Comments on: Splitting a multiple sequence FASTA file http://python.genedrift.org/2007/10/09/splitting-a-multiple-sequence-fasta-file/ a step-by-step guide to create Python applications in bioinformatics Sun, 02 May 2010 04:24:01 +0000 hourly 1 http://wordpress.org/?v=3.1-alpha By: Daniel Swan » Python, bioinformatics and ‘open blogging’ http://python.genedrift.org/2007/10/09/splitting-a-multiple-sequence-fasta-file/comment-page-1/#comment-4282 Daniel Swan » Python, bioinformatics and ‘open blogging’ Thu, 18 Oct 2007 10:23:28 +0000 http://python.genedrift.org/2007/10/09/splitting-a-multiple-sequence-fasta-file/#comment-4282 [...] the site has drifted away from the book, and I was compelled to comment on this article here. This caused, I think, some annoyance to the author who felt the need not only to rebut me in the [...] [...] the site has drifted away from the book, and I was compelled to comment on this article here. This caused, I think, some annoyance to the author who felt the need not only to rebut me in the [...]

]]> By: nuin http://python.genedrift.org/2007/10/09/splitting-a-multiple-sequence-fasta-file/comment-page-1/#comment-3926 nuin Wed, 10 Oct 2007 12:49:43 +0000 http://python.genedrift.org/2007/10/09/splitting-a-multiple-sequence-fasta-file/#comment-3926 Hi Daniel Maybe you have misunderstood the real focus of this blog/tutorial. I am not trying to reinvent the wheel, but create real-life examples with Python and bioinformatics. The main objective here is to expose people to Python. If the intention of this site was to show Unix/Linux commands I would be writing about sed, awk, cat, grep, etc that would in the end replace everything that I posted here and more. Remember that not everyone is like you with access to a Unix/Linux workstation and knowledge of all Unix/Linux commands. Some people (at least 69%) access this site from a Windows machine and have no access to a bash shell. You could easily mirror all posts here and transform them into a Unix/Linux string of commands, just to show people how to do it from the command line in your blog. And if reinventing the wheel was a problem, we shouldn't have so many redundant programming languages, should we? Hi Daniel

Maybe you have misunderstood the real focus of this blog/tutorial. I am not trying to reinvent the wheel, but create real-life examples with Python and bioinformatics. The main objective here is to expose people to Python.

If the intention of this site was to show Unix/Linux commands I would be writing about sed, awk, cat, grep, etc that would in the end replace everything that I posted here and more.

Remember that not everyone is like you with access to a Unix/Linux workstation and knowledge of all Unix/Linux commands. Some people (at least 69%) access this site from a Windows machine and have no access to a bash shell. You could easily mirror all posts here and transform them into a Unix/Linux string of commands, just to show people how to do it from the command line in your blog.

And if reinventing the wheel was a problem, we shouldn’t have so many redundant programming languages, should we?

]]> By: Daniel Swan http://python.genedrift.org/2007/10/09/splitting-a-multiple-sequence-fasta-file/comment-page-1/#comment-3918 Daniel Swan Wed, 10 Oct 2007 08:30:00 +0000 http://python.genedrift.org/2007/10/09/splitting-a-multiple-sequence-fasta-file/#comment-3918 This is one of those 'bioinformatics' tasks where people are seriously guilty of reinventing the wheel. If for the moment we assume most bioinformaticians are working on a *nix workstation 'csplit' should probably be your first port of call for context based splitting of files! And it's far more widely applicable than for just this example. Remember - if it seems like a logical operation and you are in the 'why hasn't anyone made a utility to do this?' frame of mind - look around because they probably have! This is one of those ‘bioinformatics’ tasks where people are seriously guilty of reinventing the wheel. If for the moment we assume most bioinformaticians are working on a *nix workstation ‘csplit’ should probably be your first port of call for context based splitting of files! And it’s far more widely applicable than for just this example.

Remember – if it seems like a logical operation and you are in the ‘why hasn’t anyone made a utility to do this?’ frame of mind – look around because they probably have!

]]>