SQLite数据库简单操作

SQLite数据库整体查询命令

dot-commands

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$sqlite3 
sqlite> .help
.backup ?DB? FILE Backup DB (default "main") to FILE
.bail ON|OFF Stop after hitting an error. Default OFF
.databases List names and files of attached databases
.dump ?TABLE? ... Dump the database in an SQL text format
If TABLE specified, only dump tables matching
LIKE pattern TABLE.
.echo ON|OFF Turn command echo on or off
.exit Exit this program
.explain ON|OFF Turn output mode suitable for EXPLAIN on or off.
.genfkey ?OPTIONS? Options are:
--no-drop: Do not drop old fkey triggers.
--ignore-errors: Ignore tables with fkey errors
--exec: Execute generated SQL immediately
See file tool/genfkey.README in the source
distribution for further information.
.header(s) ON|OFF Turn display of headers on or off
.help Show this message
.import FILE TABLE Import data from FILE into TABLE
.indices ?TABLE? Show names of all indices
If TABLE specified, only show indices for tables
matching LIKE pattern TABLE.
.load FILE ?ENTRY? Load an extension library
.mode MODE ?TABLE? Set output mode where MODE is one of:
csv Comma-separated values
column Left-aligned columns. (See .width)
html HTML <table> code
insert SQL insert statements for TABLE
line One value per line
list Values delimited by .separator string
tabs Tab-separated values
tcl TCL list elements
.nullvalue STRING Print STRING in place of NULL values
.output FILENAME Send output to FILENAME
.output stdout Send output to the screen
.prompt MAIN CONTINUE Replace the standard prompts
.quit Exit this program
.read FILENAME Execute SQL in FILENAME
.restore ?DB? FILE Restore content of DB (default "main") from FILE
.schema ?TABLE? Show the CREATE statements
If TABLE specified, only show tables matching
LIKE pattern TABLE.
.separator STRING Change separator used by output mode and .import
.show Show the current values for various settings
.tables ?TABLE? List names of tables
If TABLE specified, only list tables matching
LIKE pattern TABLE.
.timeout MS Try opening locked tables for MS milliseconds
.width NUM NUM ... Set column widths for "column" mode
.timer ON|OFF Turn the CPU timer measurement on or off

SQLite数据类型

  • text
  • integer
  • real
  • NULL, used for missing data, or no value
  • BLOB, which stands for binary large object, and stores any type of object as bytes

  • 注:SQLite并没有强制同列必须使用相同类型的数据,每个表的每一列都有优先类型(type affinity),但为了下游分析方便,最好同一列保持相同数据类型。
    当某一列是混合数据类型时,排序原则为:NULL values, integer and real values (sorted numerically), text values, and finally blob values。

    数据库内容查询

    万能的SELECT命令

    语法:

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    SELECT <columns> FROM <tablename>;

    基本形式:SELECT选择指令从一个table中抓取所有列的所有行(columns设定为*)。
    选取特定列:不同列之间逗号分隔(SELECT trait, chrom, position, strongest_risk_snp, pvalue FROM gwascat LIMIT 5;)
    SELECT语句除了在sqlite中交互查询外,还可在命令行中直接查询

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    #交互
    sqlite> SELECT * FROM gwascat;
    #命令行
    sqlite3 gwascat.db "SELECT * FROM gwascat" > results.txt

    SQLite默认输出不规则,可做以下设置输出排列整齐易读输出:

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    sqlite> SELECT trait, chrom, position, strongest_risk_snp, pvalue
    ...> FROM gwascat LIMIT 5;
    trait|chrom|position|strongest_risk_snp|pvalue
    Asthma and hay fever|6|32658824|rs9273373|4.0e-14
    Asthma and hay fever|4|38798089|rs4833095|5.0e-12
    Asthma and hay fever|5|111131801|rs1438673|3.0e-11
    Asthma and hay fever|2|102350089|rs10197862|4.0e-11
    Asthma and hay fever|17|39966427|rs7212938|4.0e-10
    sqlite> .header on
    sqlite> .mode column
    sqlite> SELECT trait, chrom, position, strongest_risk_snp, pvalue
    ...> FROM gwascat LIMIT 5;
    trait chrom position strongest_risk_snp pvalue
    -------------------- ---------- ---------- ------------------ ----------
    Asthma and hay fever 6 32658824 rs9273373 4.0e-14
    Asthma and hay fever 4 38798089 rs4833095 5.0e-12
    Asthma and hay fever 5 111131801 rs1438673 3.0e-11
    Asthma and hay fever 2 102350089 rs10197862 4.0e-11
    Asthma and hay fever 17 39966427 rs7212938 4.0e-10

