ Martel.AnyEol()
</pre></td></tr></table>
</dd>
</dl>
</td></tr></table>
</div>
<a name="fq_dbxref"></a>
<div>
<table class="details" border="1" cellpadding="3"
cellspacing="0" width="100%" bgcolor="white">
<tr><td>
<h3 class="epydoc">fq_dbxref</h3>
<dl class="fields">
</dl>
<dl class="fields">
<dt>Value:</dt>
<dd><table><tr><td><pre class="variable">
Std.feature_qualifier_name(Martel.Str("db_xref"))+ Martel.Str('=')+ St<span class="variable-linewrap"><img src="crarr.png" alt="\" /></span>
d.feature_qualifier_description(Martel.Str('"')+ Std.dbxref(Std.dbxref<span class="variable-linewrap"><img src="crarr.png" alt="\" /></span>
_dbname(Martel.UntilSep(None, ":"))+ Martel.Str(":")+ Std.dbxref_dbid(<span class="variable-linewrap"><img src="crarr.png" alt="\" /></span>
Martel.UntilSep(None, '"')))+ Martel.Str('"'))+ Martel.AnyEol()
</pre></td></tr></table>
</dd>
</dl>
</td></tr></table>
</div>
<a name="fq_generic"></a>
<div>
<table class="details" border="1" cellpadding="3"
cellspacing="0" width="100%" bgcolor="white">
<tr><td>
<h3 class="epydoc">fq_generic</h3>
<dl class="fields">
</dl>
<dl class="fields">
<dt>Value:</dt>
<dd><table><tr><td><pre class="variable">
Martel.Assert(Martel.Word()+ Martel.Str("="))+ Std.feature_qualifier_n<span class="variable-linewrap"><img src="crarr.png" alt="\" /></span>
ame(Martel.Word())+ Martel.Str("=")+ Std.feature_qualifier_description<span class="variable-linewrap"><img src="crarr.png" alt="\" /></span>
(Martel.UntilEol())+ Martel.AnyEol()+ Martel.Rep(Martel.Str("FT <span class="variable-linewrap"><img src="crarr.png" alt="\" /></span>
")+(Martel.AssertNot(Martel.Str("/")) | Martel.AssertNot(M<span class="variable-linewrap"><img src="crarr.png" alt="\" /></span>
artel.Re(r"/\w+=")))+ Std.feature_qualifier_description(Martel.UntilEo<span class="variable-linewrap"><img src="crarr.png" alt="\" /></span>
l())+ Martel.AnyEol())
</pre></td></tr></table>
</dd>
</dl>
</td></tr></table>
</div>
<a name="feature_qualifier"></a>
<div>
<table class="details" border="1" cellpadding="3"
cellspacing="0" width="100%" bgcolor="white">
<tr><td>
<h3 class="epydoc">feature_qualifier</h3>
<dl class="fields">
</dl>
<dl class="fields">
<dt>Value:</dt>
<dd><table><tr><td><pre class="variable">
Std.feature_qualifier(Martel.Str("FT /")+(fq_dbxref <span class="variable-linewrap"><img src="crarr.png" alt="\" /></span>
| fq_generic))
</pre></td></tr></table>
</dd>
</dl>
</td></tr></table>
</div>
<a name="feature"></a>
<div>
<table class="details" border="1" cellpadding="3"
cellspacing="0" width="100%" bgcolor="white">
<tr><td>
<h3 class="epydoc">feature</h3>
<dl class="fields">
</dl>
<dl class="fields">
<dt>Value:</dt>
<dd><table><tr><td><pre class="variable">
Std.feature(Martel.Str("FT ")+ Std.feature_name(Martel.UntilSep(sep=<span class="variable-linewrap"><img src="crarr.png" alt="\" /></span>
" "))+ whitespace+ Std.feature_location(Martel.UntilEol())+ Martel.An<span class="variable-linewrap"><img src="crarr.png" alt="\" /></span>
yEol()+ Martel.Rep(Martel.Str("FT ")+ Martel.AssertN<span class="variable-linewrap"><img src="crarr.png" alt="\" /></span>
ot(Martel.Str("/"))+ Std.feature_location(Martel.UntilEol())+ Martel.A<span class="variable-linewrap"><img src="crarr.png" alt="\" /></span>
nyEol())+ Martel.Rep(feature_qualifier))
</pre></td></tr></table>
</dd>
</dl>
</td></tr></table>
</div>
<a name="FT_block"></a>
<div>
<table class="details" border="1" cellpadding="3"
cellspacing="0" width="100%" bgcolor="white">
<tr><td>
<h3 class="epydoc">FT_block</h3>
