biogo

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v0.0.0-...-25502c3 Latest Latest Go to latest Published: Oct 9, 2012 License: GPL-3.0 Imports: 0 Imported by: 0

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README ¶

bíogo

#bíogo

##Installation

    $ go get code.google.com/p/biogo/...

##Overview

bíogo is a bioinformatics library for the Go language. It is a work in progress.

##The Purpose of bíogo

bíogo stems from the need to address the size and structure of modern genomic and metagenomic data sets. These properties enforce requirements on the libraries and languages used for analysis:

speed - size of data sets
concurrency - problems often embarrassingly parallelisable

In addition to the computational burden of massive data set sizes in modern genomics there is an increasing need for complex pipelines to resolve questions in tightening problem space and also a developing need to be able to develop new algorithms to allow novel approaches to interesting questions. These issues suggest the need for a simplicity in syntax to facilitate:

ease of coding
checking for correctness in development and particularly in peer review

Related to the second issue is the reluctance of some researchers to release code because of quality concerns.

The issue of code release is the first of the principles formalised in the Science Code Manifesto.

Code  All source code written specifically to process data for a published
      paper must be available to the reviewers and readers of the paper.

A language with a simple, yet expressive, syntax should facilitate development of higher quality code and thus help reduce this barrier to research code release.

##Yet Another Bioinformatics Library

It seems that nearly every language has it own bioinformatics library, some of which are very mature, for example BioPerl and BioPython. Why add another one?

The different libraries excel in different fields, acting as scripting glue for applications in a pipeline (much of [1, 2, 3]) and interacting with external hosts [1, 2, 4, 5], wrapping lower level high performance languages with more user friendly syntax [1, 2, 3, 4] or providing bioinformatics functions for high performance languages [5, 6].

The intended niche for bíogo lies somewhere between the scripting libraries and high performance language libraries in being easy to use for both small and large projects while having reasonable performance with computationally intensive tasks.

The intent is to reduce the level of investment required to develop new research software for computationally intensive tasks.

##Library Structure and Coding Style

The bíogo library structure is influenced both by the structure of BioPerl and the Go core libraries.

The coding style is increasingly aligning itself with the style of Go core library (I hope), although the use of 'self' as the receiver variable is aligned with the BioPerl and BioPython coding styles. While this complicates refactoring, I currently feel that it provides a more informative description of the underlying intent of the code. The alignment with the BioPerl and BioPython styles is also intended to ease adoption by bioinformatics researchers, many of whom use these libraries.

##Quality Scores

Quality scores are supported for all sequence types, including protein. Phred and Solexa scoring systems are able to be read from files, however internal representation of quality scores is with Phred, so there will be precision loss in conversion. A Solexa quality score type is provided for use where this will be a problem.

##Copyright and License

This program is free software: you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.

This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details.

You should have received a copy of the GNU General Public License along with this program. If not, see http:www.gnu.org/licenses/.

BITSTREAM CHARTER is a registered trademark of Bitstream Inc.

Documentation ¶

Overview ¶

bíogo is a bioinformatics library for the Go language. It is a work in progress.

The Purpose of bíogo ¶

bíogo stems from the need to address the size and structure of modern genomic and metagenomic data sets. These properties enforce requirements on the libraries and languages used for analysis:

speed - size of data sets
concurrency - problems often embarrassingly parallelisable

In addition to the computational burden of massive data set sizes in modern genomics there is an increasing need for complex pipelines to resolve questions in tightening problem space and also a developing need to be able to develop new algorithms to allow novel approaches to interesting questions. These issues suggest the need for a simplicity in syntax to facilitate:

ease of coding
checking for correctness in development and particularly in peer review

Related to the second issue is the reluctance of some researchers to release code because of quality concerns http://www.nature.com/news/2010/101013/full/467753a.html

The issue of code release is the first of the principles formalised in the Science Code Manifesto http://sciencecodemanifesto.org/

 Code	All source code written specifically to process data for a published
	paper must be available to the reviewers and readers of the paper.