    SELECT可选参数:
    LIMIT 输出查询行数

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    sqlite> SELECT * FROM gwascat LIMIT 2;

    ORDER BY 输出结果排序

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    SELECT author, trait, journal FROM <tablename> ORDER BY author DESC LIMIT 5; 
    #(按author降序排序),排序有助于异常值检测。
    #若所指定排序列含由NULL值,可通过 IS NOT NULL 排除NULL值
    SELECT chrom, position, trait, strongest_risk_snp, pvalue FROM <tablename> WHERE pvalue IS NOT NULL ORDER BY pvalue LIMIT 5;

    WHERE 数据筛选

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    SELECT chrom, position, trait, strongest_risk_snp, pvalue FROM <tablename> WHERE lower(strongest_risk_snp) = "rs429358";
    #SQLite大小写敏感,所以匹配时最好用lower() 转换。

    多条件筛选:

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    sqlite> SELECT chrom, position, strongest_risk_snp, pvalue FROM gwascat
    ...> WHERE chrom IN ("1", "2", "3") AND pvalue < 10e-11
    ...> ORDER BY pvalue LIMIT 5;
    #或者
    sqlite> SELECT chrom, position, strongest_risk_snp, pvalue
    ...> FROM gwascat WHERE chrom = "22"
    ...> AND position BETWEEN 24000000 AND 25000000
    ...> AND pvalue IS NOT NULL ORDER BY pvalue LIMIT 5;

    AS 对原始数据的修改:

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    sqlite> SELECT lower(trait) AS trait,
    ...> "chr" || chrom || ":" || position AS region FROM gwascat LIMIT 5;
    #||为连接运算符,用来连接两个字符串
    #NULL的替换,ifnull()函数
    sqlite> SELECT ifnull(chrom, "NA") AS chrom, ifnull(position, "NA") AS position,
    ...> strongest_risk_snp, ifnull(pvalue, "NA") AS pvalue FROM gwascat
    ...> WHERE strongest_risk_snp = "rs429358";

    更多SQLite内置函数
    Function Description
    ifnull(x, val) If x is NULL, return with val, otherwise return x; shorthand for coalesce() with two arguments
    min(a, b, c, …) Return minimum in a, b, c, …
    max(a, b, c, …) Return maximum in a, b, c, …
    abs(x) Absolute value
    coalesce(a, b, c, …) Return first non-NULL value in a, b, c, … or NULL if all values are NULL
    length(x) Returns number of characters in x
    lower(x) Return x in lowercase
    upper(x) Return x in uppercase
    replace(x, str, repl) Return x with all occurrences of str replaced with repl
    round(x, digits) Round x to digits (default 0)
    trim(x, chars), ltrim(x, chars), rtrim(x, chars) Trim off chars (spaces if chars is not specified) from both sides, left side, and right side of x, respectively.
    substr(x, start, length) Extract a substring from x starting from character start and is length characters long

    集合函数(Aggregate)

    count(colname)函数:
    返回总行数(无视NULL的存在):sqlite> SELECT count(*) FROM gwascat;
    若colname是具体某列则返回出去NULL值的总行数.
    其他相似函数:avg(x),max(x),min(x),sum(x),total(x)
    计算列非重复值(unique)个数

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    sqlite> SELECT count(DISTINCT 列) AS unique_rs FROM gwascat;

    行分组(GROUP BY)

