Package Bio :: Package expressions :: Package embl :: Module embl65
[hide private]
[frames] | no frames]

Module embl65

source code

Format from EMBL Nucleotide Sequence Database Release 65, December 2000

Variables [hide private]
  whitespace = Martel.Spaces()
  divisions = Martel.Re("EST|PHG|FUN|GSS|HTC|HTG|HUM|INV|ORG|MAM...
  ID_line = Martel.Str("ID ")+ Std.dbid(Martel.UntilSep("entry...
  accession = Std.dbid(Martel.UntilSep("accession", ";"), {"type...
  AC_line = Martel.Str("AC ")+ accession+ Martel.Rep(Martel.St...
  AC_block = Martel.Rep1(AC_line)
  SV_line = Martel.Str("SV ")+ Martel.Group("sequence_version"...
  date = Time.make_expression("%(day)-%(Jan)-%(year)")
  DT_created_line = Martel.Str("DT ")+ Martel.Group("date_crea...
  DT_updated_line = Martel.Str("DT ")+ Martel.Group("date_upda...
  DT_block = DT_created_line+ DT_updated_line
  DE_line = Martel.Str("DE ")+ Std.description(Martel.UntilEol...
  DE_block = Std.description_block(Martel.Group("description_blo...
  KW_line = Martel.Str("KW ")+ Martel.ToEol("keyword_data")
  KW_block = Martel.Rep1(KW_line)
  OS_block = sprot38.OS_block
  OC_block = sprot38.OC_block
  OG_block = sprot38.OG_block
  organism = Martel.Group("organism", OS_block+ OC_block+ Martel...
  RN_line = sprot38.RN
  RC_block = sprot38.RC_block
  RP_line = sprot38.RP
  RX_line = sprot38.RX
  RX_block = Martel.Group("RX_block", Martel.Rep1(RX_line))
  RA_block = sprot38.RA_block
  RT_block = sprot38.RT_block
  RL_block = sprot38.RL_block
  reference = Martel.Group("reference", RN_line+ Martel.Opt(RC_b...
  DR_block = sprot38.DR_block
  FH_block = Martel.Str("FH Key Location/Qualifier...
  fq_dbxref = Std.feature_qualifier_name(Martel.Str("db_xref"))+...
  fq_generic = Martel.Assert(Martel.Word()+ Martel.Str("="))+ St...
  feature_qualifier = Std.feature_qualifier(Martel.Str("FT ...
  feature = Std.feature(Martel.Str("FT ")+ Std.feature_name(Ma...
  FT_block = Std.feature_block(Martel.Rep(feature), {"location-s...
  CC_line = Martel.Str("CC ")+ Martel.ToEol("comment")
  CC_block = Martel.Rep1(CC_line)
  XX = Martel.Str("XX")+ Martel.AnyEol()
  SQ_line = Martel.Str("SQ Sequence ")+ Martel.Digits("num_BP"...
  SQ_data = Martel.Str(" ")+ Std.sequence(Martel.Re(".{65}")...
  SQ_block = Std.sequence_block(SQ_line+ Martel.Rep1(SQ_data))
  end = Martel.Str("//")+ Martel.AnyEol()
  record = Martel.Group("record", ID_line+ Martel.Opt(XX)+ AC_bl...
  format_expression = Martel.Group("dataset", Martel.Rep1(record...
  format = Martel.ParseRecords("dataset", {"format": "embl/65"},...
  __warningregistry__ = {('Bio.expressions was deprecated, as it...
Variables Details [hide private]

divisions

Value:
Martel.Re("EST|PHG|FUN|GSS|HTC|HTG|HUM|INV|ORG|MAM|VRT|PLN|"+ "PRO|ROD\
|SYN|STS|UNC|VRL|[A-Z]{3}")

ID_line

Value:
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()

accession

Value:
Std.dbid(Martel.UntilSep("accession", ";"), {"type": "accession", "dbn\
ame": "embl"})+ Martel.Str(";")

AC_line

Value:
Martel.Str("AC   ")+ accession+ Martel.Rep(Martel.Str(" ")+ accession)\
+ Martel.AnyEol()

SV_line

Value:
Martel.Str("SV   ")+ Martel.Group("sequence_version", Martel.ToSep("ac\
cession", ".")+ Martel.Digits("version"))+ Martel.AnyEol()

DT_created_line

Value:
Martel.Str("DT   ")+ Martel.Group("date_created", date)+ Martel.Str(" \
(Rel. ")+ Martel.Digits("release_created")+ Martel.Str(", Created)")+ \
Martel.AnyEol()

DT_updated_line

Value:
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()

DE_line

Value:
Martel.Str("DE   ")+ Std.description(Martel.UntilEol("description"))+ \
Martel.AnyEol()

DE_block

Value:
Std.description_block(Martel.Group("description_block", Martel.Rep1(DE\
_line)))

organism

Value:
Martel.Group("organism", OS_block+ OC_block+ Martel.Opt(OG_block))

reference

Value:
Martel.Group("reference", RN_line+ Martel.Opt(RC_block)+ Martel.Opt(RP\
_line)+ Martel.Opt(RX_block)+ RA_block+ RT_block+ RL_block)

FH_block

Value:
Martel.Str("FH   Key             Location/Qualifiers")+ Martel.AnyEol(\
)+ Martel.Str("FH")+ Martel.AnyEol()

fq_dbxref

Value:
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()

fq_generic

Value:
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())

feature_qualifier

Value:
Std.feature_qualifier(Martel.Str("FT                   /")+(fq_dbxref \
| fq_generic))

feature

Value:
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))

FT_block

Value:
Std.feature_block(Martel.Rep(feature), {"location-style": "genbank"})

SQ_line

Value:
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()

SQ_data

Value:
Martel.Str("     ")+ Std.sequence(Martel.Re(".{65}"))+ whitespace+ Mar\
tel.Digits("end_position")+ Martel.AnyEol()

record

Value:
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"})

format_expression

Value:
Martel.Group("dataset", Martel.Rep1(record), {"format": "embl/65"})

format

Value:
Martel.ParseRecords("dataset", {"format": "embl/65"}, record, RecordRe\
ader.EndsWith, ("//\n",))

__warningregistry__

Value:
{('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}