Poetry setup, tests moved, refactoring and imports

tahiri-lab · Sep 26, 2023 · 7fb5549 · 7fb5549
1 parent 66df976
commit 7fb5549
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Showing 313 changed files with 834 additions and 25 deletions.
diff --git a/.gitignore b/.gitignore
@@ -7,6 +7,19 @@ output*
 *newick
 temp.ipynb
 debug*
-/aPhyloGeoEnv
+*.egg-info
+
+#Ignore virtual environments
+.env
+.venv
+env/
+venv/
+ENV/
 /scripts/aPhyloGeo_env
-*.egg-info
+/aPhyloGeoEnv
+
+#Ignore the build directory (and its sub-directories):
+build
+
+#Ignore the distribution directory
+dist
diff --git a/aPhyloGeo/Test/__init__.py → Tests/__init__.py b/aPhyloGeo/Test/__init__.py → Tests/__init__.py
diff --git a/aPhyloGeo/Test/params_small.yaml → Tests/params_small.yaml b/aPhyloGeo/Test/params_small.yaml → Tests/params_small.yaml
@@ -1,4 +1,4 @@
-file_name: '../datasets/5seq/geo.csv'
+file_name: './datasets/5seq/geo.csv'
 specimen: 'id'   #"Please enter the name of the colum containing the specimens names: "
 names: ['id', 'ALLSKY_SFC_SW_DWN', 'T2M', 'PRECTOTCORR', 'QV2M', 'WS10M']
 bootstrap_threshold: 0
@@ -7,7 +7,7 @@ window_size: 200
 step_size: 100
 bootstrap_amount: 100
 data_names: ['ALLSKY_SFC_SW_DWN_newick', 'T2M_newick', 'QV2M_newick', 'PRECTOTCORR_newick', 'WS10M_newick']
-reference_gene_dir: '../datasets/5seq'
+reference_gene_dir: './datasets/5seq'
 reference_gene_file: 'seq small.fasta'
 makeDebugFiles: False
 alignment_method: '1'
diff --git a/aPhyloGeo/Test/params_very_small.yaml → Tests/params_very_small.yaml b/aPhyloGeo/Test/params_very_small.yaml → Tests/params_very_small.yaml
@@ -1,4 +1,4 @@
-file_name: '../datasets/5seq/geo.csv'
+file_name: './datasets/5seq/geo.csv'
 specimen: 'id'   #"Please enter the name of the colum containing the specimens names: "
 names: ['id', 'ALLSKY_SFC_SW_DWN', 'T2M', 'PRECTOTCORR', 'QV2M', 'WS10M']
 bootstrap_threshold: 0
@@ -7,7 +7,7 @@ window_size: 200
 step_size: 100
 bootstrap_amount: 100
 data_names: ['ALLSKY_SFC_SW_DWN_newick', 'T2M_newick', 'QV2M_newick', 'PRECTOTCORR_newick', 'WS10M_newick']
-reference_gene_dir: '../datasets/5seq'
+reference_gene_dir: './datasets/5seq'
 reference_gene_file: 'seq very small.fasta'
 makeDebugFiles: False
 alignment_method: '1'
diff --git a/...ence/seq small/OM739053 vs OL989074.fasta → ...ence/seq small/OM739053 vs OL989074.fasta b/...ence/seq small/OM739053 vs OL989074.fasta → ...ence/seq small/OM739053 vs OL989074.fasta
diff --git a/...ence/seq small/ON129429 vs OL989074.fasta → ...ence/seq small/ON129429 vs OL989074.fasta b/...ence/seq small/ON129429 vs OL989074.fasta → ...ence/seq small/ON129429 vs OL989074.fasta
diff --git a/...ence/seq small/ON134852 vs OL989074.fasta → ...ence/seq small/ON134852 vs OL989074.fasta b/...ence/seq small/ON134852 vs OL989074.fasta → ...ence/seq small/ON134852 vs OL989074.fasta
diff --git a/...ence/seq small/OU471040 vs OL989074.fasta → ...ence/seq small/OU471040 vs OL989074.fasta b/...ence/seq small/OU471040 vs OL989074.fasta → ...ence/seq small/OU471040 vs OL989074.fasta
diff --git a/...seq very small/OM739053 vs OL989074.fasta → ...seq very small/OM739053 vs OL989074.fasta b/...seq very small/OM739053 vs OL989074.fasta → ...seq very small/OM739053 vs OL989074.fasta
