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ChangeLog

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  • To find the state of this project's repository at the time of any of these versions, check out the tags.
    ChangeLog 15.05 KiB
    Version XX
    	From the 'View' menu added 'Adjust panel heights...' option in ACT 
    	for adjusting their heights (BAM, VCF, plots, comparisons) by giving 
    	them different weights in order to distribute the space between each 
    	component.
    
    	Labels can optionally be added to the header of base position plots
    	and these are used in the legend, e.g.
    	# colour 5:150:55 255:0:0 0:255:0 0:0:255 100:100:100 50:150:50
    	# label lab1 lab2 lab3 lab4 lab5 lab6
    	176 2204.8 848.23 0 0 0 536.04
    	...
    	
    	In the Feature Editor there is now a button ('User Qualifiers') which
    	opens a tool for maintaining user defined lists of qualifiers (i.e. 
    	qualifiers in the form tag = value pairs on separate lines) and the 
    	option to read qualifiers from OBO formatted files or URLs. These can
    	be saved between sessions in the file '.artemis.qualifiers' in the
    	home directory.
    	
    	Automatic addition of history qualifier in chado database mode.
    
    	Added RNASeq strand specific option to the BAM popup menu ('Colour By' -> 
    	'RNASeq Strand Specific Tag (XS)'). Reads colours are based on the XS 
    	tag (used by TopHat). The RNA strand is then used in the coverage plots.
    	
    	Added the following flags:
      		-Dshow_snps			Show SNP marks in BamView
      		-Dshow_snp_plot		Open SNP plot in BamView
      		-Dshow_cov_plot		Open coverage plot in BamView
      
    	Add validation checks. This will check the following:
    		All file types:
    	    	- CDS have no internal stop codon
          		- CDS have valid stop codon
    		GFF / Chado:
    	    	- check complete gene model
            	- check boundaries are valid
            	- check all features are on the same strand
            	- check CDS features have a phase
            	- check attribute column 
                - qualifiers have a value (not empty)
                - only reserved tags start with uppercase
    	
    		Validation can be run in two ways: 
    			1. using the option in View->Feature Filters->Validation checks... which shows 
    			'failed' features in feature list windows
    			2. selecting 'Validation report ...' option in the popup menu when right clicking 
    			on the feature display. This produces a report with an option to auto-fix gene 
    			boundaries and stop codons. 
    
    Version 15
    
    	Multiple BAM panels can be opened using the bamClone flag this is used with 
    	the -Dbam flag:
    	art -Dbam='/pathToFile/file1.bam,/pathToFile/file2.bam' -DbamClone=n  
    	(where n is an integer greater than 1). All BAM files are then shown in	each 
    	panel. Alternatively the following will open BAM files in separate panels
    	(using -Dbam[1,2,3...]):
    	art -Dbam1=fileA.bam -Dbam2=fileB.bam
    	
    	Add SVG (scalable vector graphics) support for Artemis, ACT and DNAPlotter.
    
    	Option added to adjust VCF row height.
    		
    	Add support for indexed user graphs using tabix. For example file.plot is a tab
    	delimited file with column 1 containing the sequence name and column 2 the
    	positions:
    	(grep ^"#" file.plot; grep -v ^"#" file.plot | sort -k1,1 -k2,2n) | bgzip > sorted.plot.gz ;
    	tabix -s 1 -b 2 -e 2 sorted.plot.gz
    	
    	Option added to show or hide the average line in the graphs.
    	
    	BAM coverage heatmap view added.
    
    	Add Rfam sequence search from the RUN menu.
    	
    	Base similarity graph for each VCF added to the VCF view.
    	
    	Sense and anti-sense read counts and RPKM values are now reported.
    	
    	Option added to create features from BAM peaks, i.e. above a threshold of the 
    	number aligned reads.
    
    	Option included for defining groups of BAM files so that they can be
    	switched on and off by their group.
    	