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    sqlite> SELECT chrom, count(*) FROM gwascat GROUP BY chrom;
    chrom count(*)
    ---------- ----------
    70
    1 1458
    10 930
    11 988
    12 858
    13 432
    [...]
    #列重命名,降序,分组计算
    sqlite> SELECT chrom, count(*) as nhits FROM gwascat GROUP BY chrom
    ...> ORDER BY nhits DESC;
    chrom nhits
    ---------- ----------
    6 1658
    1 1458
    2 1432
    3 1033
    11 988
    10 930
    [...]
    #多列分组,不同列之间逗号分隔
    sqlite> select strongest_risk_snp, strongest_risk_allele, count(*) AS count
    ...> FROM gwascat GROUP BY strongest_risk_snp, strongest_risk_allele
    ...> ORDER BY count DESC LIMIT 10;
    strongest_risk_snp strongest_risk_allele count
    ------------------ --------------------- ----------
    rs1260326 T 22
    rs2186369 G 22
    rs1800562 A 20
    rs909674 C 20
    rs11710456 G 19

    自己动手写数据库

    we’ll use the basic SQL syntax to create tables and insert records into tables. Then load data into SQLite using Python’s sqlite3 module.

    创建tables

    基本语法:

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    CREATE TABLE tablename(
    id integer primary key,
    column1 column1_type,
    column2 column2_type,
    ...
    );

    注意到所有SQLite数据库第一列总是id integer primary key,primary key是非重复整数来识别table中每一条记录。
    创建table:

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    $ sqlite3 practice.dbsqlite> CREATE TABLE variants(
    ...> id integer primary key,
    ...> chrom text,
    ...> start integer,
    ...> end integer,
    ...> strand text,
    ...> name text);

    数据写入table

    基本语法:

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    INSERT INTO tablename(column1, column2)
    VALUES (value1, value2);

    建立索引

    基本语法:

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    sqlite> CREATE INDEX <columns-name_idx> ON <tablename>(<columns-name>);
    #察看索引
    sqlite> .indices
    columns-name_idx
    #删除索引
    sqlite> DROP INDEX columns-name_idx;

    修改/删除table

    删除:DROP TABLE
    修改:ALTER TABLE

    python中交互操作SQLite

    连接SQLite数据库并创建table

    create_table.py

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    import sqlite3

    # the filename of this SQLite database
    db_filename = "variants.db"

    # initialize database connection
    conn = sqlite3.connect(db_filename) #connect() 连接数据库

    c = conn.cursor() #在python中用cursor()与SQLite数据库交互

    table_def = """\
    CREATE TABLE variants(
    id integer primary key,
    chrom test,
    start integer,
    end integer,
    strand text,
    rsid text);
    """


    c.execute(table_def) #SQL语法,相当于确认
    conn.commit() #提交跟新内容到SQLite数据库
    conn.close() #关闭与数据库的连接

    数据载入table

    load_variants.py

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    ##load_variants.py data.txt
    import sys
    import sqlite3
    from collections import OrderedDict

    # the filename of this SQLite database
    db_filename = "variants.db"

    # initialize database connection
    conn = sqlite3.connect(db_filename)
    c = conn.cursor()

    ## Load Data
    # columns (other than id, which is automatically incremented
    tbl_cols = OrderedDict([("chrom", str), ("start", int),
    ("end", int), ("strand", str),
    ("rsid", str)])

    with open(sys.argv[1]) as input_file:
    for line in input_file:
    # split a tab-delimited line
    values = line.strip().split("\t")

    # pair each value with its column name
    cols_values = zip(tbl_cols.keys(), values)
    # use the column name to lookup an appropriate function to coerce each
    # value to the appropriate type
    coerced_values = [tbl_cols[col](value) for col, value in cols_values]

    # create an empty list of placeholders
    placeholders = ["?"] * len(tbl_cols)

    # create the query by joining column names and placeholders quotation
    # marks into comma-separated strings
    colnames = ", ".join(tbl_cols.keys())
    placeholders = ", ".join(placeholders)
    query = "INSERT INTO variants(%s) VALUES (%s);"%(colnames, placeholders)

    # execute query
    c.execute(query, coerced_values)

    conn.commit() # commit these inserts
    conn.close()

    本文固定链接:http://tiramisutes.github.io/2016/03/22/SQLite.html 转载请注明出处!

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