| move annotation.reformat.rename() to formats.gff |
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over 13 years ago
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| add formats.gff.format() option --gsac; formats.gff.load() option --attribute; |
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over 13 years ago
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| add support for "conserved hypothetical protein" |
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over 13 years ago
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| add duplicate removal in annotation.ahrd.merge() |
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over 13 years ago
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| add utils.ordereddict and make gff attributes into OrderedDict |
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over 13 years ago
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| Minor RegExp fixes to annotation.ahrd.fix() |
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over 13 years ago
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| fix bug in annotation.reformat.rename() |
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over 13 years ago
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| Added in RegExps (loosely based upon GenBank regulations) to trim out unwanted content from AHRDs. Updated formats.ace.extract() to include new param that checks 'singlets' file for unassembled reads |
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over 13 years ago
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| add annotation.ahrd.fix() |
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over 13 years ago
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| add support for AGP spec v2.0 |
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over 13 years ago
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| add annotation.ahrd |
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over 13 years ago
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| add option --ids to generate labels when translating cds |
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over 13 years ago
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| make gff.load() output features in order with original gff file |
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over 13 years ago
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| move apps.command.less() and blast() into apps.base |
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over 13 years ago
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| merge apps.setop into formats.base |
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over 13 years ago
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| add option --samesize in annotation.maker.longest() |
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over 13 years ago
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| add annotation.maker.longest() and formats.gff.parents() |
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over 13 years ago
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| minor formatting changes when reporting overlapping models |
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over 13 years ago
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| write to scores fiel in annnotation.maker.batcheval() |
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over 13 years ago
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| add batch evaluator in annotation.maker.batcheval() |
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over 13 years ago
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| accept integer qv in formats.fasta.fastq() |
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over 13 years ago
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| add --qv option to formats.fasta.fastq() |
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over 13 years ago
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| add formats.bed.pile() and formats.gff.children() |
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over 13 years ago
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| simplify update_attributes() in formats.gff |
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over 13 years ago
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| add --rc to formats.fastq.splitread() |
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over 13 years ago
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| add option --genomesize to assembly.simulate.wgsim() |
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over 13 years ago
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| add option --noerrors for assembly.simulate.wgsim() |
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over 13 years ago
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| fix bug in apps.grid that prevents some jobs to be run |
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over 13 years ago
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| add option --nogaps in formats.agp.reindex() and formats.agp.tidy() |
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over 13 years ago
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| fix bug in utils.range.range_interleave() |
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over 13 years ago
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