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Evan Parker's Blog

Wednesday, August 27, 2014. I wanted to add performance metrics for fasta format files since their simplicity means that they are often used to transmit large sequences; the main intended use case of the lazy loading parsers. Fasta files don't contain extensive annotations or any features so the primary task of parsing a fasta file is parsing the sequence. Included below are the compared times for both a large file and a medium sized file. Wednesday, August 20, 2014. While the lazy loading classes and so...

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Wednesday, August 27, 2014. I wanted to add performance metrics for fasta format files since their simplicity means that they are often used to transmit large sequences; the main intended use case of the lazy loading parsers. Fasta files don't contain extensive annotations or any features so the primary task of parsing a fasta file is parsing the sequence. Included below are the compared times for both a large file and a medium sized file. Wednesday, August 20, 2014. While the lazy loading classes and so...

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Evan Parker's Blog | blog.evanaparker.com Reviews

https://blog.evanaparker.com

Wednesday, August 27, 2014. I wanted to add performance metrics for fasta format files since their simplicity means that they are often used to transmit large sequences; the main intended use case of the lazy loading parsers. Fasta files don't contain extensive annotations or any features so the primary task of parsing a fasta file is parsing the sequence. Included below are the compared times for both a large file and a medium sized file. Wednesday, August 20, 2014. While the lazy loading classes and so...

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blog.evanaparker.com

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Evan Parker's Blog

http://blog.evanaparker.com/2014_07_01_archive.html

Skip to main content. Showing posts from July, 2014. Indexing XML files in Python. Parsing EMBL and performance testing. Lazy loading of GenBank format. Back to coding: storage of the index dictionary. After a period of relatively low activity due to my obligations in graduate school and recently due to my presentation at the ASMS conference, I am now doing full-time coding for Biopython! Working with the Fasta format. Designing an abstract base for lazy loading proxies. Building Biopython on Windows.

2

Evan Parker's Blog

http://blog.evanaparker.com/2014_08_01_archive.html

Skip to main content. Showing posts from August, 2014. Pre-pull-request performance tests and documentation. Preparing the lazy loading parser for public review. Lazy loading of Uniprot-XML.

3

Indexing XML files in Python

http://blog.evanaparker.com/2014/07/indexing-xml-files-in-python.html

Skip to main content. Indexing XML files in Python. XML provides some unique challenges for file indexing. Up to now, the sequence file formats I have worked with used line-based data where newline characters have concrete meaning. This is useful since an easy way to iterate over a text file is through the. Call Conversely it is possible that a single chunk of valid data is separated by many newlines while remaining XML compliant. Stream-based parsers are an attractive option for indexing since, by their...

4

Lazy loading of Uniprot-XML

http://blog.evanaparker.com/2014/08/lazy-loading-of-uniprot-xml.html

Skip to main content. Lazy loading of Uniprot-XML. We are closing in on the pencils down date for Google Summer of Code but I'm still busy cleaning up my code and adding the last of my features. Previously I developed a method of indexing XML files using Python's expat bindings. This helped tremendously with the task of indexing and lazy-loading of Uniprot-XML files. May 20, 2016 at 5:05 AM. Salesforce training in Chennai. Popular posts from this blog. Indexing XML files in Python.

5

Parsing EMBL and performance testing

http://blog.evanaparker.com/2014/07/parsing-embl-and-performance-testing.html

Skip to main content. Parsing EMBL and performance testing. As an update to my performance evaluation, the elimination of the unnecessary file. Below I have included the raw results for the GenBank file. And for the EMBL file. Each performance test was run twice in a row before saving results to account any potential performance boost given by OS-level file caching. Popular posts from this blog. Indexing XML files in Python.

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Google Summer of Code · Biopython

http://biopython.org/wiki/Google_Summer_of_Code

Biopython version 1.67. Edit this page on GitHub. Google Summer of Code. For the past several years, Biopython-related GSoC projects have been successfully run under the mentorship of the Open Bioinformatics Foundation (OBF). And the National Evolutionary Synthesis Center (NESCent). Please read those organizations’ GSoC pages and the main Google Summer of Code page. For more details about the program. See the Open Bioinformatics Foundation (OBF) GSoC wiki page. And OBF GSoC page. Object. This works w...

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Evan Parker's Blog

Wednesday, August 27, 2014. I wanted to add performance metrics for fasta format files since their simplicity means that they are often used to transmit large sequences; the main intended use case of the lazy loading parsers. Fasta files don't contain extensive annotations or any features so the primary task of parsing a fasta file is parsing the sequence. Included below are the compared times for both a large file and a medium sized file. Wednesday, August 20, 2014. While the lazy loading classes and so...

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