A language with a simple, yet expressive, syntax should facilitate development of higher quality code and thus help reduce this barrier to research code release.

Yet Another Bioinformatics Library ¶

It seems that nearly every language has it own bioinformatics library, some of which are very mature, for example BioPerl and BioPython. Why add another one?

The different libraries excel in different fields, acting as scripting glue for applications in a pipeline (much of [1-3]) and interacting with external hosts [1, 2, 4, 5], wrapping lower level high performance languages with more user friendly syntax [1-4] or providing bioinformatics functions for high performance languages [5, 6].

The intended niche for bíogo lies somewhere between the scripting libraries and high performance language libraries in being easy to use for both small and large projects while having reasonable performance with computationally intensive tasks.

The intent is to reduce the level of investment required to develop new research software for computationally intensive tasks.

 [1] BioPerl http://bioperl.org/
 	http://genome.cshlp.org/content/12/10/1611.full
 	http://www.springerlink.com/content/pp72033m171568p2

 [2] BioPython http://biopython.org/
	http://bioinformatics.oxfordjournals.org/content/25/11/1422

 [3] BioRuby http://bioruby.org/
 	http://bioinformatics.oxfordjournals.org/content/26/20/2617

 [4] PyCogent http://pycogent.sourceforge.net/
 	http://genomebiology.com/2007/8/8/R171

 [5] BioJava http://biojava.org/
	http://bioinformatics.oxfordjournals.org/content/24/18/2096

 [6] SeqAn http://www.seqan.de/
 	http://www.biomedcentral.com/1471-2105/9/11

Library Structure and Coding Style ¶

The bíogo library structure is influenced both by the structure of BioPerl and the Go core libraries.

The coding style is increasingly aligning itself with the style of Go core library (I hope), although the use of 'self' as the receiver variable is aligned with the BioPerl and BioPython coding styles. While this complicates refactoring, I currently feel that it provides a more informative description of the underlying intent of the code. The alignment with the BioPerl and BioPython styles is also intended to ease adoption by bioinformatics researchers, many of whom use these libraries.

Position Numbering ¶

Position numbering in the bíogo library conforms to the zero-based indexing of Go and range indexing conforms to Go's half-open zero-based slice indexing. This is at odds with the 'normal' inclusive indexing used by molecular biologists. This choice was made to avoid inconsistent indexing spaces being used — one-based inclusive for bíogo functions and methods and zero-based for native Go slices and arrays — and so avoid errors that this would otherwise facilitate. Note that the GFF package does allow, and defaults to, one-based inclusive indexing in its input and output of GFF files.

EWD831 Why numbering should start at zero

To denote the subsequence of natural numbers 2, 3, ..., 12 without the
pernicious three dots, four conventions are open to us

a) 2 ≤ i< 13
b) 1 < i≤ 12
c) 2 ≤ i≤ 12
d) 1 < i< 13

Are there reasons to prefer one convention to the other? Yes, there are.
The observation that conventions a) and b) have the advantage that the
difference between the bounds as mentioned equals the length of the
subsequence is valid. So is the observation that, as a consequence, in
either convention two subsequences are adjacent means that the upper
bound of the one equals the lower bound of the other. Valid as these
observations are, they don't enable us to choose between a) and b); so
let us start afresh.

There is a smallest natural number. Exclusion of the lower bound —as in
b) and d)— forces for a subsequence starting at the smallest natural
number the lower bound as mentioned into the realm of the unnatural
numbers. That is ugly, so for the lower bound we prefer the ≤ as in a)
and c). Consider now the subsequences starting at the smallest natural
number: inclusion of the upper bound would then force the latter to be
unnatural by the time the sequence has shrunk to the empty one. That is
ugly, so for the upper bound we prefer < as in a) and d). We conclude
that convention a) is to be preferred.

