id2url

id2url opens a set of websites for a list of identifiers or other search terms. The preset websites are primarily useful for (computational) biologists. Command line options allow:

• flexible specification of search terms
• multiple websites for each term, allowing combinations of both preset and user-supplied URLs

See below for usage instructions.

Install id2url

Download the source code and run id2url:

• wget https://github.com/robinvanderlee/id2url/archive/<version>.zip
• unzip id2url-<version>.zip
• cd id2url-<version>
• ./id2url.pl

Run id2url

Instructions from id2url.pl --help:

  v1.1
Open a set of web pages for a list of identifiers or other search terms, which can be supplied as a file, or entered by pasting under the -l flag.

    Examples:
      $ ./id2url.pl uniprot_identifiers.txt
      $ cut -f 2 biomart_with_entrez_idenfiers.txt | sort | perl id2url.pl -p 2
      $ ./id2url.pl -b 5 -o 2 -v 1 -l
      $ perl id2url.pl -u \"http:\/\/www.ncbi.nlm.nih.gov\/pubmed?cmd=search&term=%s%20immunity\"
          pubmed_identifiers_search_with_immunity.txt
      $ ./id2url.pl -l -p 2,7,10 -u \"http://www.genome.jp/dbget-bin/www_bget?hsa:%s\"
    
    By default, identifiers should be on different lines (separated by a newline, \n).

    General options. Default values in square brackets []:
               -h        Display this usage help information

               -l        Asks for a list of identifiers on the command line rather 
                           than reading in from a file; execute script with ^D (ctrl+D)
                           after pasting the identifiers
               -i <id>   Open the (single) identifier that is supplied as argument
               
               -v <x>    Verbosity [0]:
                           0 print only dots
                           1 print identifiers
                           2 print full URLs

               -e <expr> Split expression for identifiers [newline ("\n")]
               -b <x>    Batchsize, open <x> URLs at a time [all]
               -o <x>    Go to the URL of every other <x> identifiers [1]
               -s <x>    Sleep time (<x> seconds) before opening next URL, can 
                           be a floating point number [0]
               -r        Open identifier URLs in reversed order
               -unq      Only open unique identfiers from the entered list

    URL options. Multiple URLs, separated by ",", can be supplied using both the -u and -p flags:
               -u <url>  Custom URL, %s will be replaced by the identifier - 
                           e.g. "http://www.uniprot.org/uniprot/%s"
               -p <x>    Preset URLs, <x>:
                           1 UniProt [default]
                           2 Entrez human (9606)
                           3 Ensembl
                           4 RefSeq
                           5 PudMed
                           6 UCSC Genome Browser
                           7 Google (careful, might cause temporary ban!)
                           8 UniProt human search
                           9 Entrez human (9606) search
                           10 GeneCards
                           11 Pfam
                           12 OMIM
                           13 QuickGO
                           14 PDB
                           15 Saccharomyces Genome Database
                           16 dbSNP
                           17 Ensembl variation
                           18 Wikipedia
                           19 InnateDB

    Other options.
               -f        Open a set of URLs in the browser as is (i.e. without any
                           identifier inserted or any other modification)

Browser compatibility and OS-specific instructions

id2url has been tested on OSX, Windows and Linux. The application was developed for graphical browsers. Command line browers are therefore not supported.

Additional information for Linux

The application uses the command x-www-browser, which opens the default web browser. To list the available web browsers for the command x-www-browser:

sudo update-alternatives --list x-www-browser

If you have a browser installed that should be compatible with x-www-browser, but is not visible in the list (e.g. firefox), install it using

sudo update-alternatives --install /usr/bin/x-www-browser x-www-browser /usr/bin/firefox 90

To change the default web browser, type

sudo update-alternatives --config x-www-browser

and select your preferred browser.