The cl-gene-searcher Reference Manual

Table of Contents

The cl-gene-searcher Reference Manual

This is the cl-gene-searcher Reference Manual, version 0.1, generated automatically by Declt version 3.0 "Montgomery Scott" on Tue Apr 28 10:57:48 2020 GMT+0.

1 Introduction

cl-gene-searcher is a very simple library to allow searching for information available through UCSC, in a local form.  The current database utilized is sqlite, with eventual support for utilizing the API interface for UCSC.  

Installation
1) git clone the repository
2) Symlink the asd file to your central asdf systems directory
3) Download hg18.sqlite (hg19 coming soon) - Location: (still working on this)

Sample Usage:

(require :cl-gene-searcher)

You can create your own package that uses cl-gene-searcher, or just (in-package :cl-gene-searcher)

You will need to point the library to your hg18 database:
(setDatabasePath "/Users/dthole/programming/cl-gene-searcher/data/hg18.sqlite")

To search by a gene name (or multiple gene names):
CL-GENE-SEARCHER> (loop for x in (query-gene-by-name "RPS6KA2" "FAM20C") do (format t "name: ~a~%" (name x)))
name: RPS6KA2
name: RPS6KA2
name: FAM20C
NIL


To look up genes based off some genomic location:
CL-GENE-SEARCHER> (query-gene-by-range :chr "chr1" :start 1 :stop 5000)
(# # #
 # # #
 # # #
 # # #
 # # #)

And to get their useful information:
CL-GENE-SEARCHER> (loop for x in (query-gene-by-range :chr "chr1" :start 1 :stop 5000) do (format t "chr: ~a | start: ~a | end: ~a | name: ~a~%" (chr x) (start_region x) (stop_region x) (name x)))
chr: chr1 | start: 1115 | end: 4121 | name: uc001aaa.2
chr: chr1 | start: 1115 | end: 4272 | name: uc009vip.1
chr: chr1 | start: 4268 | end: 6628 | name: uc009vis.1
chr: chr1 | start: 4268 | end: 9622 | name: uc009vit.1
chr: chr1 | start: 4268 | end: 9622 | name: uc009viu.1
chr: chr1 | start: 4268 | end: 9622 | name: uc001aae.2
chr: chr1 | start: 4268 | end: 14764 | name: uc001aab.2
chr: chr1 | start: 4268 | end: 19221 | name: uc009viq.1
chr: chr1 | start: 4268 | end: 19221 | name: uc009vir.1
chr: chr1 | start: 4268 | end: 19221 | name: uc001aac.2
chr: chr1 | start: 4269 | end: 19221 | name: uc009viv.1
chr: chr1 | start: 4269 | end: 19221 | name: uc009viw.1
chr: chr1 | start: 4832 | end: 19672 | name: uc001aaf.1
chr: chr1 | start: 4224 | end: 7502 | name: LOC100288778
chr: chr1 | start: 4224 | end: 19233 | name: WASH7P
NIL


If you wanted just the refFlat version of this information:
CL-GENE-SEARCHER> (loop for x in (query-refflat-gene-by-range :chr "chr1" :start 1 :stop 5000) do (format t "chr: ~a | start: ~a | end: ~a | name: ~a~%" (chr x) (start_region x) (stop_region x) (name x)))
chr: chr1 | start: 4224 | end: 7502 | name: LOC100288778
chr: chr1 | start: 4224 | end: 19233 | name: WASH7P
NIL

2 Systems

The main system appears first, followed by any subsystem dependency.

2.1 cl-gene-searcher

Maintainer

David Thole

Author

David Thole

License

LGPL

Description

A simple interface to a SQLite database for querying information for genes, and DGV Tracks.

Version

0.1

Dependency

clsql-sqlite3

Source

cl-gene-searcher.asd (file)

Components

• lib/cl-gene-searcher/package.lisp (file)
• lib/cl-gene-searcher/db-connections.lisp (file)
• lib/cl-gene-searcher/db-defs.lisp (file)
• lib/cl-gene-searcher/cl-gene-searcher.lisp (file)

3 Files

Files are sorted by type and then listed depth-first from the systems components trees.

