Comments on: Reading FASTA files: introduction http://python.genedrift.org/2007/07/03/reading-fasta-files/ 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: Druthi http://python.genedrift.org/2007/07/03/reading-fasta-files/comment-page-1/#comment-15551 Druthi Fri, 04 Jul 2008 05:33:53 +0000 http://python.genedrift.org/2007/07/03/reading-fasta-files/#comment-15551 how to create a module to read a fasta sequenec in Biopython .send the code for this how to create a module to read a fasta sequenec in Biopython .send the code for this

]]> By: nuin http://python.genedrift.org/2007/07/03/reading-fasta-files/comment-page-1/#comment-551 nuin Thu, 05 Jul 2007 16:34:38 +0000 http://python.genedrift.org/2007/07/03/reading-fasta-files/#comment-551 Hi Animesh I understood your point of view and thanks for linking to this site. I think that evolutionary biology software are more C/C++ based to take advantage of the speed of computation. Python can be slow sometimes and I don't see it very well geared to calculate large phylogenetic trees, for instance. One drawback of writing large Python software for distribution is actually how to distribute it and how to distribute portable solutions. I have some (little) experience writing wxPython interfaces and although Windows and Linux executables are not very large (~8 Mb), OSX standalone packages are huge, around 70 Mb in size for a 500-line program. Regarding the functional programming, I am planning to add some entries regarding it with some ("funny") examples for bioinformatics stuff. Thanks a lot for your comments and please keep commenting and visiting the website. Every opinion is important. Paulo Hi Animesh

I understood your point of view and thanks for linking to this site.

I think that evolutionary biology software are more C/C++ based to take advantage of the speed of computation. Python can be slow sometimes and I don’t see it very well geared to calculate large phylogenetic trees, for instance.

One drawback of writing large Python software for distribution is actually how to distribute it and how to distribute portable solutions. I have some (little) experience writing wxPython interfaces and although Windows and Linux executables are not very large (~8 Mb), OSX standalone packages are huge, around 70 Mb in size for a 500-line program.

Regarding the functional programming, I am planning to add some entries regarding it with some (“funny”) examples for bioinformatics stuff.

Thanks a lot for your comments and please keep commenting and visiting the website. Every opinion is important.

Paulo

]]> By: Animesh Sharma http://python.genedrift.org/2007/07/03/reading-fasta-files/comment-page-1/#comment-550 Animesh Sharma Thu, 05 Jul 2007 15:28:04 +0000 http://python.genedrift.org/2007/07/03/reading-fasta-files/#comment-550 Yes I agree with you, one should have choice :) I have shamelessly (without asking you) suggested your link as a good alternative to the pasteur thing I clipped for my blog. I have seen lot of things where people have used Python for Structure related jobs and some places where they have used it for Sequence related job as well, but one thing I have never seen is Python being used for Gene Expression and Evolutionary Biology related work... given the strong numerical (with NumPY) character of Python, better support with OOPs (can actually make good software instead of throwaway scripts I feel) and a flavor of functional programming I am sure it will be a good idea to use these as well as an example. Yes I agree with you, one should have choice :) I have shamelessly (without asking you) suggested your link as a good alternative to the pasteur thing I clipped for my blog.
I have seen lot of things where people have used Python for Structure related jobs and some places where they have used it for Sequence related job as well, but one thing I have never seen is Python being used for Gene Expression and Evolutionary Biology related work… given the strong numerical (with NumPY) character of Python, better support with OOPs (can actually make good software instead of throwaway scripts I feel) and a flavor of functional programming I am sure it will be a good idea to use these as well as an example.

]]> By: nuin http://python.genedrift.org/2007/07/03/reading-fasta-files/comment-page-1/#comment-531 nuin Wed, 04 Jul 2007 17:50:19 +0000 http://python.genedrift.org/2007/07/03/reading-fasta-files/#comment-531 Hi Animesh I am not trying to replicate what the Pasteur people is (was) doing. This is just another tutorial on how to write simple Python scripts for Bioinformatics use. It is like the many different Python programming books available: you choose what fits you best. Clearly, BioPython is one way to go to create Python scripts for bioinfo, but sometimes (1) one wants to know how to do things her/himself and (2) BioPython is not available. I recommend BioPython to whoever wants to get serious about Python and bioinfo. I don't know if there is something interesting coming up. It might not be for you but it might be very interesting to someone else. Keep checking and commenting and if you want to see something else here, just let me know. Paulo Hi Animesh

I am not trying to replicate what the Pasteur people is (was) doing. This is just another tutorial on how to write simple Python scripts for Bioinformatics use. It is like the many different Python programming books available: you choose what fits you best.

Clearly, BioPython is one way to go to create Python scripts for bioinfo, but sometimes (1) one wants to know how to do things her/himself and (2) BioPython is not available. I recommend BioPython to whoever wants to get serious about Python and bioinfo.

I don’t know if there is something interesting coming up. It might not be for you but it might be very interesting to someone else. Keep checking and commenting and if you want to see something else here, just let me know.

Paulo

]]> By: Animesh Sharma http://python.genedrift.org/2007/07/03/reading-fasta-files/comment-page-1/#comment-529 Animesh Sharma Wed, 04 Jul 2007 16:00:13 +0000 http://python.genedrift.org/2007/07/03/reading-fasta-files/#comment-529 Hey are you trying to replicate what http://www.pasteur.fr/recherche/unites/sis/formation/python/index.html guys are doing? Reading this post, it reminds me of their http://www.pasteur.fr/recherche/unites/sis/formation/python/ch11s03.html#d0e3774 . I feel if one is serious about using Python [ http://www.python.org/ ] in Bioinformatics, one should check out Biopython [ http://www.biopython.org/ ] as early as possible. Or there is something interesting coming up here later and this is just the teaser to the big event :) Hey are you trying to replicate what http://www.pasteur.fr/recherche/unites/sis/formation/python/index.html guys are doing? Reading this post, it reminds me of their http://www.pasteur.fr/recherche/unites/sis/formation/python/ch11s03.html#d0e3774 . I feel if one is serious about using Python [ http://www.python.org/ ] in Bioinformatics, one should check out Biopython [ http://www.biopython.org/ ] as early as possible. Or there is something interesting coming up here later and this is just the teaser to the big event :)

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