    	Coverage plots from read alignments (BAM) can be plotted by their strand.
    
    	Addition of a Project File Manager used to group files together for
    	launching in Artemis. When a project has been added or updated the details 
    	are saved at the end of each session in '.artemis.project.properties' 
    	in the user's home directory. 
    
    	Fix for saving user defined shortcuts between sessions on windows.
    	
    	Add preliminary support for the CRAM format:
    	http://www.ebi.ac.uk/ena/about/cram_toolkit
    	This requires the cramtools.jar to be added to the start of the CLASSPATH.
    
    	Improved support for matching GFF feature coordinates to the correct
    	contig in a multiple FASTA sequences. This works now whether
    	the sequence is part of the GFF file or a separate multiple-FASTA file.
    
    	Add 'Feature Stack View' to visualise overlapping gene features.
    
    	Add support for read-only indexed GFF. Features in GFF format are
    	sorted and indexed with tabix:
    	http://samtools.sourceforge.net/tabix.shtml
    
    Version 14
    	Add options in the navigator for searching the forward and 
    	reverse strands individually for base / amino acid patterns.
    	
    	Add an option to the navigator for searching for matches that
    	overlap a selected region or feature.
    	
    	New translation table 24 (Pterobranchia mitochondrial) added.
    	
    	If the BAM index file is missing then Artemis uses the picard library to
    	attempt to create the index.
    
    	Variant (VCF / BCF) filtering now uses the meta-data in the header to
    	enable filtering based on INFO, FILTER and FORMAT columns.
    	
    	Shortcut changes made in the 'Preferences' menu are saved between sessions (the 
    	shortcut_cache flag in the options file can be used to turn this on/off).
    	
    	More support for GTF format to show CDS and exons as joined features. 
    
    	BAM record list option added to display as a list the reads and their
    	properties.
    	
    	Add options for loading graph, BAM and VCF files into ACT from the 
    	command line. Numbers are used to associate the file with a particular
    	sequence. e.g. add a BAM to the first (top) sequence in ACT:
    	act -Dbam1=/pathToFile/file.bam 
    	or, to add a userplot to the second sequence:
    	act -Duserplot2=/pathToFile/userPlot
    
    Version 13.2.0
    	Added option to provide overview of the variation sites.
    
    	Change BamView filter to enable filtering in and out based on
    	reads flag.
    	
    	Add read count and RPKM calculations to BamView.
    
    	Add option in BamView to clone the alignment panel.
    	
    	Create features option for VCF records.
    	
    	Unit tests added for writing VCF/BCF sequences.
    
    	Add new Coverage view to BamView. It automatically switches to this view
    	on zooming out.
    
    	Add options to write out or view FASTA sequences from VCF/BVF variation
    	data.
    
    Version 13
    	Add support for reading in indexed BCF (Binary VCF) files.
    	
    	Memory optimisation of codon caching, reducing the memory footprint.
    	
    	It is now possible to add BAM, VCF and BCF files from the command line using the 
    	JVM bam option, e.g. art -Dbam=/pathToFile/file.bam 
    	and for multiple BAM's/VCF's this is comma separated
    	art -Dbam='/pathToFile/file1.bam,/pathToFile/file2.bam', it
    	can also read the BAM's from URL's.
    	
    	Added option to display orientation of reads in BamView.
    
    	In Bamview, display reads that are split over introns so that the exon boundaries can 
    	be identified by colouring the line between the aligned blocks grey.
    	
    	Add VCF panel to ACT.
    	
    	Support added to read indexed fasta sequence files. An index file is created
    	using SAMtools.
    
    	Add support for VCF v3.3 and v4.0.
    
    	Add option to show combined coverage plots for multiple BAMs.
    
    	Add show_forward_lines and show_reverse_lines as options for switching
    	frame lines on and off.
    	
    	Add an option to delete qualifiers in the Find/Replace tool.
    
    	Artemis can read in a set of zipped search results (e.g. blastp/blastp.zip).
    
