Module tfasta_templates
source code
This is automatically generated documentation and should not be relied
on for the API. Please see the official documentation at
http://pythonhosted.org/tfasta/.
The only things that should be used externally from this module are
TEMPLATES, a dict
of FastaTemplate
instances, or FastaTemplate
itself. A dictionary is used so
that templates can be selected dynamically at run-time.
Template types registered in TEMPLATES are:
-
default - plain old fasta line
-
name - everything after the ">"
-
swissprot - fasta files from swissprot
-
gi_num - between first set of "|"s
-
accession - between 3rd and 4th "|"
-
description - after last "|"
-
pdb - the fasta file of the entire pdb
-
idCode - first four characters after ">"
-
chainID - any non-whitespace characters after first
"_"
-
type - non-whitespace immediately following first
":"
-
numRes - numbers immediatly following first ":"
-
description - stripped characters after numRes
-
nr - the protein non-redundant database
-
gi - between first set of "|"s
-
accession - between 3rd and 4th "|"
-
description - stripped characters before brackets
-
source - stripped characters inside brackets
-
nrblast - fasta file produced from blast output of the
nr
-
gi - between first set of "|"s
-
accession - between 3rd and 4th "|"
|
FastaTemplate
This class encapsulates template information for parsing fasta
files.
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_t
This class is essentially a namespace to hold some
values that will be used to provide templates for the
TEMPLATES dict .
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TEMPLATES = {"default": _t._default_template, "swissprot": _t....
a dict holding instances of FastaTemplate
used for parsing
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__package__ = ' tfasta '
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TEMPLATES
a dict holding instances of FastaTemplate used
for parsing
- Value:
{"default": _t._default_template, "swissprot": _t._swissprot_template,
"pdb": _t._pdb_template, "nr": _t._nr_template, "nrblast": _t._nrblas
t_template}
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