Core 0.4.3 0.4.4 delta

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These are detailed notes on changes made between release-0-04-3 and release-0-04-4.

Bio::DB::Abstract: Added the GenBank.pm DB module for retrieving nucleotide and protein sequences from GenBank (uses Tools::WWW and LWP:Simple qw(get)) and currently returns a Seq object (perhaps an EMBL-SeqIO parsed Entry/?? object soon).; Removed AutoLoader usage.

Bio::DB::GenBank: This is the GenBank.pm module, uses Bio::Tools::WWW and LWP::Simple qw(get) to retrieve nucleotide/protein entries (in genbank format) from GenBank, via Entrez. Returns a Seq object.; Removed AutoLoader usage.; Overhauled a bit to use IO::Socket instead of LWP and Bio::SeqIO instead of Seq->parse_genbank(). Probably not functional yet.; Getting things to work still using IO::Socket. Perhaps painfully.; Added documentation. Yee haw.; Made a small fix to SeqIO::Fasta.pm - it was grabbing the next character from the filehandle (getc($fh)) and checking to see if it's a '>' (if so, quit), and if not, just add it willy nilly to the sequence. However, it's possible that this character is neither '>' nor /\w/ (like if its a space or newline or such). In this case, we shouldn't add it. And now DB::GenBank.pm works ducky.

Bio::Root::Global: Added NEWLINE global. Changed default timeout to 20 seconds.; Changes for the 0.04.4 release (see the Changes file in the central distribution).; Declaring TIMEOUT_SECS to avoid warnings with -w (only with 5.003).

Bio::Root::IOManager: Added NEWLINE global. Changed default timeout to 20 seconds.; Changes for the 0.04.4 release (see the Changes file in the central distribution).; Bumped up VERSION number and moved modification notes to bottom of file.

Bio::Root::Object: Changes for the 0.04.4 release (see the Changes file in the central distribution).

Bio::Root::Utilities: Added NEWLINE global. Changed default timeout to 20 seconds.; Changes for the 0.04.4 release (see the Changes file in the central distribution).; Declaring $buffer in taste_file() to prevent uninitialized warning (5.003 only).

Bio::Seq: Added parse_genbank to deal with individual sequence files coming from an Entrez query.; Fixed type() so that it always returns a string and no longer stores an uninformative 'unknown' string.

Bio::SeqIO: Added in SeqIO system; Changed SeqIO stuff for new mechanism; Added in test suite for seqio, fixed things to work ;); Fixed docs

Bio::SeqIO::EMBL: Moved SeqFeature down one, added in EMBL.pm; Added in test suite for seqio, fixed things to work ;)

Bio::SeqIO::Fasta: Added in SeqIO system; Changed SeqIO stuff for new mechanism; Added in test suite for seqio, fixed things to work ;); Made a small fix to SeqIO::Fasta.pm - it was grabbing the next character from the filehandle (getc($fh)) and checking to see if it's a '>' (if so, quit), and if not, just add it willy nilly to the sequence. However, it's possible that this character is neither '>' nor /\w/ (like if its a space or newline or such). In this case, we shouldn't add it. And now DB::GenBank.pm works ducky.; Changed $c =~ /[\n\l\r\f\s]/ to $c =~ /\W/ - no big deal.; Fixed up uc($c)

Bio::SeqIO::Handler: Added in SeqIO system; Changed SeqIO stuff for new mechanism; Added in test suite for seqio, fixed things to work ;)

Bio::SeqIO::Raw: First commit of SeqIO::Raw.pm basically it is SeqIO::Fasta.pm with a few trivial modifications.

Bio::SimpleAlign: Fixed a write_fasta bug and beefed up the test suite thingy; Added RCS Id tag.

Bio::Tools::Blast: Minor formatting of docs; Fixed a variety of bugs the most glaring of which was in postclient.pl. See the CHANGES file for Blast version 0.075 in the bioperl 0.04.4 release.

Bio::Tools::Fasta: Fixed bug regarding call to the former Util->get_newline_char and fixed num_seqs().

SeqFeature.pm: Added in SeqFeature; Moved SeqFeature down one, added in EMBL.pm

examples/psw.pl: Fixed bugs in the blast examples and in root_object/utilities.pl. Added RCS revision line (Id) and changed shebang lines to /usr/bin/perl (more standard).

examples/rev_and_trans.pl: Fixed bugs in the blast examples and in root_object/utilities.pl. Added RCS revision line (Id) and changed shebang lines to /usr/bin/perl (more standard).

examples/seq_pattern.pl: Fixed bugs in the blast examples and in root_object/utilities.pl. Added RCS revision line (Id) and changed shebang lines to /usr/bin/perl (more standard).

examples/simplealign.pl: Fixed bugs in the blast examples and in root_object/utilities.pl. Added RCS revision line (Id) and changed shebang lines to /usr/bin/perl (more standard).