diff --git a/...seq very small/ON129429 vs OL989074.fasta → ...seq very small/ON129429 vs OL989074.fasta b/...seq very small/ON129429 vs OL989074.fasta → ...seq very small/ON129429 vs OL989074.fasta
diff --git a/...seq very small/ON134852 vs OL989074.fasta → ...seq very small/ON134852 vs OL989074.fasta b/...seq very small/ON134852 vs OL989074.fasta → ...seq very small/ON134852 vs OL989074.fasta
diff --git a/...seq very small/OU471040 vs OL989074.fasta → ...seq very small/OU471040 vs OL989074.fasta b/...seq very small/OU471040 vs OL989074.fasta → ...seq very small/OU471040 vs OL989074.fasta
diff --git a/...est/testFiles/bootstrapList/seq small.txt → Tests/testFiles/bootstrapList/seq small.txt b/...est/testFiles/bootstrapList/seq small.txt → Tests/testFiles/bootstrapList/seq small.txt
diff --git a/...estFiles/bootstrapList/seq very small.txt → ...estFiles/bootstrapList/seq very small.txt b/...estFiles/bootstrapList/seq very small.txt → ...estFiles/bootstrapList/seq very small.txt
diff --git a/...t/testFiles/createBootstrap/seq small.xml → ...s/testFiles/createBootstrap/seq small.xml b/...t/testFiles/createBootstrap/seq small.xml → ...s/testFiles/createBootstrap/seq small.xml
diff --git a/...tFiles/createBootstrap/seq very small.xml → ...tFiles/createBootstrap/seq very small.xml b/...tFiles/createBootstrap/seq very small.xml → ...tFiles/createBootstrap/seq very small.xml
diff --git a/...Files/createClimaticList/geo.csv/list.txt → ...Files/createClimaticList/geo.csv/list.txt b/...Files/createClimaticList/geo.csv/list.txt → ...Files/createClimaticList/geo.csv/list.txt
diff --git a/...testFiles/createGeneticList/seq small.txt → ...testFiles/createGeneticList/seq small.txt b/...testFiles/createGeneticList/seq small.txt → ...testFiles/createGeneticList/seq small.txt
diff --git a/...iles/createGeneticList/seq very small.txt → ...iles/createGeneticList/seq very small.txt b/...iles/createGeneticList/seq very small.txt → ...iles/createGeneticList/seq very small.txt
diff --git a/.../createTree/geo.csv/ALLSKY_SFC_SW_DWN.txt → .../createTree/geo.csv/ALLSKY_SFC_SW_DWN.txt b/.../createTree/geo.csv/ALLSKY_SFC_SW_DWN.txt → .../createTree/geo.csv/ALLSKY_SFC_SW_DWN.txt
diff --git a/...tFiles/createTree/geo.csv/PRECTOTCORR.txt → ...tFiles/createTree/geo.csv/PRECTOTCORR.txt b/...tFiles/createTree/geo.csv/PRECTOTCORR.txt → ...tFiles/createTree/geo.csv/PRECTOTCORR.txt
diff --git a/...est/testFiles/createTree/geo.csv/QV2M.txt → Tests/testFiles/createTree/geo.csv/QV2M.txt b/...est/testFiles/createTree/geo.csv/QV2M.txt → Tests/testFiles/createTree/geo.csv/QV2M.txt
diff --git a/...Test/testFiles/createTree/geo.csv/T2M.txt → Tests/testFiles/createTree/geo.csv/T2M.txt b/...Test/testFiles/createTree/geo.csv/T2M.txt → Tests/testFiles/createTree/geo.csv/T2M.txt
diff --git a/...st/testFiles/createTree/geo.csv/WS10M.txt → Tests/testFiles/createTree/geo.csv/WS10M.txt b/...st/testFiles/createTree/geo.csv/WS10M.txt → Tests/testFiles/createTree/geo.csv/WS10M.txt
diff --git a/...ssimilarity/geo.csv/ALLSKY_SFC_SW_DWN.csv → ...ssimilarity/geo.csv/ALLSKY_SFC_SW_DWN.csv b/...ssimilarity/geo.csv/ALLSKY_SFC_SW_DWN.csv → ...ssimilarity/geo.csv/ALLSKY_SFC_SW_DWN.csv