3.1 Lisp

3.1.1 cl-gene-searcher.asd

Location

cl-gene-searcher.asd

Systems

cl-gene-searcher (system)

Packages

cl-gene-searcher-asd

3.1.2 cl-gene-searcher/lib/cl-gene-searcher/package.lisp

Parent

cl-gene-searcher (system)

Location

lib/cl-gene-searcher/package.lisp

Packages

cl-gene-searcher

3.1.3 cl-gene-searcher/lib/cl-gene-searcher/db-connections.lisp

Dependency

lib/cl-gene-searcher/package.lisp (file)

Parent

cl-gene-searcher (system)

Location

lib/cl-gene-searcher/db-connections.lisp

Internal Definitions

• *global-db-connection-object* (special variable)
• connect-db (generic function)
• connect-db (method)
• db-connection (class)
• db-connection-sqlite (class)
• db-type (method)
• db-type (method)
• (setf db-type) (method)
• disconnect-db (function)
• path (method)
• (setf path) (method)

3.1.4 cl-gene-searcher/lib/cl-gene-searcher/db-defs.lisp

Dependency

lib/cl-gene-searcher/db-connections.lisp (file)

Parent

cl-gene-searcher (system)

Location

lib/cl-gene-searcher/db-defs.lisp

Exported Definitions

• chr (method)
• (setf chr) (method)
• chr (method)
• (setf chr) (method)
• id (method)
• id (method)
• name (method)
• (setf name) (method)
• name (method)
• (setf name) (method)
• platform (method)
• (setf platform) (method)
• powner (method)
• (setf powner) (method)
• start_region (method)
• (setf start_region) (method)
• start_region (method)
• (setf start_region) (method)
• stop_region (method)
• (setf stop_region) (method)
• stop_region (method)
• (setf stop_region) (method)
• strand (method)
• (setf strand) (method)
• strand (method)
• (setf strand) (method)

Internal Definitions

• dgv (class)
• geneplatform (class)
• genes (class)

3.1.5 cl-gene-searcher/lib/cl-gene-searcher/cl-gene-searcher.lisp

Dependency

lib/cl-gene-searcher/db-defs.lisp (file)

Parent

cl-gene-searcher (system)

Location

lib/cl-gene-searcher/cl-gene-searcher.lisp

Exported Definitions

• getdatabasepath (function)
• query-dgv-by-range (function)
• query-gene-by-name (function)
• query-gene-by-range (function)
• query-refflat-gene-by-range (function)
• query-ucsc-gene-by-range (function)
• setdatabasepath (function)

Internal Definitions

• *database-path* (special variable)
• query-error (condition)
• text (method)
• with-generic-sqlite-db (macro)

4 Packages

Packages are listed by definition order.

4.1 cl-gene-searcher-asd

Source

cl-gene-searcher.asd

Use List

common-lisp

4.2 cl-gene-searcher

Source

lib/cl-gene-searcher/package.lisp (file)

Use List

• clsql-sqlite3
• common-lisp

Exported Definitions

• chr (generic function)
• chr (method)
• (setf chr) (method)
• chr (method)
• (setf chr) (method)
• (setf chr) (generic function)
• getdatabasepath (function)
• id (generic function)
• id (method)
• id (method)
• name (generic function)
• name (method)
• (setf name) (method)
• name (method)
• (setf name) (method)
• (setf name) (generic function)
• platform (generic function)
• platform (method)
• (setf platform) (method)
• (setf platform) (generic function)
• powner (generic function)
• powner (method)
• (setf powner) (method)
• (setf powner) (generic function)
• query-dgv-by-range (function)
• query-gene-by-name (function)
• query-gene-by-range (function)
• query-refflat-gene-by-range (function)
• query-ucsc-gene-by-range (function)
• setdatabasepath (function)
• start_region (generic function)
• start_region (method)
• (setf start_region) (method)
• start_region (method)
• (setf start_region) (method)
• (setf start_region) (generic function)
• stop_region (generic function)
• stop_region (method)
• (setf stop_region) (method)
• stop_region (method)
• (setf stop_region) (method)
• (setf stop_region) (generic function)
• strand (generic function)
• strand (method)
• (setf strand) (method)
• strand (method)
• (setf strand) (method)
• (setf strand) (generic function)

Internal Definitions

• *database-path* (special variable)
• *global-db-connection-object* (special variable)
• connect-db (generic function)
• connect-db (method)
• db-connection (class)
• db-connection-sqlite (class)
• db-type (generic function)
• db-type (method)
• db-type (method)
• (setf db-type) (method)
• (setf db-type) (generic function)
• dgv (class)
• disconnect-db (function)
• geneplatform (class)
• genes (class)
• path (generic function)
• path (method)
• (setf path) (method)
• (setf path) (generic function)
• query-error (condition)
• text (generic function)
• text (method)
• with-generic-sqlite-db (macro)

5 Definitions

Definitions are sorted by export status, category, package, and then by lexicographic order.