Remark  The programming language Mesa, developed at Xerox PARC, has
special notations for intervals of integers in all four conventions.
Extensive experience with Mesa has shown that the use of the other three
conventions has been a constant source of clumsiness and mistakes, and
on account of that experience Mesa programmers are now strongly advised
not to use the latter three available features. I mention this
experimental evidence —for what it is worth— because some people feel
uncomfortable with conclusions that have not been confirmed in practice.
(End of Remark.)

			*                *
				*

When dealing with a sequence of length N, the elements of which we wish
to distinguish by subscript, the next vexing question is what subscript
value to assign to its starting element. Adhering to convention a)
yields, when starting with subscript 1, the subscript range 1 ≤  i <
N+1; starting with 0, however, gives the nicer range 0 ≤   i <  N. So
let us let our ordinals start at zero: an element's ordinal (subscript)
equals the number of elements preceding it in the sequence. And the
moral of the story is that we had better regard —after all those
centuries!— zero as a most natural number.

Remark  Many programming languages have been designed without due
attention to this detail. In FORTRAN subscripts always start at 1; in
ALGOL 60 and in PASCAL, convention c) has been adopted; the more recent
SASL has fallen back on the FORTRAN convention: a sequence in SASL is at
the same time a function on the positive integers. Pity! (End of
Remark.)

			*                *
				*

The above has been triggered by a recent incident, when, in an emotional
outburst, one of my mathematical colleagues at the University —not a
computing scientist— accused a number of younger computing scientists of
"pedantry" because —as they do by habit— they started numbering at zero.
He took consciously adopting the most sensible convention as a
provocation. (Also the "End of ..." convention is viewed of as
provocative; but the convention is useful: I know of a student who
almost failed at an examination by the tacit assumption that the
questions ended at the bottom of the first page.) I think Antony Jay is
right when he states: "In corporate religions as in others, the heretic
must be cast out not because of the probability that he is wrong but
because of the possibility that he is right."

Plataanstraat 5		11 August 1982
5671 AL NUENEN		prof.dr. Edsger W. Dijkstra
The Netherlands		Burroughs Research Fellow

Quality Scores ¶

Quality scores are supported for all sequence types, including protein. Phred and Solexa scoring systems are able to be read from files, however internal representation of quality scores is with Phred, so there will be precision loss in conversion. A Solexa quality score type is provided for use where this will be a problem.

Copyright and License ¶

This program is free software: you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.

This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details.

You should have received a copy of the GNU General Public License along with this program. If not, see <http:www.gnu.org/licenses/>.

Index ¶

Constants

Constants ¶

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const Version = "alpha"

Variables ¶

This section is empty.

Functions ¶

This section is empty.

Types ¶

This section is empty.

