Ductape

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UPGRADE URGENCY: MODERATE; many features have changed, especially for the genomic analysis

FEATURES:
* Reactions copy number is no more analyzed: for pangenome and mutants experiments the program now focus on exclusive and distinct reaction IDs
* dgenome stats/export, dape start/map have been changed accordingly
* dgenome annotate: new command to transfer kegg annotations inside an orthologous group
* dgenome deannotate: revert the annotation transfer
* Added a test directory with a simple script to test the three modules

BUGFIXES:
* PM data: prevent crashes in the clusterization step
* PM data: prevent crashes when parsing csv files
* kegg: final fix to handle correctly HTMLs from kegg
* DB: speed improvements on big pangenomes
* Other small bugfixes

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UPGRADE URGENCY: HIGH; in some cases the KEGG html maps could not be retrieved correctly

kegg:
BUGFIX: the preparation of some kegg html maps resulted in failures

dgenome start:
FEATURE: roughly 3X speed improvements on BBH pangenome calculation, thanks to in-memory Blast searches

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UPGRADE URGENCY: HIGH; in some cases the KEGG data could not be retrieved correctly

kegg:
FEATURE: an improved connectivity check
BUGFIX: the insertion in the database of some kegg maps resulted in failures

dgenome start:
BUGFIX: in a corner case the pangenome calculation was performed twice

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UPGRADE URGENCY: HIGH; the control signal subtraction has been fixed on PM plate PM04A

dgenome start
FEATURE: roughly 3X speed improvements on BBH pangenome calculation

dphenome zero
BUGFIX: the control signal subtraction has been fixed on PM plate PM04A

dphenome export
BUGFIX: the table with the average AV shouldn't contain the column "replica"

kegg:
FEATURE: fetch also the EC numbers for the Kegg reactions
BUGFIX: add some spaces when a tag retrieved with the "info" request spans multiple lines

dape start
BUGFIX: fixing again the compound duplication bug when creating metabolic networks

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UPGRADE URGENCY: HIGH; dphenome users may be unable to load some PM data

dphenome
FEATURE: import/export plates data
BUGFIX: biolog parser shouldn't fail on unknown plates
BUGFIX: handle new possible plate names some plates names

dape
FEATURE: add-multi lets the user to provide multiple orgID
Fixed some typos

dape/dgenome/dphenome start:
FEATURE: added options to skip kegg map and phenomics parameters calculation

kegg:
FEATURE: internet connectivity is checked before the kegg mapping is performed

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dape start
FEATURE: added AV color to KEGG compounds (GML graph output)
BUGFIX: avoid duplicated nodes in the metabolic graphs