5.1 Exported definitions

5.1.1 Functions

Function: getdatabasepath ()

Package

cl-gene-searcher

Source

lib/cl-gene-searcher/cl-gene-searcher.lisp (file)

Function: query-dgv-by-range &key CHR START STOP

Package

cl-gene-searcher

Source

lib/cl-gene-searcher/cl-gene-searcher.lisp (file)

Function: query-gene-by-name NAME &rest NAMES

Package

cl-gene-searcher

Source

lib/cl-gene-searcher/cl-gene-searcher.lisp (file)

Function: query-gene-by-range &key CHR START STOP

Package

cl-gene-searcher

Source

lib/cl-gene-searcher/cl-gene-searcher.lisp (file)

Function: query-refflat-gene-by-range &key CHR START STOP

Package

cl-gene-searcher

Source

lib/cl-gene-searcher/cl-gene-searcher.lisp (file)

Function: query-ucsc-gene-by-range &key CHR START STOP

Package

cl-gene-searcher

Source

lib/cl-gene-searcher/cl-gene-searcher.lisp (file)

Function: setdatabasepath PATH

Package

cl-gene-searcher

Source

lib/cl-gene-searcher/cl-gene-searcher.lisp (file)

5.1.2 Generic functions

Generic Function: chr OBJECT

Generic Function: (setf chr) NEW-VALUE OBJECT

Package

cl-gene-searcher

Methods

Method: chr (DGV dgv)

automatically generated reader method

Source

lib/cl-gene-searcher/db-defs.lisp (file)

Method: (setf chr) NEW-VALUE (DGV dgv)

automatically generated writer method

Source

lib/cl-gene-searcher/db-defs.lisp (file)

Method: chr (GENES genes)

automatically generated reader method

Source

lib/cl-gene-searcher/db-defs.lisp (file)

Method: (setf chr) NEW-VALUE (GENES genes)

automatically generated writer method

Source

lib/cl-gene-searcher/db-defs.lisp (file)

Generic Function: id OBJECT

Package

cl-gene-searcher

Methods

Method: id (DGV dgv)

automatically generated reader method

Source

lib/cl-gene-searcher/db-defs.lisp (file)

Method: id (GENEPLATFORM geneplatform)

automatically generated reader method

Source

lib/cl-gene-searcher/db-defs.lisp (file)

Generic Function: name OBJECT

Generic Function: (setf name) NEW-VALUE OBJECT

Package

cl-gene-searcher

Methods

Method: name (GENES genes)

automatically generated reader method

Source

lib/cl-gene-searcher/db-defs.lisp (file)

Method: (setf name) NEW-VALUE (GENES genes)

automatically generated writer method

Source

lib/cl-gene-searcher/db-defs.lisp (file)

Method: name (GENEPLATFORM geneplatform)

automatically generated reader method

Source

lib/cl-gene-searcher/db-defs.lisp (file)

Method: (setf name) NEW-VALUE (GENEPLATFORM geneplatform)

automatically generated writer method

Source

lib/cl-gene-searcher/db-defs.lisp (file)

Generic Function: platform OBJECT

Generic Function: (setf platform) NEW-VALUE OBJECT

Package

cl-gene-searcher

Methods

Method: platform (GENES genes)

automatically generated reader method

Source

lib/cl-gene-searcher/db-defs.lisp (file)

Method: (setf platform) NEW-VALUE (GENES genes)

automatically generated writer method

Source

lib/cl-gene-searcher/db-defs.lisp (file)

Generic Function: powner OBJECT

Generic Function: (setf powner) NEW-VALUE OBJECT

Package

cl-gene-searcher

Methods

Method: powner (GENES genes)

automatically generated reader method

Source

lib/cl-gene-searcher/db-defs.lisp (file)

Method: (setf powner) NEW-VALUE (GENES genes)

automatically generated writer method

Source

lib/cl-gene-searcher/db-defs.lisp (file)

