文件列表:

LICENSE (1079, 2014-06-04)
index.html (1076, 2014-06-04)
ncbiconnect.js (13357, 2014-06-04)

NCBIConnect.js ============== Introduction ------------ NCBIConnect.js is a client-side JavaScript library that provides a simple, hassle-free interface to some of the National Center for Biotechnology Information's databases. Right now, the *nucleotide* (nuccore) and *protein* databases are supported (you can search for nucleic acid or protein sequences by name). Support for gene data should arrive in the next build. Primary Objective ----------------- The primary objective of this project is to encourage talented bioinformaticians and web developers to find more common ground and begin taking more projects to the beautiful, dynamic, modern web with JavaScript. NCBIConnect can be used as a starting point to develop webapps that rely on NCBI's databases without having to set up a server environment - all processing is done client-side. NCBIConnect can also be used to write simple data collection scripts (in much fewer lines) that can be shared easily as .html files. No Perl required! (You can also consider writing your own data processing applications and scripts without having to save or load from local data!) Installation ------------ Simply download ```ncbiconnect.js``` and incorporate it into your webpage using: ```html ``` Voila! (Make sure it's in the same directory, otherwise specify the relative path.) Example Usage ------------- Let's say I'm interested in the genome of a specific virus. In this case, it's the much-studied bacteriophage T4. I want to grab the top 5 hits from NCBI's nucleotide database for T4's genome, and store it in a single FASTA file. Easy! ```javascript var nucDB = new NCBIConnect('nucleotide'); nucDB.query( 'Bacteriophage T4', // My search term {'limit': 5, 'offset': 0}, // Give 5 results, starting at 0 function(err, result) { if(err) { throw err; } result.getFASTA(function(err, fasta) { if(err) { throw err; } fasta.save(); }); } ); ``` Assuming we don't hit any errors with NCBI's servers, a file should automatically be downloaded to our computer's ```Downloads``` folder when we run this script. **What about listing results?** Simple! ```javascript nucDB.query( 'Bacteriophage T4', // My search term {'limit': 5, 'offset': 0}, // Give 5 results, starting at 0 function(err, result) { if(err) { throw err; } result.each(function(row) { console.log(row.get('id') + ', ' + row.get('name')); }); } ); ``` We now see a lovely output in our console: ```javascript 29366675, Enterobacteria phage T4, complete genome 422934005, Enterobacteria phage Bp7, complete genome 161622381, Enterobacteria phage JS98, complete genome 291290213, Enterobacteria phage AR1 DNA, complete genome 345450514, Enterobacteria phage Bp7, complete genome ``` **New to HTML?** You may have written some Perl but you're unfamiliar with throwing together a webpage. No problem! Included with this package is ```index.html```, a sample index page containing the latter example above. It will execute on page load so make sure you have your web console open to see it work! There are also a number of useful methods to be used with results (and FASTA files). Explore them in the documentation! **Happy building!** Documentation ============= NCBIConnect.js contains the following objects: ```NCBIConnect``` is the main connection object, it manages queries to NCBI's servers ```NCBIConnectRow``` is a result row (from a query to NCBI's databases) ```NCBIConnectSet``` is a set of ```NCBIConnectRow```s ```NCBIConnectResult``` inherits from ```NCBIConnectSet``` and is the result object that contains one or many results of a specific query from ```NCBIConnect``` ```NCBIConnectCollection``` inherits from ```NCBIConnectSet``` and can contain any collection of results from a number of queries ```NCBIConnectFASTA``` is a special interface that provides some nifty tools for dealing with FASTA files NCBIConnect ----------- ### Constructor Instantiate using ```var myConn = new NCBIConnect('[database]')``` where *[database]* is one of: *nucleotide*, *protein*. ### Methods **query** ```javascript query( str_searchTerm, obj_filters, fn_callback [ context NCBIConnect, params [ Error, NCBIConnectResult ] ] ) ``` Supported filters are ```limit``` to provide a max number of records to return, and ```offset``` to indicate which record to begin at. **queryFASTA** ```javascript queryFASTA( str_id OR arr_idList, str_fileIdentifier, fn_callback [ context NCBIConnect, params [ Error, NCBIConnectFASTA ] ] ) ``` ```id``` is a specific gene identifier (Gi) or an array of them, and ```fileIdentifer``` should be a unique string that can be used to identify the file. **createCollection** ```javascript createCollection() ``` Creates