diff --git a/...les/dissimilarity/geo.csv/PRECTOTCORR.csv → ...les/dissimilarity/geo.csv/PRECTOTCORR.csv b/...les/dissimilarity/geo.csv/PRECTOTCORR.csv → ...les/dissimilarity/geo.csv/PRECTOTCORR.csv
diff --git a/.../testFiles/dissimilarity/geo.csv/QV2M.csv → .../testFiles/dissimilarity/geo.csv/QV2M.csv b/.../testFiles/dissimilarity/geo.csv/QV2M.csv → .../testFiles/dissimilarity/geo.csv/QV2M.csv
diff --git a/...t/testFiles/dissimilarity/geo.csv/T2M.csv → ...s/testFiles/dissimilarity/geo.csv/T2M.csv b/...t/testFiles/dissimilarity/geo.csv/T2M.csv → ...s/testFiles/dissimilarity/geo.csv/T2M.csv
diff --git a/...testFiles/dissimilarity/geo.csv/WS10M.csv → ...testFiles/dissimilarity/geo.csv/WS10M.csv b/...testFiles/dissimilarity/geo.csv/WS10M.csv → ...testFiles/dissimilarity/geo.csv/WS10M.csv
diff --git a/...eo/Test/testFiles/getSequenceCentroid/seq → Tests/testFiles/getSequenceCentroid/seq b/...eo/Test/testFiles/getSequenceCentroid/seq → Tests/testFiles/getSequenceCentroid/seq
diff --git a/...t/testFiles/getSequenceCentroid/seq small → ...s/testFiles/getSequenceCentroid/seq small b/...t/testFiles/getSequenceCentroid/seq small → ...s/testFiles/getSequenceCentroid/seq small
diff --git a/...tFiles/getSequenceCentroid/seq very small → ...tFiles/getSequenceCentroid/seq very small b/...tFiles/getSequenceCentroid/seq very small → ...tFiles/getSequenceCentroid/seq very small
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diff --git a/...slidingWindow/seq small/11700_11899.fasta → ...slidingWindow/seq small/11700_11899.fasta b/...slidingWindow/seq small/11700_11899.fasta → ...slidingWindow/seq small/11700_11899.fasta
diff --git a/...slidingWindow/seq small/11800_11999.fasta → ...slidingWindow/seq small/11800_11999.fasta b/...slidingWindow/seq small/11800_11999.fasta → ...slidingWindow/seq small/11800_11999.fasta
diff --git a/...slidingWindow/seq small/11900_12036.fasta → ...slidingWindow/seq small/11900_12036.fasta b/...slidingWindow/seq small/11900_12036.fasta → ...slidingWindow/seq small/11900_12036.fasta
diff --git a/...slidingWindow/seq small/12000_12036.fasta → ...slidingWindow/seq small/12000_12036.fasta b/...slidingWindow/seq small/12000_12036.fasta → ...slidingWindow/seq small/12000_12036.fasta
diff --git a/...s/slidingWindow/seq small/1200_1399.fasta → ...s/slidingWindow/seq small/1200_1399.fasta b/...s/slidingWindow/seq small/1200_1399.fasta → ...s/slidingWindow/seq small/1200_1399.fasta
diff --git a/...s/slidingWindow/seq small/1300_1499.fasta → ...s/slidingWindow/seq small/1300_1499.fasta b/...s/slidingWindow/seq small/1300_1499.fasta → ...s/slidingWindow/seq small/1300_1499.fasta
diff --git a/...s/slidingWindow/seq small/1400_1599.fasta → ...s/slidingWindow/seq small/1400_1599.fasta b/...s/slidingWindow/seq small/1400_1599.fasta → ...s/slidingWindow/seq small/1400_1599.fasta
diff --git a/...s/slidingWindow/seq small/1500_1699.fasta → ...s/slidingWindow/seq small/1500_1699.fasta b/...s/slidingWindow/seq small/1500_1699.fasta → ...s/slidingWindow/seq small/1500_1699.fasta
