This script fetches sequences from MycorWeb Blast result links.

getMycorSequences.coffee

# getMycorSequences.coffee
# This script fetches sequences from MycorWeb Blast result links.
#
# links file must be provided and can be obtained with getMycorLinks.coffee:
# https://gist.github.com/4683065
#
# Dependencies: casperjs
# Usage: casperjs getMycorSequences.coffee fileWithLinks
# Example: casperjs getMycorSequences.coffee sequencesLinks:0-4275.txt
# Author: Bruno Vieira ([email protected])
# License: MIT

fs = require 'fs'
casper = require('casper').create()

sequencesLinks = fs.read(casper.cli.args[0]).toString().split('\n')
outputFile = "#{casper.cli.args[0]}.fasta"

casper.start()

casper.then ->
  for sequenceLink in sequencesLinks
    @thenOpen sequenceLink, ->
      if sequenceLink isnt ''
        sequence = @getHTML('pre').replace('&gt;', '>').replace(/<br>/g, '\n')
        fs.write outputFile, "#{sequence}\n", 'a'

casper.run()