becavin-lab / bacnet Goto Github PK

Update transcriptomes.txt table with new transcriptomics file found on ArrayExpress

qzdqzd

EGDe genome has specific annotation to be added, need to run specific methods for that.
also add small RNAs

This is very much Listeria centered for the moment

• Remove Srna static variable and replace with database management variable

PATHTABLE_Srna -> Database.getInstance().getDatabaseFeatures().get("EGDe_SRNA")

Listeriomics website has a wiki found here

We need to move it on GitHub Pages

Only 1 (gawk) out of the 4 (mash, req, fastme) dependencies needed to use FigTree to create the phylogenomic tree is available for a Windows installation. So impossible with a Windows computer to create the files from the phylogeny tab in Bacnet.

👀 Some source code analysis tools can help to find opportunities for improving software components.
💭 I propose to increase the usage of compound operators accordingly.

Would you like to integrate anything from a transformation result which can be generated by a command like the following?
(:point_right: Please check also for questionable change suggestions because of an evolving search pattern.)

lokal$ perl -p -i.orig -0777 -e 's#\b(?<target>\S+)\s*=\s*\k<target>[ \t]*(?<operator>[+\-*/%^]|&(?!&)|\|(?!\|)|<<|>>>?)#$+{target} $+{operator}=#gm' $(find ~/Projekte/BACNET/lokal -name '*.java')

🔮 How will development interests evolve further also according to update candidates in 100 lines of this software?

Create Homolog tables
Issue #31

Run new database creation with updated Listeriomics omics datasets

• update genomes
• update transcriptomes
• update proteomes
• update homolog
• update phylogeny tree
• update co-expression network
• update nterminomics
• update small RNA integration

Instead of having BioJava integrated in bacnet plugin, one should have BioJava has an external dependency.

Think about a progressive integration of BACNET packages to BioJava

Update Transcriptomic datasets

• Add RNASeq datasets

Fix all errors

Create all transcriptomes
Issue #10

After 9 years of development need to reformat, reorganize input, suppress warnings

In Eclipse, right-click :

• Source > Format
• Source > Organize Imports
• Refactor > Infer Generic Type Arguments

Plus, fix all Problems in Problems View.
Right Click on each problem and select Quick Fix

More than 400 problems are found!
Pull request #17

Add a tool to create phylogenomic tree

Using IQTree (http://www.iqtree.org/) we need to generate 'PhylogenyGenomes.svg' (also 'Phylogenomic.PHYLO_GENOME_SVG')

• Implement IQTree
• Run it in 'GenomesCreation'
• Extract Phylogenomic.PHYLO_GENOME_SVG file

package bacnet.datamodel.dataset

In RNASeq.convertWIGFile(RNASeq data, boolean logTransformed) only Raw and variableStep are accepted. We need to add fixedStep parsing.

https://genome.ucsc.edu/goldenPath/help/wiggle.html

A button existed in the past to send genes and proteins to Blast search. But the integration did not work anymore.
Need to put it back.

• copy BlastN.html website in bacnet
• modify it to add sequence
• find a way to add in the resource BLASTN_files for having proper visualization
• display blast page

Add new proteomics datasets found on PubMed

TSS and TermSeq creation are Listeria specific for the moment

TSS.createTSS(exp);
TermSeq.createTermSeq(exp);

Change that and make it uniform with the way RNASeq are read.
Need to manage:

• .bed files for TSS and TermSeq
• WIG files for RNASeq and RibosSeq
• Count files for RNASeq

• Remove hardcoding of BacnetDatabases.ini
• Add googleId code and Website title management in BasicApplication

No easy way for the moment to manage log transformed representation of RNASeq datasets. Wig files are by default log transformed, and when displayed values are unloged for displaying scale.

Co-expression network creation
Issu #29

Need to be able to load human and mouse genomes. For that the 'Genome.load()' method should be change to add more pre-processed loading.

• All genes from a genome are loaded right now, need to change that.

Run BBH search (Best bidirectional search)

Part of the scripts are already present in bacnet.scripts.database.HomologCreation

Update genomes.txt with new genomes

• update genomes
• update phylogenomic tree
• update homologs

Create Phylogenomic tree
Issue #31

Create all proteomes
Issue #1

test issue

Need to implement creation of javadoc

Use Eclipse tools for that

Run with Ant the file bacnet-doc/javadoc.xml

Using MANIFEST and tools for automatic deployment in war in Eclipse

Create all Genomes
Fix ProteinId parsing #32

Re-run database creation with updated BACNET tools and re-deploy Listeriomics website

• update genomes
• update transcriptomes
• update proteomes
• update homolog
• update phylogeny tree
• update co-expression network
• update nterminomics
• update small RNA integration

Put underscore in the genome name on the database

• " " for human readable tables
• "_" for database organisation

Try to add an automatic manipulation of this changes

These tools for co-expression network construction exists already but only for Listeriomics datasets. It needs to be generalized.

Need to use bacnet.scripts.listeriomics.SystemsBiologyListeriomics and create bacnet.scripts.database.SystemsBiologyCreation

Remove/archived/clean old scripts in bacnet.scripts.listeriomics

They were used for creation of Listeriomics and NBTerminomics paper but are now mostly obslote and will not be reused.

No unit is implemented, coverage calculation is impossible

For the moment only coding sequences, tRNA and rRNA are included.
If no CDS, exon is available the element is not included.
We should include:

• pseudogene without CDS
• non-coding elements = gene without CDS

Test on eukaryotes with exon, intron and specific stuff

Modify specifically:
GFFNCBIReader.addSequences(LinkedHashMap<String, ChromosomeBacteriaSequence> chromosomes,HashMap<String, ArrayList<FeatureI>> listLocusTag)
In package bacnet.reader

Specifically if only one GFF line is available per feature !
Manage both cases

• Radial network display was working but should be updated because of creating new circlar genome view.

Need to fix:
GenomesCreation.createCircularGenomeView(Genome.loadGenome(genomeName), genomeName);
Bacnet.lib should be fixed ?
Or Maybe search for update solution ?

• Add also capability to display different genome in co-expression network, for the moment only one genome is selected per website in :
  CoExprNetworkView.initComboGenome()

Add Vaccinology tools