    	Add BamView panel to ACT.
    
    	Fix for writing EMBL files out from GFF entries.
    
    	An option has been added in BamView to colour reads by the colour 
    	used in the coverage plot - useful when looking at multiple BAM files.
    	
    	Plot multiple coverage plots in BamView when multiple BAM files are
    	loaded in.
    
    Version 12
    	It is now possible to add user plots from the command line using the 
    	JVM userplot option, e.g. art -Duserplot=/pathToFile/userPlot 
    	and for multiple plots this is comma separated
    	art -Duserplot='/pathToFile/userPlot1,/pathToFile/userPlot2', it
    	can also read the plots from URL's.
    
    	Added support to be able to read BAM files to display read alignments.
    	It uses picard (http://picard.sourceforge.net/) to read from the BAM file
    	and so requires Artemis to be run with Java 1.6.
    
    	All graphs can now be configured to be plotted as line graphs
    	or heat maps.
    	
    	Added support for BLAST tabular format (-m 8 option) and MSPcrunch 
    	format to plot scores.
    	
    	Added support for wiggle (variableStep/fixedStep) plots that can be 
    	displayed as histograms or heat maps. 
    	
    	Added a new user plot file format with the first column specifying
    	a base position.
    	
    	More configure options have been added to the graphs to enable
    	configuration of the graph line style and size.
    	
    	GoTo directory option added to file manager to assist navigation.
    	
        The database manager is cached between sessions (this can is on by default 
        and can be switched off with -Ddatabase_manager_cache_off). There is an 
        option under the File menu to clear this cache.
        
        A checkbox has been added to the window for adding ortholog/paralog links
        in the Gene Builder. If this is selected it adds links between existing 
        ortholog/paralogs and the new ortholog/paralog. By default this is off.
        
        An option has been added to the database manager to display polypeptide 
        domains in the feature display (as well as the protein map in the Gene
        Builder).
        
        An option has been added to the Run menu for doing a search of the Pfam
        database.
        
    	Added an option to the Write menu for writing a combination of upstream 
    	+ feature + downstream bases for selected features.
    
        Option added in the View->Filter Features menu to search for Duplicate
        Systematic Name Qualifier.
    
        LookSeq analysis panel can be displayed by setting the lookseq 
        value in the options file. An option under the Display menu then
        is used to shows the LookSeq read alignment panel in Artemis.
    
        Added options to set the minimum and maximum values of the plots.
    
        Transfer Annotation Tool (TAT) added to feature editor and Gene
        Builder.
    
    	New graph popup menu option to show the values and average for
    	a selected range.
    	
    	Added product_cv database option to define if the product is
    	stored as a controlled vocabulary or as a feature property (featureprop).
    
    Version 11
    
        Use black_belt_mode to suppress warnings when opening Artemis.
        
        Script (writedb_entry) added to make it easier to write out 
        multiple entries as EMBL / GFF files from chado. This uses Artemis 
        read-write libraries and does not require each sequence to be 
        launched from the database. For command line help run: 
        etc/writedb_entry -help
    
    	On MacOSX - enable dropping files on Artemis application to open sequences
    	with file extensions: gff, embl, EMBL, genbank, gbk, fasta, seq, art and 
    	dna (defined in Artemis.app/Contents/Info.plist).
    
    	Add NCBI search link to run menu. This transfers the sequence automatically
    	to the NCBI web page.
    	
    	Add support for writing Sequin table format.
    	
    	Added print to PostScript option in Artemis and ACT.
    
        Optimisation of reading in user graphs.
    
    	New Edit->Selected Feature(s)->Convert Keys option to convert
    	keys of selected features.
    
    	New Edit menu option for finding and replacing qualifier text. This
    	has an option for boolean searches (e.g. and, or, &, |) of qualifier
    	text. This includes an option to search for duplicate qualifiers.
    
    	Implemented a commit manager for the database mode. This
    	highlights transactions that produce an error.
    	
