| Added "-T" option to formats.gff/bed/blast.sort() to allow user to specify tmp directory used by unix sort |
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about 12 years ago
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| add --cscore to algorithms.catalog.omgparse() |
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about 12 years ago
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| add assembly.allpaths.automaton to streamline assembly in a folder of paired reads |
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about 12 years ago
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| Update assembly.preprocess.trim() to use tv0.30. In formats.fasta.format(), when ID mapping file and annotation file are both provided, convert old to new ID first and lookup the new ID in the annotation file. Update formats.gff.filter() to lookup GFF3 attributes in a case-insensitive manner |
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about 12 years ago
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| add assembly.allpaths.automaton() and fix option --hsps for formats.blast.best() |
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about 12 years ago
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| add formats.bed.some() to extract subset of bed features |
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about 12 years ago
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| move --chain to a separate function in formats.gff.chain(); add option --fixphase to translate between Ensembl phase and standard GFF phase |
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over 12 years ago
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| minor adjustments in formats.gff.format() |
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over 12 years ago
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| change annotation.snp.frommaf() to output vcf format |
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over 12 years ago
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| use gffutils rather than old GFFutils (updated by daler); add field options for formats.gff.fromgtf() |
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over 12 years ago
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| apps.bwa default no longer reports uniquely mapped reads |
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over 12 years ago
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| Updated formats.fasta.identical() to allow more than 2 input fasta files |
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over 12 years ago
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| Added formats.fasta.identical() to identify "exactly identical" sequences between 2 sets of input fasta sequences based on their computed MD5 hexdigest |
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over 12 years ago
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| Merge branch 'master' of github.com:tanghaibao/jcvi |
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over 12 years ago
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| Minor modification to grouper RegExp in annotation.reformat.annotate(). Minor fix to formats.blast.rbbh(). Allow other translation tables in formats.fasta.translate() |
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over 12 years ago
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| add formats.sam.fpkm to convert BAM file to FPKM values |
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over 12 years ago
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| add annotation.snp and formats.excel; change default FASTA index=False |
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over 12 years ago
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| Added formats.blast.rbbh() to pick reciprocal best blast hits from 2 input BLAST tab files (A vs B and B vs A) |
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over 12 years ago
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| add algorithms.ml to make format for machine learning |
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over 12 years ago
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| add formats.blast.score() to add up score per query |
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over 12 years ago
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| add pseudocounts in log-ratio in assembly.kmer.logodds() |
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over 12 years ago
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| add K-mer based classification pipeline in assembly.kmer |
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over 12 years ago
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| Add option to formats.gff.load() to generate full header (partly based upon Athaliana FASTA headers) which contain seqid, start/end coords and datestamp (for generating annotation release). Add option to formats.gff.format() to allow appending a `Name` attribute from a two-column lookup table. Rename `--switch` option to `--seqid`. Add option to annotation.reformat.annotate() which lets user specify if identifiers in the the BED file used for annotation follow the ATG naming convention or not (eg. Medtr1g0010000, At2g00348, etc.) |
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over 12 years ago
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| add graphics.base.markup() to allow inline markup of text |
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over 12 years ago
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| add utils.cbook.Registry to help counting, used in algorithms.fractionation.summary() |
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over 12 years ago
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| Update command line options for annotation.reformat.annotate(), slight tweak to the logic used for the ID transfer. Update formats.gff.format() command line options to add `-o` outfile parameter. |
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over 12 years ago
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| fix glitch in formats.gff.bed --source |
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over 12 years ago
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| Merge branch 'master' of github.com:tanghaibao/jcvi |
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over 12 years ago
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| Added option to formats.gff.bed() to allow filtering of gff file by `source` name for situations where a certain feature `type` may be associated with multiple sources. Renamed the `--pasa` option in formats.gff.format() to `--chain`. Minor code formatting. |
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over 12 years ago
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| Merge branch 'master' of github.com:tanghaibao/jcvi |
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over 12 years ago
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