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Ready for Biopython 1.50 beta release

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peterjc committed Apr 3, 2009
1 parent 2a51f4d commit f73c5c0a03d7049c3e14eaaf2da509f7e792262b
Showing with 15 additions and 8 deletions.
  1. +1 −1 Bio/__init__.py
  2. +1 −1 Doc/Tutorial.tex
  3. +1 −1 Martel/__init__.py
  4. +12 −5 NEWS
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@@ -10,7 +10,7 @@
http://biopython.org
"""
-__version__ = "1.49+" #The plus indicates this is unreleased CVS code
+__version__ = "1.50b" #This is a beta release!
class MissingExternalDependencyError(Exception):
pass
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@@ -81,7 +81,7 @@
\author{Jeff Chang, Brad Chapman, Iddo Friedberg, Thomas Hamelryck, \\
Michiel de Hoon, Peter Cock, Tiago Ant\~ao}
-\date{Last Update -- 3 April 2009 (Biopython 1.49+)}
+\date{Last Update -- 3 April 2009 (Biopython 1.50 \textit{beta})}
%Hack to get the logo at the start of the HTML front page:
%(hopefully this isn't going to be too wide for most people)
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@@ -18,7 +18,7 @@
are now deprecated. They are no longer used in any of the current Biopython
parsers, and are likely to be removed in a future release of Biopython.
"""
-__version__ = "1.49"
+__version__ = "1.50b"
import warnings
warnings.warn("Martel and those parts of Biopython depending on it" \
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17 NEWS
@@ -9,13 +9,24 @@ The latest news is at the top.
===================================================================
+April 3, 2008: Biopython 1.50 beta released.
+
The SeqRecord object has a new dictionary attribute, letter_annotations,
which is for holding per-letter-annotation information like sequence
quality scores or secondary structure predictions. As part of this work,
the SeqRecord object can now be sliced to give a new SeqRecord covering
just part of the sequence. This will slice the per-letter-annotation to
match, and will also include any SeqFeature objects as appropriate.
+Bio.SeqIO can now read and write FASTQ and QUAL quality files using PHRED
+quality scores (Sanger style, also used for Roche 454 sequencing), and FASTQ
+files using Solexa/Illumina quality scores.
+
+The Bio.Seq module now has an UnknownSeq object, used for when we have a
+sequence of known length, but unknown content. This is used in parsing
+GenBank and EMBL files where the sequence may not be present (e.g. for a
+contig record) and when parsing QUAL files (which don't have the sequence)
+
GenomeDiagram by Leighton Pritchard has been integrated into Biopython as
the Bio.Graphics.GenomeDiagram module If you use this code, please cite the
publication Pritchard et al. (2006), Bioinformatics 22 616-617. Note that
@@ -24,16 +35,12 @@ like Bio.Graphics, this requires the ReportLab python library.
A new module Bio.Motif has been added, which is intended to replace the
existing Bio.AlignAce and Bio.MEME modules.
-Bio.SeqIO can now read and write FASTQ and QUAL quality files using PHRED
-quality scores (Sanger style, also used for Roche 454 sequencing), and FASTQ
-files using Solexa/Illumina quality scores.
-
The set of NCBI DTD files included with Bio.Entrez has been updated with the
revised files the NCBI introduced on 1 Jan 2009.
Minor fix to BioSQL for retrieving references and comments.
-We've also make some changes to our test framework, which is now given a
+We've also made some changes to our test framework, which is now given a
whole chapter in the tutorial. This intended to help new developers or
contributors wanting to improve our unit test coverage.

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