Generic Function: start_region OBJECT

Generic Function: (setf start_region) NEW-VALUE OBJECT

Package

cl-gene-searcher

Methods

Method: start_region (DGV dgv)

automatically generated reader method

Source

lib/cl-gene-searcher/db-defs.lisp (file)

Method: (setf start_region) NEW-VALUE (DGV dgv)

automatically generated writer method

Source

lib/cl-gene-searcher/db-defs.lisp (file)

Method: start_region (GENES genes)

automatically generated reader method

Source

lib/cl-gene-searcher/db-defs.lisp (file)

Method: (setf start_region) NEW-VALUE (GENES genes)

automatically generated writer method

Source

lib/cl-gene-searcher/db-defs.lisp (file)

Generic Function: stop_region OBJECT

Generic Function: (setf stop_region) NEW-VALUE OBJECT

Package

cl-gene-searcher

Methods

Method: stop_region (DGV dgv)

automatically generated reader method

Source

lib/cl-gene-searcher/db-defs.lisp (file)

Method: (setf stop_region) NEW-VALUE (DGV dgv)

automatically generated writer method

Source

lib/cl-gene-searcher/db-defs.lisp (file)

Method: stop_region (GENES genes)

automatically generated reader method

Source

lib/cl-gene-searcher/db-defs.lisp (file)

Method: (setf stop_region) NEW-VALUE (GENES genes)

automatically generated writer method

Source

lib/cl-gene-searcher/db-defs.lisp (file)

Generic Function: strand OBJECT

Generic Function: (setf strand) NEW-VALUE OBJECT

Package

cl-gene-searcher

Methods

Method: strand (DGV dgv)

automatically generated reader method

Source

lib/cl-gene-searcher/db-defs.lisp (file)

Method: (setf strand) NEW-VALUE (DGV dgv)

automatically generated writer method

Source

lib/cl-gene-searcher/db-defs.lisp (file)

Method: strand (GENES genes)

automatically generated reader method

Source

lib/cl-gene-searcher/db-defs.lisp (file)

Method: (setf strand) NEW-VALUE (GENES genes)

automatically generated writer method

Source

lib/cl-gene-searcher/db-defs.lisp (file)

5.2 Internal definitions

5.2.1 Special variables

Special Variable: *database-path*

Package

cl-gene-searcher

Source

lib/cl-gene-searcher/cl-gene-searcher.lisp (file)

Special Variable: *global-db-connection-object*

Package

cl-gene-searcher

Source

lib/cl-gene-searcher/db-connections.lisp (file)

5.2.2 Macros

Macro: with-generic-sqlite-db (VAR) &body BODY

Package

cl-gene-searcher

Source

lib/cl-gene-searcher/cl-gene-searcher.lisp (file)

5.2.3 Functions

Function: disconnect-db ()

Package

cl-gene-searcher

Source

lib/cl-gene-searcher/db-connections.lisp (file)

5.2.4 Generic functions

Generic Function: connect-db DB-CONNECTION

Generic method for which the various database types will be supported

Package

cl-gene-searcher

Source

lib/cl-gene-searcher/db-connections.lisp (file)

Methods

Method: connect-db (DB db-connection-sqlite)

Generic Function: db-type OBJECT

Generic Function: (setf db-type) NEW-VALUE OBJECT

Package

cl-gene-searcher

Methods

Method: db-type (DB-CONNECTION-SQLITE db-connection-sqlite)

automatically generated reader method

Source

lib/cl-gene-searcher/db-connections.lisp (file)

Method: db-type (DB-CONNECTION db-connection)

automatically generated reader method

Source

lib/cl-gene-searcher/db-connections.lisp (file)

Method: (setf db-type) NEW-VALUE (DB-CONNECTION db-connection)

automatically generated writer method

Source

lib/cl-gene-searcher/db-connections.lisp (file)

Generic Function: path OBJECT

Generic Function: (setf path) NEW-VALUE OBJECT

Package

cl-gene-searcher

Methods

Method: path (DB-CONNECTION-SQLITE db-connection-sqlite)

automatically generated reader method

Source

lib/cl-gene-searcher/db-connections.lisp (file)

Method: (setf path) NEW-VALUE (DB-CONNECTION-SQLITE db-connection-sqlite)

automatically generated writer method

Source

lib/cl-gene-searcher/db-connections.lisp (file)

Generic Function: text CONDITION

Package

cl-gene-searcher

Methods

Method: text (CONDITION query-error)