Source Files ¶

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Directories ¶

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Path	Synopsis
align Sequence Alignment packages	Sequence Alignment packages
nw Needleman-Wunsch sequence alignment package	Needleman-Wunsch sequence alignment package
pals Package implementing functions required for PALS sequence alignment	Package implementing functions required for PALS sequence alignment
pals/dp Package providing PALS dynamic programming alignment routines.	Package providing PALS dynamic programming alignment routines.
pals/filter Package providing PALS sequence hit filter routines based on 'Efficient q-gram filters for finding all 𝛜-matches over a given length.' Kim R. Rasmussen, Jens Stoye, and Eugene W. Myers.	Package providing PALS sequence hit filter routines based on 'Efficient q-gram filters for finding all 𝛜-matches over a given length.' Kim R. Rasmussen, Jens Stoye, and Eugene W. Myers.
sw Smith-Waterman sequence alignment package	Smith-Waterman sequence alignment package
alphabet
bio
concurrent Package to apply a function over an array or stream of data.	Package to apply a function over an array or stream of data.
exp
alphabet Package alphabet describes biological sequence letters, including quality scores.	Package alphabet describes biological sequence letters, including quality scores.
seq Package seq provides the base for storage and manipulation of biological sequence information.	Package seq provides the base for storage and manipulation of biological sequence information.
seq/nucleic Package nucleic provides support for manipulation of single nucleic acid sequences with and without quality data.	Package nucleic provides support for manipulation of single nucleic acid sequences with and without quality data.
seq/nucleic/alignment Package alignment handles aligned sequences stored as columns.	Package alignment handles aligned sequences stored as columns.
seq/nucleic/multi Package multi handles collections of sequences as alignments or sets.	Package multi handles collections of sequences as alignments or sets.
seq/nucleic/packed Package packed provides support for manipulation of single nucleic acid sequences with and without quality data.	Package packed provides support for manipulation of single nucleic acid sequences with and without quality data.
seq/protein Package protein provides support for manipulation of single protein sequences with and without quality data.	Package protein provides support for manipulation of single protein sequences with and without quality data.
seq/protein/alignment Package alignment handles aligned sequences stored as columns.	Package alignment handles aligned sequences stored as columns.
seq/protein/multi Package multi handles collections of sequences as alignments or sets.	Package multi handles collections of sequences as alignments or sets.
seq/quality Package quality provides support for manipulation of quality data in generic Phred format.	Package quality provides support for manipulation of quality data in generic Phred format.
seq/quality/illumina Package illumina provides support for manipulation of quality data in Illumina format.	Package illumina provides support for manipulation of quality data in Illumina format.
seq/quality/sanger Package sanger provides support for manipulation of quality data in Sanger format.	Package sanger provides support for manipulation of quality data in Sanger format.
seq/quality/solexa Package solexa provides support for manipulation of quality data in Solexa format.	Package solexa provides support for manipulation of quality data in Solexa format.
seq/sequtils Package sequtils provides generic functions for manipulation of slices used in the seq types.	Package sequtils provides generic functions for manipulation of slices used in the seq types.
seqio Packages for reading and writing sequence files	Packages for reading and writing sequence files
seqio/fasta Package to read and write FASTA format files	Package to read and write FASTA format files
seqio/fastq Package to read and write FASTQ format files	Package to read and write FASTQ format files
feat Basic Feature package	Basic Feature package
graphics
color Hue Saturation Value Alpha color package	Hue Saturation Value Alpha color package
kmercolor Package to represent k-mer sequences as a color	Package to represent k-mer sequences as a color
index Sequence indexing packages	Sequence indexing packages
kmerindex Kmer indexing package based on Bob Edgar and Gene Meyers' approach used in PALS.	Kmer indexing package based on Bob Edgar and Gene Meyers' approach used in PALS.
interval Package to find intersections between intervals or to sort intervals.	Package to find intersections between intervals or to sort intervals.
io
alignio Package for reading and writing multiple sequence alignment files	Package for reading and writing multiple sequence alignment files
featio Packages for reading and writing features	Packages for reading and writing features
featio/bed Package to read and write BED file formats	Package to read and write BED file formats
featio/gff Package to read and write GFF format files	Package to read and write GFF format files
seqio Packages for reading and writing sequence files	Packages for reading and writing sequence files
seqio/fasta Package to read and write FASTA format files	Package to read and write FASTA format files
seqio/fastq Package to read and write FASTQ format files	Package to read and write FASTQ format files
matrix Packages providing basic linear algebra operations	Packages providing basic linear algebra operations
sparse Sparse matrix operations N.B. There is fairly extensive use of unrecovered panics in sparse to avoid unreadable matrix formulae.	Sparse matrix operations N.B. There is fairly extensive use of unrecovered panics in sparse to avoid unreadable matrix formulae.
morass Use morass when you don't want your data to be a quagmire.	Use morass when you don't want your data to be a quagmire.
nmf Implementation of NMF by alternative non-negative least squares using projected gradients Chih-Jen Lin (2007) Projected Gradient Methods for Nonnegative Matrix Factorization.	Implementation of NMF by alternative non-negative least squares using projected gradients Chih-Jen Lin (2007) Projected Gradient Methods for Nonnegative Matrix Factorization.
pwm Position weight matrix search based on algorithm by Deborah Toledo Flores	Position weight matrix search based on algorithm by Deborah Toledo Flores
seq Basic sequence package	Basic sequence package
util Commonly used functions	Commonly used functions