    	Make the chado transaction log messages more human readable.
    
        Add ability to write file formats from Artemis in database mode.
        With option to collapse the gene hierarchy (gene, transcript, exon) 
        into a CDS feature.
    
    	Graphs are now added to a split pane. So that their size can be 
    	defined by dragging the divider at the bottom of the graphs.
    
    	Provide option to log transform user data plot.
    	
    	Improved error reporting for contig reordering.
    
       	Fix for creating intergenic features for overlapping CDS's. Also
       	add note based on which one of the 4 cases with respect to the 
       	flanking CDS it belongs to, i.e.:
     	IGR-F (forward):  cds> IGR cds>
    	IGR-R (reverse): <cds IGR <cds
    	IGR-B (both): <cds IGR cds>
    	IGR-X: cds> IGR <cds
    	
    	Add option to preferences for defining contig ordering features.
    
    	Added option to "Create features from graph peaks". For a graph 
    	this creates features in regions above a given cut-off and above 
    	a given feature size.
    	
    	Add -Dread_only option for read only databases.
    	
    	Add option to lazy load feature data from database.
    	
    Version 10
    
    	Add redo function to 'Edit' menu. Also enable/disable undo and
    	redo menu items when available/not available.
    	
    	Add option to replace selected bases in 'Edit' menu.
    	
    	Option to create features in intergenic regions added.
    
    	Feature editor now marks hyperlinks to SWALL, EMBL, UniProt, 
    	PMID, PubMed, InterPro, OrthoMCLDB, Pfam that are opened in 
    	the browser. Now configured in the options file.
    	
    	Added "Convert Qualifier of Selected..." option to the Edit menu.
    	This allows the user to change the names of qualifiers for all
    	selected features.
    	
    	Now using new release of j2ssh (0.2.9). This requires Java1.5+.
    
    	Implemented option for ORF creation to take into account boundaries
    	of multiple fasta sequences, so that they do not cross them.
    
    	Implemented the ability to run and store fasta and blast search 
    	results for multiple databases... E.g. fasta searches on uniprot 
    	and on user's own database, stored in multiple fasta_file qualifiers.
    
     	"Set Score Cutoffs" in Artemis popup menu uses existing /scores as
     	the initial min and max values (rather than just 0 and 100).
    
    	Added cache to store the entries retrieved for the object editor.
    	
    	Implement log4j logging to be displayed in log viewer. Using colour
    	coding depending on level of logging.
    	
    	Added -Doffset so that Artemis can be opened at a given base.
    
    Version 9
    
    	Feature selector can be used to look for features with introns 
    	that do no contain the GT/GC start or AG end.
    
    	Contig tool now checks for contigs that contain features that
    	span the boundaries of the contigs. These features have to be 
    	removed or restricted to the contig boundary before it can 
    	carry out contig reordering.
    
    	Fix for converting files from other file formats to
    	genbank format.
    
    	Fix rounding problem for long sequences when writting 
    	out all bases in FASTA or raw format.
    
    	Cache the start codons (as per stop codon caching),
    	to speed their display.
    
    	Combine the extend to next exon and the fix stop codons
      	into one option.
    
    	The feature types that appear on the frame lines can be defined
    	by the user via an option ("Frame Line Features...") in the 
    	feature display popup menu.
    	
    	Added to File -> Preferences a user defined selection for display names
    	and systematic names. Also extended popup menu option in feature lists 
    	to allow the user to be able to select multiple qualifiers to display.
    
    	For entries opened from the remote side of an SSH connection will search
    	for results on the remote file system if they are not found locally. They
    	are transferred via SSH and then stored locally.
    
    	For Mac users, the option to send search results to the browser will
    	display the results in the default browser.
    
    	When automatically generating gene names (under the Edit menu), the user
    	can specify the number of zeros to pad the numbering with. e.g if 5 digits are
    	selected the format will look like : 00001, 00002 etc.