Moved all the conversion scripts to src/ with a new naming scheme

checkAgoraIntegrity.sh

@@ -40,9 +40,9 @@ print_title 'check the preprocessing scripts'
 
 preProcessCommandLines=(
 # convet a .nhx tree into a protTree (forest of gene trees)
-"src/preprocessing/nhxGeneTrees2phylTreeGeneTrees.py example/data/GeneTreeForest.nhx.bz2 > tmp/geneTrees.protTree"
+"src/convert.geneTrees.NHX-phylTree.py example/data/GeneTreeForest.nhx.bz2 > tmp/geneTrees.protTree"
 # convet a .nwk tree into a phylTree
-"src/preprocessing/newickSpeciesTree2phylTreeSpeciesTree.py example/data/Species.nwk > tmp/speciesTree.phylTree"
+"src/convert.speciesTree.Newick-phylTree.py example/data/Species.nwk > tmp/speciesTree.phylTree"
 )
 print_and_run_commands "${preProcessCommandLines[@]}"
 
@@ -86,7 +86,7 @@ print_title 'check the postprocessing script'
 
 mkdir tmp/ancGenomes
 convertAncGenomesCommandLines=(
-"src/postprocessing/misc.convertContigsToGenome.py tmp/speciesTree.phylTree A0 -IN.ancDiags=tmp/integrDiags/final/diags.%s.list.bz2 -OUT.ancGenomes=tmp/ancGenomes/ancGenome.%s.list.bz2 -ancGenesFiles=tmp/ancGenes/all/ancGenes.%s.list.bz2"
+"src/convert.ancGenomes.diags-genes.py tmp/speciesTree.phylTree A0 -IN.ancDiags=tmp/integrDiags/final/diags.%s.list.bz2 -OUT.ancGenomes=tmp/ancGenomes/ancGenome.%s.list.bz2 -ancGenesFiles=tmp/ancGenes/all/ancGenes.%s.list.bz2"
 )
 print_and_run_commands "${convertAncGenomesCommandLines[@]}"
 

doc/HowTo.md

@@ -617,7 +617,7 @@ To convert the _diags_ files to the _ancGenome_ format, run this script:
 
 ```bash
 mkdir -p example/results/ancGenomes/final
-src/postprocessing/misc.convertContigsToGenome.py \
+src/convert.ancGenomes.diags-genes.py \
   example/data/Species.conf \
   A0 \
   -IN.ancDiags=example/results/integrDiags/final/diags.%s.list.bz2 \

src/postprocessing/misc.convertContigsToGenome.py → src/convert.ancGenomes.diags-genes.py

@@ -10,7 +10,7 @@
     Transform reconstructed ancestral lists of blocks (diags) in formated ancestral genomes (lists of genes)
 
     usage:
-        src/postprocessing/misc.convertContigsToGenome.py example/data/Species.conf A0 \
+        src/convert.ancGenomes.diags-genes.py example/data/Species.conf A0 \
                 -IN.ancDiags=example/results/integrDiags/final/diags.%s.list.bz2 \
                 -OUT.ancGenomes=example/results/ancGenomes/final/ancGenome.%s.list.bz2 \
                 -ancGenesFiles=example/results/ancGenes/all/ancGenes.%s.list.bz2

src/preprocessing/newickSpeciesTree2phylTreeSpeciesTree.py → src/convert.speciesTree.Newick-phylTree.py

@@ -9,8 +9,8 @@
 __doc__ = """ Convert a species phylogenetic tree from/to newick or phyltree text format
 
      usage:
-        ALL.convertNewickTree.py Species.conf -fromNewick > Species.nwk
-        ALL.convertNewickTree.py Species.nwk +fromNewick > Species.conf """
+        convert.SpeciesTree.Newick-phylTree.py Species.conf -fromNewick > Species.nwk
+        convert.SpeciesTree.Newick-phylTree.py Species.nwk +fromNewick > Species.conf """
 
 import utils.myFile as myFile
 import utils.myPhylTree as myPhylTree