Source

lib/cl-gene-searcher/cl-gene-searcher.lisp (file)

5.2.5 Conditions

Condition: query-error ()

Package

cl-gene-searcher

Source

lib/cl-gene-searcher/cl-gene-searcher.lisp (file)

Direct superclasses

error (condition)

Direct methods

text (method)

Direct slots

Slot: text

Initargs

:text

Readers

text (generic function)

5.2.6 Classes

Class: db-connection ()

The foundation datbase connection class, that the others will inherit

Package

cl-gene-searcher

Source

lib/cl-gene-searcher/db-connections.lisp (file)

Direct superclasses

standard-object (class)

Direct subclasses

db-connection-sqlite (class)

Direct methods

• db-type (method)
• db-type (method)

Direct slots

Slot: type

Initargs

:type

Readers

db-type (generic function)

Writers

(setf db-type) (generic function)

Class: db-connection-sqlite ()

The specific connection object for SQLite

Package

cl-gene-searcher

Source

lib/cl-gene-searcher/db-connections.lisp (file)

Direct superclasses

db-connection (class)

Direct methods

• connect-db (method)
• path (method)
• path (method)
• db-type (method)

Direct slots

Slot: type

Initform

"sqlite3"

Readers

db-type (generic function)

Slot: path

Initargs

:path

Readers

path (generic function)

Writers

(setf path) (generic function)

Class: dgv ()

Package

cl-gene-searcher

Source

lib/cl-gene-searcher/db-defs.lisp (file)

Direct superclasses

standard-db-object (class)

Direct methods

• strand (method)
• strand (method)
• stop_region (method)
• stop_region (method)
• start_region (method)
• start_region (method)
• chr (method)
• chr (method)
• id (method)

Direct slots

Slot: id

Type

(or null integer)

Readers

id (generic function)

Slot: chr

Type

(or null string)

Initargs

:chr

Readers

chr (generic function)

Writers

(setf chr) (generic function)

Slot: start_region

Type

(or null integer)

Initargs

:start_region

Readers

start_region (generic function)

Writers

(setf start_region) (generic function)

Slot: stop_region

Type

(or null integer)

Initargs

:stop_region

Readers

stop_region (generic function)

Writers

(setf stop_region) (generic function)

Slot: strand

Type

(or null string)

Initargs

:strand

Readers

strand (generic function)

Writers

(setf strand) (generic function)

Class: geneplatform ()

Package

cl-gene-searcher

Source

lib/cl-gene-searcher/db-defs.lisp (file)

Direct superclasses

standard-db-object (class)

Direct methods

• name (method)
• name (method)
• id (method)

Direct slots

Slot: id

Type

(or null integer)

Readers

id (generic function)

Slot: name

Type

(or null string)

Initargs

:name

Readers

name (generic function)

Writers

(setf name) (generic function)

Class: genes ()

Package

cl-gene-searcher

Source

lib/cl-gene-searcher/db-defs.lisp (file)

Direct superclasses

standard-db-object (class)

Direct methods

• powner (method)
• powner (method)
• platform (method)
• platform (method)
• strand (method)
• strand (method)
• stop_region (method)
• stop_region (method)
• start_region (method)
• start_region (method)
• chr (method)
• chr (method)
• name (method)
• name (method)

Direct slots

Slot: name

Type

(or null string)

Initargs

:name

Readers

name (generic function)

Writers

(setf name) (generic function)

Slot: chr

Type

(or null string)

Initargs

:chr

Readers

chr (generic function)

Writers

(setf chr) (generic function)

Slot: start_region

Type

(or null integer)

Initargs

:start_region

Readers

start_region (generic function)

Writers

(setf start_region) (generic function)

Slot: stop_region

Type

(or null integer)

Initargs

:stop_region

Readers

stop_region (generic function)

Writers

(setf stop_region) (generic function)

Slot: strand

Type

(or null string)

Initargs

:strand

Readers

strand (generic function)

Writers

(setf strand) (generic function)

Slot: platform

Type

(or null integer)

Initargs

:platform

Readers

platform (generic function)

Writers

(setf platform) (generic function)

Slot: powner

Readers

powner (generic function)

Writers

(setf powner) (generic function)

Appendix A Indexes

A.1 Concepts

A.2 Functions

A.3 Variables

A.4 Data types