an empty ```NCBIConnectCollection``` which can then be used to store result sets for future use. NCBIConnectRow -------------- ### Constructor Inaccessible, created only as a result of a query from ```NCBIConnect``` ### Methods **set** ```javascript set( str_field, var_value ) ``` Sets a given field of the row to a specific value. **get** ```javascript get( str_field, var_defaultValue ) ``` Gets the value of the row associated with a specific field. If no value is present, defaultValue is returned. **getFASTA** ```javascript getFASTA( fn_callback [ context NCBIConnect, params [ Error, NCBIConnectFASTA ] ] ) ``` Alias for ```NCBIConnect.queryFASTA``` for this specific result row. NCBIConnectSet -------------- ### Constructor Inaccessible, created only as a result of selecting values from ```NCBIConnectResult``` or ```NCBIConnectCollection``` ### Methods **each** ```javascript each( fn_callback [ context NCBIConnect, params [ NCBIConnectRow ] ] ) ``` Executes a provided callback function for each row in the set, starting with the first result. **count** ```javascript count() ``` Returns the number of items in the set. **item** ```javascript item( int_index ) ``` Returns the item at ```index``` from the set (```NCBIConnectRow```). **first** ```javascript first() ``` Returns the first item of the set. Throws an error if the set is empty. **last** ```javascript last() ``` Returns the last item of the set. Throws an error if the set is empty. **range** ```javascript range( int_start, int_end ) ``` Returns ```NCBIConnectSet``` with values beginning at index ```start``` and ending at index ```end``` (**inclusive**). **subset** ```javascript subset( int_start, int_length ) ``` Returns ```NCBIConnectSet``` with values beginning at index ```start``` that is ```length``` items long. **toArray** ```javascript toArray() ``` Converts the set into a native Array of native Objects. (These objects are *not* copies! They contain referential row data.) **list** ```javascript list( str_field ) ``` Returns a native Array of all values associated with ```field``` for each row in the set. **getFASTA** ```javascript getFASTA( fn_callback [ context NCBIConnect, params [ Error, NCBIConnectFASTA ] ] ) ``` Alias for ```NCBIConnect.queryFASTA``` for all rows in the set - returns an aggregated (multi-FASTA) file. NCBIConnectResult ----------------- ### Inherits This Object inherits from ```NCBIConnectSet``` ### Constructor Inaccessible, returned as a result of ```NCBIConnect.query``` NCBIConnectCollection ---------------------- ### Inherits This Object inherits from ```NCBIConnectSet``` ### Constructor Inaccessible, returned as a result of ```NCBIConnect.createCollection``` ### Methods **add** ```javascript add( [NCBIConnectRow or NCBIConnectSet or NCBIConnectResult or NCBIConnectCollection], ... ) ``` Accepts any number of arguments of the above specified kinds. Adds the rows from these objects, in order, to the collection. Returns current collection. **remove** ```javascript remove( int_index ) ``` Removes the row at specified index from the current collection, and returns the current collection. NCBIConnectFASTA ---------------- ### Constructor Inaccessible, returned as a result of ```NCBIConnect.queryFASTA```'s callback. ### Methods **size** ```javascript size() ``` Returns the total size, in bytes, of the raw FASTA (or multiFASTA) file. **raw** ```javascript raw() ``` Returns a string containing the raw FASTA (or multiFASTA) file. **data** ```javascript data( opt_int_index ) ``` If ```index``` is supplied, provides a native Object containing both the header (comments) and content data of the FASTA file at the specified index (useful for multiFASTA files). Otherwise provides a native Array containing all such Objects. (Single FASTA files will use an index of 0). **header** ```javascript header( opt_int_index ) ``` Similar to ```data()```, but provides the specific header (comment) information for FASTA file at specified index. **content** ```javascript content( opt_int_index ) ``` Similar to ```header```, but provides the specific content information for FASTA file at specified index. (No whitespace.) **save** ```javascript save( opt_str_name ) ``` Automatically saves the full FASTA or multiFASTA file to the user's browser-specified "Downloads" folder. If ```name``` is provided, it will attempt to save the file as ```name + '.seq'```, otherwise the name will be automatically generated. Thanks ====== Thanks for checking out NCBIConnect.js :) You can check out my other projects on my GitHub account: http://github.com/keithwhor View my personal website at: http://keithwhor.com Or follow me on Twitter: @keithwhor http://twitter.com/keithwhor Cheers!

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