Comments for Biorelated http://biorelated.com Sat, 28 Jan 2012 06:27:28 +0000 hourly 1 http://wordpress.com/ Comment on My first Bioruby plugin calculates the isoelectric point of a protein by George http://biorelated.com/2011/01/06/my-first-bioruby-plugin-calculates-the-isoelectric-point-of-a-protein/#comment-836 Sat, 28 Jan 2012 06:27:28 +0000 http://biorelated.com/?p=255#comment-836 Thanks for pointing it out! I edited the post to reflect the changes! :)

]]> Comment on My first Bioruby plugin calculates the isoelectric point of a protein by Ben Woodcroft http://biorelated.com/2011/01/06/my-first-bioruby-plugin-calculates-the-isoelectric-point-of-a-protein/#comment-835 Fri, 27 Jan 2012 22:17:02 +0000 http://biorelated.com/?p=255#comment-835 Sure – just wanted to lessen confusion. But you did change it anyway, didn’t you!

]]> Comment on My first Bioruby plugin calculates the isoelectric point of a protein by George http://biorelated.com/2011/01/06/my-first-bioruby-plugin-calculates-the-isoelectric-point-of-a-protein/#comment-834 Fri, 27 Jan 2012 18:01:30 +0000 http://biorelated.com/?p=255#comment-834 The code in this blog post was posted a year ago and I had not updated the post. for more accurate update please follow the github repo README.

]]> Comment on My first Bioruby plugin calculates the isoelectric point of a protein by Ben Woodcroft http://biorelated.com/2011/01/06/my-first-bioruby-plugin-calculates-the-isoelectric-point-of-a-protein/#comment-833 Fri, 27 Jan 2012 00:40:26 +0000 http://biorelated.com/?p=255#comment-833 Cool, good luck with that. I noticed just then that the code you have above Bio::Sequence::AA#calculate_iep should be Bio::Sequence::AA#isoelectric_point by the way.

]]> Comment on My first Bioruby plugin calculates the isoelectric point of a protein by George http://biorelated.com/2011/01/06/my-first-bioruby-plugin-calculates-the-isoelectric-point-of-a-protein/#comment-832 Thu, 26 Jan 2012 05:13:50 +0000 http://biorelated.com/?p=255#comment-832 Thanks Ben! and am glad that the plugin is useful. There is no formal publication for the plugin yet, though am planning to prepare one. The only reference so far is the github repository URL(https://github.com/georgeG/bioruby-isoelectric_point)

]]> Comment on My first Bioruby plugin calculates the isoelectric point of a protein by Ben Woodcroft http://biorelated.com/2011/01/06/my-first-bioruby-plugin-calculates-the-isoelectric-point-of-a-protein/#comment-831 Thu, 26 Jan 2012 04:21:00 +0000 http://biorelated.com/?p=255#comment-831 Good stuff. I’m likely to use this in a publication – is there a recommended reference?

]]> Comment on Converting sequence data from csv to fasta format by biorelated http://biorelated.com/2011/01/26/converting-sequence-data-from-csv-to-fasta-format/#comment-361 Thu, 01 Sep 2011 05:53:31 +0000 http://biorelated.com/?p=280#comment-361 You would run the script all at once. you would change the name of the file, i.e the path to the csv file and the name of the new fasta file. seq_name_col is the column number with the names of the sequences and the seq_data_col is the column number for the sequences.

]]> Comment on Converting sequence data from csv to fasta format by a http://biorelated.com/2011/01/26/converting-sequence-data-from-csv-to-fasta-format/#comment-328 Wed, 31 Aug 2011 08:02:20 +0000 http://biorelated.com/?p=280#comment-328 Okay I am new to Ruby (downloaded it about half an hour ago!) I am using windows and have read the brief Ruby tutorial.

This page is perfect as I want to convert a CSV fle to fasta…I am just a bit confused with this script…is it pasted into Ruby all at once? would you be able to highlight the bits where things should be edited to make it run correctly with my own files?

Sorry to be a pain but it would be so uselful to me right now!

x

]]> Comment on Convert a fastA file to a hash by Rob Syme http://biorelated.com/2011/06/25/convert-a-fasta-file-to-a-hash/#comment-203 Mon, 27 Jun 2011 01:57:47 +0000 http://biorelated.com/?p=358#comment-203 In a similar vein:

def fasta_to_hash(filename)
Hash[ Bio::FlatFile.auto(filename).map{|entry| [entry.definition, entry.seq] } ]
end

To take a filename and return a hash keyed by sequence definitions that contains Bio::Sequence objects. This is be Ruby 1.9 ony though…

]]> Comment on Standalone BLAST with Ruby (windows) by yannick http://biorelated.com/2007/10/03/standalone-blast-with-ruby-part-1/#comment-202 Wed, 22 Jun 2011 12:35:54 +0000 http://biorelated.wordpress.com/2007/10/03/standalone-blast-with-ruby-part-1/#comment-202 You can also use ruby to set up a local BLAST server, much easier than would be using NCBI’s wwwblast.
Cheers!

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