diff --git a/...s/slidingWindow/seq small/1600_1799.fasta → ...s/slidingWindow/seq small/1600_1799.fasta b/...s/slidingWindow/seq small/1600_1799.fasta → ...s/slidingWindow/seq small/1600_1799.fasta
diff --git a/...s/slidingWindow/seq small/1700_1899.fasta → ...s/slidingWindow/seq small/1700_1899.fasta b/...s/slidingWindow/seq small/1700_1899.fasta → ...s/slidingWindow/seq small/1700_1899.fasta
diff --git a/...s/slidingWindow/seq small/1800_1999.fasta → ...s/slidingWindow/seq small/1800_1999.fasta b/...s/slidingWindow/seq small/1800_1999.fasta → ...s/slidingWindow/seq small/1800_1999.fasta
diff --git a/...s/slidingWindow/seq small/1900_2099.fasta → ...s/slidingWindow/seq small/1900_2099.fasta b/...s/slidingWindow/seq small/1900_2099.fasta → ...s/slidingWindow/seq small/1900_2099.fasta
diff --git a/...s/slidingWindow/seq small/2000_2199.fasta → ...s/slidingWindow/seq small/2000_2199.fasta b/...s/slidingWindow/seq small/2000_2199.fasta → ...s/slidingWindow/seq small/2000_2199.fasta
diff --git a/...les/slidingWindow/seq small/200_399.fasta → ...les/slidingWindow/seq small/200_399.fasta b/...les/slidingWindow/seq small/200_399.fasta → ...les/slidingWindow/seq small/200_399.fasta
diff --git a/...s/slidingWindow/seq small/2100_2299.fasta → ...s/slidingWindow/seq small/2100_2299.fasta b/...s/slidingWindow/seq small/2100_2299.fasta → ...s/slidingWindow/seq small/2100_2299.fasta
diff --git a/...s/slidingWindow/seq small/2200_2399.fasta → ...s/slidingWindow/seq small/2200_2399.fasta b/...s/slidingWindow/seq small/2200_2399.fasta → ...s/slidingWindow/seq small/2200_2399.fasta
diff --git a/...s/slidingWindow/seq small/2300_2499.fasta → ...s/slidingWindow/seq small/2300_2499.fasta b/...s/slidingWindow/seq small/2300_2499.fasta → ...s/slidingWindow/seq small/2300_2499.fasta
diff --git a/...s/slidingWindow/seq small/2400_2599.fasta → ...s/slidingWindow/seq small/2400_2599.fasta b/...s/slidingWindow/seq small/2400_2599.fasta → ...s/slidingWindow/seq small/2400_2599.fasta
diff --git a/...s/slidingWindow/seq small/2500_2699.fasta → ...s/slidingWindow/seq small/2500_2699.fasta b/...s/slidingWindow/seq small/2500_2699.fasta → ...s/slidingWindow/seq small/2500_2699.fasta
diff --git a/...s/slidingWindow/seq small/2600_2799.fasta → ...s/slidingWindow/seq small/2600_2799.fasta b/...s/slidingWindow/seq small/2600_2799.fasta → ...s/slidingWindow/seq small/2600_2799.fasta
diff --git a/...s/slidingWindow/seq small/2700_2899.fasta → ...s/slidingWindow/seq small/2700_2899.fasta b/...s/slidingWindow/seq small/2700_2899.fasta → ...s/slidingWindow/seq small/2700_2899.fasta
diff --git a/...s/slidingWindow/seq small/2800_2999.fasta → ...s/slidingWindow/seq small/2800_2999.fasta b/...s/slidingWindow/seq small/2800_2999.fasta → ...s/slidingWindow/seq small/2800_2999.fasta
diff --git a/...s/slidingWindow/seq small/2900_3099.fasta → ...s/slidingWindow/seq small/2900_3099.fasta b/...s/slidingWindow/seq small/2900_3099.fasta → ...s/slidingWindow/seq small/2900_3099.fasta
diff --git a/...s/slidingWindow/seq small/3000_3199.fasta → ...s/slidingWindow/seq small/3000_3199.fasta b/...s/slidingWindow/seq small/3000_3199.fasta → ...s/slidingWindow/seq small/3000_3199.fasta
diff --git a/...les/slidingWindow/seq small/300_499.fasta → ...les/slidingWindow/seq small/300_499.fasta b/...les/slidingWindow/seq small/300_499.fasta → ...les/slidingWindow/seq small/300_499.fasta
diff --git a/...s/slidingWindow/seq small/3100_3299.fasta → ...s/slidingWindow/seq small/3100_3299.fasta b/...s/slidingWindow/seq small/3100_3299.fasta → ...s/slidingWindow/seq small/3100_3299.fasta
diff --git a/...s/slidingWindow/seq small/3200_3399.fasta → ...s/slidingWindow/seq small/3200_3399.fasta b/...s/slidingWindow/seq small/3200_3399.fasta → ...s/slidingWindow/seq small/3200_3399.fasta
diff --git a/...s/slidingWindow/seq small/3300_3499.fasta → ...s/slidingWindow/seq small/3300_3499.fasta b/...s/slidingWindow/seq small/3300_3499.fasta → ...s/slidingWindow/seq small/3300_3499.fasta
diff --git a/...s/slidingWindow/seq small/3400_3599.fasta → ...s/slidingWindow/seq small/3400_3599.fasta b/...s/slidingWindow/seq small/3400_3599.fasta → ...s/slidingWindow/seq small/3400_3599.fasta
diff --git a/...s/slidingWindow/seq small/3500_3699.fasta → ...s/slidingWindow/seq small/3500_3699.fasta b/...s/slidingWindow/seq small/3500_3699.fasta → ...s/slidingWindow/seq small/3500_3699.fasta
diff --git a/...s/slidingWindow/seq small/3600_3799.fasta → ...s/slidingWindow/seq small/3600_3799.fasta b/...s/slidingWindow/seq small/3600_3799.fasta → ...s/slidingWindow/seq small/3600_3799.fasta
diff --git a/...s/slidingWindow/seq small/3700_3899.fasta → ...s/slidingWindow/seq small/3700_3899.fasta b/...s/slidingWindow/seq small/3700_3899.fasta → ...s/slidingWindow/seq small/3700_3899.fasta
diff --git a/...s/slidingWindow/seq small/3800_3999.fasta → ...s/slidingWindow/seq small/3800_3999.fasta b/...s/slidingWindow/seq small/3800_3999.fasta → ...s/slidingWindow/seq small/3800_3999.fasta
diff --git a/...s/slidingWindow/seq small/3900_4099.fasta → ...s/slidingWindow/seq small/3900_4099.fasta b/...s/slidingWindow/seq small/3900_4099.fasta → ...s/slidingWindow/seq small/3900_4099.fasta
diff --git a/...s/slidingWindow/seq small/4000_4199.fasta → ...s/slidingWindow/seq small/4000_4199.fasta b/...s/slidingWindow/seq small/4000_4199.fasta → ...s/slidingWindow/seq small/4000_4199.fasta
diff --git a/...les/slidingWindow/seq small/400_599.fasta → ...les/slidingWindow/seq small/400_599.fasta b/...les/slidingWindow/seq small/400_599.fasta → ...les/slidingWindow/seq small/400_599.fasta
diff --git a/...s/slidingWindow/seq small/4100_4299.fasta → ...s/slidingWindow/seq small/4100_4299.fasta b/...s/slidingWindow/seq small/4100_4299.fasta → ...s/slidingWindow/seq small/4100_4299.fasta
diff --git a/...s/slidingWindow/seq small/4200_4399.fasta → ...s/slidingWindow/seq small/4200_4399.fasta b/...s/slidingWindow/seq small/4200_4399.fasta → ...s/slidingWindow/seq small/4200_4399.fasta
diff --git a/...s/slidingWindow/seq small/4300_4499.fasta → ...s/slidingWindow/seq small/4300_4499.fasta b/...s/slidingWindow/seq small/4300_4499.fasta → ...s/slidingWindow/seq small/4300_4499.fasta
diff --git a/...s/slidingWindow/seq small/4400_4599.fasta → ...s/slidingWindow/seq small/4400_4599.fasta b/...s/slidingWindow/seq small/4400_4599.fasta → ...s/slidingWindow/seq small/4400_4599.fasta
diff --git a/...s/slidingWindow/seq small/4500_4699.fasta → ...s/slidingWindow/seq small/4500_4699.fasta b/...s/slidingWindow/seq small/4500_4699.fasta → ...s/slidingWindow/seq small/4500_4699.fasta
diff --git a/...s/slidingWindow/seq small/4600_4799.fasta → ...s/slidingWindow/seq small/4600_4799.fasta b/...s/slidingWindow/seq small/4600_4799.fasta → ...s/slidingWindow/seq small/4600_4799.fasta
diff --git a/...s/slidingWindow/seq small/4700_4899.fasta → ...s/slidingWindow/seq small/4700_4899.fasta b/...s/slidingWindow/seq small/4700_4899.fasta → ...s/slidingWindow/seq small/4700_4899.fasta
diff --git a/...s/slidingWindow/seq small/4800_4999.fasta → ...s/slidingWindow/seq small/4800_4999.fasta b/...s/slidingWindow/seq small/4800_4999.fasta → ...s/slidingWindow/seq small/4800_4999.fasta
diff --git a/...s/slidingWindow/seq small/4900_5099.fasta → ...s/slidingWindow/seq small/4900_5099.fasta b/...s/slidingWindow/seq small/4900_5099.fasta → ...s/slidingWindow/seq small/4900_5099.fasta
diff --git a/...s/slidingWindow/seq small/5000_5199.fasta → ...s/slidingWindow/seq small/5000_5199.fasta b/...s/slidingWindow/seq small/5000_5199.fasta → ...s/slidingWindow/seq small/5000_5199.fasta
diff --git a/...les/slidingWindow/seq small/500_699.fasta → ...les/slidingWindow/seq small/500_699.fasta b/...les/slidingWindow/seq small/500_699.fasta → ...les/slidingWindow/seq small/500_699.fasta
diff --git a/...s/slidingWindow/seq small/5100_5299.fasta → ...s/slidingWindow/seq small/5100_5299.fasta b/...s/slidingWindow/seq small/5100_5299.fasta → ...s/slidingWindow/seq small/5100_5299.fasta
diff --git a/...s/slidingWindow/seq small/5200_5399.fasta → ...s/slidingWindow/seq small/5200_5399.fasta b/...s/slidingWindow/seq small/5200_5399.fasta → ...s/slidingWindow/seq small/5200_5399.fasta
diff --git a/...s/slidingWindow/seq small/5300_5499.fasta → ...s/slidingWindow/seq small/5300_5499.fasta b/...s/slidingWindow/seq small/5300_5499.fasta → ...s/slidingWindow/seq small/5300_5499.fasta
diff --git a/...s/slidingWindow/seq small/5400_5599.fasta → ...s/slidingWindow/seq small/5400_5599.fasta b/...s/slidingWindow/seq small/5400_5599.fasta → ...s/slidingWindow/seq small/5400_5599.fasta
diff --git a/...s/slidingWindow/seq small/5500_5699.fasta → ...s/slidingWindow/seq small/5500_5699.fasta b/...s/slidingWindow/seq small/5500_5699.fasta → ...s/slidingWindow/seq small/5500_5699.fasta
diff --git a/...s/slidingWindow/seq small/5600_5799.fasta → ...s/slidingWindow/seq small/5600_5799.fasta b/...s/slidingWindow/seq small/5600_5799.fasta → ...s/slidingWindow/seq small/5600_5799.fasta
diff --git a/...s/slidingWindow/seq small/5700_5899.fasta → ...s/slidingWindow/seq small/5700_5899.fasta b/...s/slidingWindow/seq small/5700_5899.fasta → ...s/slidingWindow/seq small/5700_5899.fasta
diff --git a/...s/slidingWindow/seq small/5800_5999.fasta → ...s/slidingWindow/seq small/5800_5999.fasta b/...s/slidingWindow/seq small/5800_5999.fasta → ...s/slidingWindow/seq small/5800_5999.fasta
diff --git a/...s/slidingWindow/seq small/5900_6099.fasta → ...s/slidingWindow/seq small/5900_6099.fasta b/...s/slidingWindow/seq small/5900_6099.fasta → ...s/slidingWindow/seq small/5900_6099.fasta
diff --git a/...s/slidingWindow/seq small/6000_6199.fasta → ...s/slidingWindow/seq small/6000_6199.fasta b/...s/slidingWindow/seq small/6000_6199.fasta → ...s/slidingWindow/seq small/6000_6199.fasta
diff --git a/...les/slidingWindow/seq small/600_799.fasta → ...les/slidingWindow/seq small/600_799.fasta b/...les/slidingWindow/seq small/600_799.fasta → ...les/slidingWindow/seq small/600_799.fasta
diff --git a/...s/slidingWindow/seq small/6100_6299.fasta → ...s/slidingWindow/seq small/6100_6299.fasta b/...s/slidingWindow/seq small/6100_6299.fasta → ...s/slidingWindow/seq small/6100_6299.fasta
diff --git a/...s/slidingWindow/seq small/6200_6399.fasta → ...s/slidingWindow/seq small/6200_6399.fasta b/...s/slidingWindow/seq small/6200_6399.fasta → ...s/slidingWindow/seq small/6200_6399.fasta
diff --git a/...s/slidingWindow/seq small/6300_6499.fasta → ...s/slidingWindow/seq small/6300_6499.fasta b/...s/slidingWindow/seq small/6300_6499.fasta → ...s/slidingWindow/seq small/6300_6499.fasta
diff --git a/...s/slidingWindow/seq small/6400_6599.fasta → ...s/slidingWindow/seq small/6400_6599.fasta b/...s/slidingWindow/seq small/6400_6599.fasta → ...s/slidingWindow/seq small/6400_6599.fasta
diff --git a/...s/slidingWindow/seq small/6500_6699.fasta → ...s/slidingWindow/seq small/6500_6699.fasta b/...s/slidingWindow/seq small/6500_6699.fasta → ...s/slidingWindow/seq small/6500_6699.fasta
diff --git a/...s/slidingWindow/seq small/6600_6799.fasta → ...s/slidingWindow/seq small/6600_6799.fasta b/...s/slidingWindow/seq small/6600_6799.fasta → ...s/slidingWindow/seq small/6600_6799.fasta
diff --git a/...s/slidingWindow/seq small/6700_6899.fasta → ...s/slidingWindow/seq small/6700_6899.fasta b/...s/slidingWindow/seq small/6700_6899.fasta → ...s/slidingWindow/seq small/6700_6899.fasta
diff --git a/...s/slidingWindow/seq small/6800_6999.fasta → ...s/slidingWindow/seq small/6800_6999.fasta b/...s/slidingWindow/seq small/6800_6999.fasta → ...s/slidingWindow/seq small/6800_6999.fasta
diff --git a/...s/slidingWindow/seq small/6900_7099.fasta → ...s/slidingWindow/seq small/6900_7099.fasta b/...s/slidingWindow/seq small/6900_7099.fasta → ...s/slidingWindow/seq small/6900_7099.fasta
diff --git a/...s/slidingWindow/seq small/7000_7199.fasta → ...s/slidingWindow/seq small/7000_7199.fasta b/...s/slidingWindow/seq small/7000_7199.fasta → ...s/slidingWindow/seq small/7000_7199.fasta
diff --git a/...les/slidingWindow/seq small/700_899.fasta → ...les/slidingWindow/seq small/700_899.fasta b/...les/slidingWindow/seq small/700_899.fasta → ...les/slidingWindow/seq small/700_899.fasta
diff --git a/...s/slidingWindow/seq small/7100_7299.fasta → ...s/slidingWindow/seq small/7100_7299.fasta b/...s/slidingWindow/seq small/7100_7299.fasta → ...s/slidingWindow/seq small/7100_7299.fasta
diff --git a/...s/slidingWindow/seq small/7200_7399.fasta → ...s/slidingWindow/seq small/7200_7399.fasta b/...s/slidingWindow/seq small/7200_7399.fasta → ...s/slidingWindow/seq small/7200_7399.fasta
diff --git a/...s/slidingWindow/seq small/7300_7499.fasta → ...s/slidingWindow/seq small/7300_7499.fasta b/...s/slidingWindow/seq small/7300_7499.fasta → ...s/slidingWindow/seq small/7300_7499.fasta