<dl class="fields">
</dl>
<dl class="fields">
<dt>Value:</dt>
<dd><table><tr><td><pre class="variable">
Std.feature_block(Martel.Rep(feature), {"location-style": "genbank"})
</pre></td></tr></table>
</dd>
</dl>
</td></tr></table>
</div>
<a name="SQ_line"></a>
<div>
<table class="details" border="1" cellpadding="3"
cellspacing="0" width="100%" bgcolor="white">
<tr><td>
<h3 class="epydoc">SQ_line</h3>
<dl class="fields">
</dl>
<dl class="fields">
<dt>Value:</dt>
<dd><table><tr><td><pre class="variable">
Martel.Str("SQ Sequence ")+ Martel.Digits("num_BP")+ Martel.Str(" BP<span class="variable-linewrap"><img src="crarr.png" alt="\" /></span>
; ")+ Martel.Digits("num_A")+ Martel.Str(" A; ")+ Martel.Digits("num_C<span class="variable-linewrap"><img src="crarr.png" alt="\" /></span>
")+ Martel.Str(" C; ")+ Martel.Digits("num_G")+ Martel.Str(" G; ")+ Ma<span class="variable-linewrap"><img src="crarr.png" alt="\" /></span>
rtel.Digits("num_T")+ Martel.Str(" T; ")+ Martel.Digits("num_other")+ <span class="variable-linewrap"><img src="crarr.png" alt="\" /></span>
Martel.Str(" other;")+ Martel.AnyEol()
</pre></td></tr></table>
</dd>
</dl>
</td></tr></table>
</div>
<a name="SQ_data"></a>
<div>
<table class="details" border="1" cellpadding="3"
cellspacing="0" width="100%" bgcolor="white">
<tr><td>
<h3 class="epydoc">SQ_data</h3>
<dl class="fields">
</dl>
<dl class="fields">
<dt>Value:</dt>
<dd><table><tr><td><pre class="variable">
Martel.Str(" ")+ Std.sequence(Martel.Re(".{65}"))+ whitespace+ Mar<span class="variable-linewrap"><img src="crarr.png" alt="\" /></span>
tel.Digits("end_position")+ Martel.AnyEol()
</pre></td></tr></table>
</dd>
</dl>
</td></tr></table>
</div>
<a name="record"></a>
<div>
<table class="details" border="1" cellpadding="3"
cellspacing="0" width="100%" bgcolor="white">
<tr><td>
<h3 class="epydoc">record</h3>
<dl class="fields">
</dl>
<dl class="fields">
<dt>Value:</dt>
<dd><table><tr><td><pre class="variable">
Martel.Group("record", ID_line+ Martel.Opt(XX)+ AC_block+ Martel.Opt(X<span class="variable-linewrap"><img src="crarr.png" alt="\" /></span>
X)+ SV_line+ Martel.Opt(XX)+ DT_block+ Martel.Opt(XX)+ DE_block+ Marte<span class="variable-linewrap"><img src="crarr.png" alt="\" /></span>
l.Opt(XX)+ KW_block+ Martel.Opt(XX)+ Martel.Rep1(organism+ Martel.Opt(<span class="variable-linewrap"><img src="crarr.png" alt="\" /></span>
XX))+ Martel.Rep(reference+ Martel.Opt(XX))+ Martel.Opt(DR_block+ Mart<span class="variable-linewrap"><img src="crarr.png" alt="\" /></span>
el.Opt(XX))+ Martel.Rep(CC_block+ Martel.Opt(XX))+ FH_block+ FT_block+<span class="variable-linewrap"><img src="crarr.png" alt="\" /></span>
Martel.Opt(XX)+ SQ_block+ end, {"format": "embl/65"})
</pre></td></tr></table>
</dd>
</dl>
</td></tr></table>
</div>
<a name="format_expression"></a>
<div>
<table class="details" border="1" cellpadding="3"
cellspacing="0" width="100%" bgcolor="white">
<tr><td>
<h3 class="epydoc">format_expression</h3>
<dl class="fields">
</dl>
<dl class="fields">
<dt>Value:</dt>
<dd><table><tr><td><pre class="variable">
Martel.Group("dataset", Martel.Rep1(record), {"format": "embl/65"})
</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">
Martel.ParseRecords("dataset", {"format": "embl/65"}, record, RecordRe<span class="variable-linewrap"><img src="crarr.png" alt="\" /></span>
ader.EndsWith, ("//\n",))
</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>
6<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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