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python-biopython  1.60
Public Member Functions | Static Public Attributes
Bio.SeqIO.InsdcIO.ImgtWriter Class Reference
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List of all members.

Public Member Functions

def write_record

Static Public Attributes

int HEADER_WIDTH = 5
int QUALIFIER_INDENT = 25
string QUALIFIER_INDENT_STR = "FT"
string QUALIFIER_INDENT_TMP = "FT %s "
string FEATURE_HEADER = "FH Key Location/Qualifiers\n"
int MAX_WIDTH = 80

Detailed Description

Definition at line 1040 of file InsdcIO.py.


Member Function Documentation

def Bio.SeqIO.InsdcIO.EmblWriter.write_record (   self,
  record 
) [inherited]
Write a single record to the output file.

Definition at line 996 of file InsdcIO.py.

00996 
00997     def write_record(self, record):
00998         """Write a single record to the output file."""
00999 
01000         handle = self.handle
01001         self._write_the_first_lines(record)
01002 
01003         #PR line (0 or 1 lines only), project identifier
01004         for xref in record.dbxrefs:
01005             if xref.startswith("Project:"):
01006                 self._write_single_line("PR", xref+";")
01007                 handle.write("XX\n")
01008                 break
01009 
01010         #TODO - DT lines (date)
01011 
01012         descr = record.description
01013         if descr == "<unknown description>" : descr = "."
01014         self._write_multi_line("DE", descr)
01015         handle.write("XX\n")
01016 
01017         #Should this be "source" or "organism"?
01018         self._write_multi_line("OS", self._get_annotation_str(record, "organism"))
01019         try:
01020             #List of strings
01021             taxonomy = "; ".join(record.annotations["taxonomy"]) + "."
01022         except KeyError:
01023             taxonomy = "."
01024         self._write_multi_line("OC", taxonomy)
01025         handle.write("XX\n")
01026 
01027         if "references" in record.annotations:
01028             self._write_references(record)
01029 
01030         if "comment" in record.annotations:
01031             self._write_comment(record)
01032 
01033         handle.write(self.FEATURE_HEADER)
01034         rec_length = len(record)
01035         for feature in record.features:
01036             self._write_feature(feature, rec_length)
01037 
01038         self._write_sequence(record)
01039         handle.write("//\n")

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Member Data Documentation

string Bio.SeqIO.InsdcIO.ImgtWriter.FEATURE_HEADER = "FH Key Location/Qualifiers\n" [static]

Reimplemented from Bio.SeqIO.InsdcIO.EmblWriter.

Definition at line 1045 of file InsdcIO.py.

Reimplemented from Bio.SeqIO.InsdcIO.EmblWriter.

Definition at line 1041 of file InsdcIO.py.

int Bio.SeqIO.InsdcIO._InsdcWriter.MAX_WIDTH = 80 [static, inherited]

Definition at line 236 of file InsdcIO.py.

Reimplemented from Bio.SeqIO.InsdcIO.EmblWriter.

Definition at line 1042 of file InsdcIO.py.

Reimplemented from Bio.SeqIO.InsdcIO.EmblWriter.

Definition at line 1043 of file InsdcIO.py.

Reimplemented from Bio.SeqIO.InsdcIO.EmblWriter.

Definition at line 1044 of file InsdcIO.py.


The documentation for this class was generated from the following file: