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SCHEMA = """
CREATE TABLE features (
id text,
seqid text,
source text,
featuretype text,
start int,
end int,
score text,
strand text,
frame text,
attributes text,
extra text,
bin int,
primary key (id)
);
CREATE TABLE relations (
parent text,
child text,
level int,
primary key (parent, child, level)
);
CREATE TABLE meta (
dialect text,
version text
);
CREATE TABLE directives (
directive text
);
CREATE TABLE autoincrements (
base text,
n int,
primary key (base)
);
CREATE TABLE duplicates (
idspecid text,
newid text,
primary key (newid)
);
"""
default_pragmas = {
"synchronous": "NORMAL",
"journal_mode": "MEMORY",
"main.page_size": 4096,
"main.cache_size": 10000,
}
_keys = [
"id",
"seqid",
"source",
"featuretype",
"start",
"end",
"score",
"strand",
"frame",
"attributes",
"extra",
"bin",
]
_gffkeys = [
"seqid",
"source",
"featuretype",
"start",
"end",
"score",
"strand",
"frame",
"attributes",
]
_gffkeys_extra = _gffkeys + ["extra"]
_SELECT = "SELECT " + ", ".join(_keys) + ", features.rowid as file_order FROM features "
_INSERT = (
"INSERT INTO features ("
+ ", ".join(_keys)
+ ") VALUES ("
+ ",".join(list("?" * len(_keys)))
+ ")"
)
_update_clause = ",".join(["%s = ?" % i for i in _keys])
_UPDATE = "UPDATE features SET " + _update_clause + " WHERE id = ?"
# TODO: create indexes once profiling figures out which ones work best....
INDEXES = []
# This dictionary keeps track of idiosyncracies to [attempt to] maintain
# invariance of file->db->file round trips.
dialect = {
# Initial semicolon, e.g.,
#
# ;ID=001;
# vs
# ID=001;
"leading semicolon": False,
# Semicolon after the last value, e.g.,
#
# ID=001; Name=gene1;
# vs
# ID=001; Name=gene1
"trailing semicolon": False,
# e.g.,
#
# gene_id "GENE1"
# vs
# gene_id GENE1
"quoted GFF2 values": False,
# Sometimes there's extra space surrounding the semicolon, e.g.,
#
# ID=001;Name=gene1
# vs
# ID=001; Name=gene1
"field separator": ";",
# Usually "=" for GFF3; " " for GTF, e.g.,
#
# gene_id "GENE1"
# vs
# gene_id="GENE1"
"keyval separator": "=",
# Usually a comma, e.g.,
#
# Parent=gene1,gene2,gene3
"multival separator": ",",
# General GTF or GFF format
"fmt": "gff3",
# How multiple values for the same key are handled, e.g.,
#
# Parent=gene1; Parent=gene2;
# vs
# Parent=gene1,gene2;
#
# (the first one has repeated keys)
"repeated keys": False,
# If these keys exist, then print them in this order.
"order": ["ID", "Name", "gene_id", "transcript_id"],
}
always_return_list = True
ignore_url_escape_characters = False
# these keyword args are used by iterators.
_iterator_kwargs = (
"data",
"checklines",
"transform",
"force_dialect_check",
"dialect",
"from_string",
)
|
