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Remove Bio::SeqIO support for abi, alf, ctf, exp, pln, and ztr.
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This trace files were wrappers to Bio::SeqIO::staden::read which is
not even indexed in CPAN (it's in the bioperl-ext repository).  So
remove this modules and move into a separate distribution (actually,
move them into the bioperl-ext repo).

Note that alf.t makes use of a test data file that no longer exists.
Looking into the history of the repo, seems that it never did.
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carandraug committed Sep 24, 2018
1 parent b3310c7 commit c98b3b5
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Showing 19 changed files with 11 additions and 1,238 deletions.
12 changes: 11 additions & 1 deletion Changes
Original file line number Diff line number Diff line change
Expand Up @@ -55,9 +55,15 @@ be removed.
Bio::DB::Expression::geo
Bio::Index::Stockholm
Bio::LiveSeq::*
Bio::Phenotype::*
Bio::Root::Build
Bio::SearchDist
Bio::Phenotype::*
Bio::SeqIO::abi
Bio::SeqIO::alf
Bio::SeqIO::ctf
Bio::SeqIO::exp
Bio::SeqIO::pln
Bio::SeqIO::ztr
Bio::Tools::AlignFactory
Bio::Tools::Phylo::Gumby
Bio::Tools::dpAlign
Expand All @@ -68,6 +74,10 @@ be removed.
bp_netinstall
bp_process_wormbase

* The following modules are no longer dependencies:

Bio::SeqIO::staden::read

[Code changes]

* The deobfuscator has been removed.
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5 changes: 0 additions & 5 deletions lib/Bio/SeqIO.pm
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Expand Up @@ -216,11 +216,6 @@ throw a fatal error.
The format name is case-insensitive: 'FASTA', 'Fasta' and 'fasta' are
all valid.
Currently, the tracefile formats (except for SCF) require installation
of the external Staden "io_lib" package, as well as the
Bio::SeqIO::staden::read package available from the bioperl-ext
repository.
=item -alphabet
Sets the alphabet ('dna', 'rna', or 'protein'). When the alphabet is
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188 changes: 0 additions & 188 deletions lib/Bio/SeqIO/abi.pm

This file was deleted.

151 changes: 0 additions & 151 deletions lib/Bio/SeqIO/alf.pm

This file was deleted.

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