diff --git a/...s/slidingWindow/seq small/7400_7599.fasta → ...s/slidingWindow/seq small/7400_7599.fasta b/...s/slidingWindow/seq small/7400_7599.fasta → ...s/slidingWindow/seq small/7400_7599.fasta
diff --git a/...s/slidingWindow/seq small/7500_7699.fasta → ...s/slidingWindow/seq small/7500_7699.fasta b/...s/slidingWindow/seq small/7500_7699.fasta → ...s/slidingWindow/seq small/7500_7699.fasta
diff --git a/...s/slidingWindow/seq small/7600_7799.fasta → ...s/slidingWindow/seq small/7600_7799.fasta b/...s/slidingWindow/seq small/7600_7799.fasta → ...s/slidingWindow/seq small/7600_7799.fasta
diff --git a/...s/slidingWindow/seq small/7700_7899.fasta → ...s/slidingWindow/seq small/7700_7899.fasta b/...s/slidingWindow/seq small/7700_7899.fasta → ...s/slidingWindow/seq small/7700_7899.fasta
diff --git a/...s/slidingWindow/seq small/7800_7999.fasta → ...s/slidingWindow/seq small/7800_7999.fasta b/...s/slidingWindow/seq small/7800_7999.fasta → ...s/slidingWindow/seq small/7800_7999.fasta
diff --git a/...s/slidingWindow/seq small/7900_8099.fasta → ...s/slidingWindow/seq small/7900_8099.fasta b/...s/slidingWindow/seq small/7900_8099.fasta → ...s/slidingWindow/seq small/7900_8099.fasta
diff --git a/...s/slidingWindow/seq small/8000_8199.fasta → ...s/slidingWindow/seq small/8000_8199.fasta b/...s/slidingWindow/seq small/8000_8199.fasta → ...s/slidingWindow/seq small/8000_8199.fasta
diff --git a/...les/slidingWindow/seq small/800_999.fasta → ...les/slidingWindow/seq small/800_999.fasta b/...les/slidingWindow/seq small/800_999.fasta → ...les/slidingWindow/seq small/800_999.fasta
diff --git a/...s/slidingWindow/seq small/8100_8299.fasta → ...s/slidingWindow/seq small/8100_8299.fasta b/...s/slidingWindow/seq small/8100_8299.fasta → ...s/slidingWindow/seq small/8100_8299.fasta
diff --git a/...s/slidingWindow/seq small/8200_8399.fasta → ...s/slidingWindow/seq small/8200_8399.fasta b/...s/slidingWindow/seq small/8200_8399.fasta → ...s/slidingWindow/seq small/8200_8399.fasta
diff --git a/...s/slidingWindow/seq small/8300_8499.fasta → ...s/slidingWindow/seq small/8300_8499.fasta b/...s/slidingWindow/seq small/8300_8499.fasta → ...s/slidingWindow/seq small/8300_8499.fasta
diff --git a/...s/slidingWindow/seq small/8400_8599.fasta → ...s/slidingWindow/seq small/8400_8599.fasta b/...s/slidingWindow/seq small/8400_8599.fasta → ...s/slidingWindow/seq small/8400_8599.fasta
diff --git a/...s/slidingWindow/seq small/8500_8699.fasta → ...s/slidingWindow/seq small/8500_8699.fasta b/...s/slidingWindow/seq small/8500_8699.fasta → ...s/slidingWindow/seq small/8500_8699.fasta
diff --git a/...s/slidingWindow/seq small/8600_8799.fasta → ...s/slidingWindow/seq small/8600_8799.fasta b/...s/slidingWindow/seq small/8600_8799.fasta → ...s/slidingWindow/seq small/8600_8799.fasta
diff --git a/...s/slidingWindow/seq small/8700_8899.fasta → ...s/slidingWindow/seq small/8700_8899.fasta b/...s/slidingWindow/seq small/8700_8899.fasta → ...s/slidingWindow/seq small/8700_8899.fasta
diff --git a/...s/slidingWindow/seq small/8800_8999.fasta → ...s/slidingWindow/seq small/8800_8999.fasta b/...s/slidingWindow/seq small/8800_8999.fasta → ...s/slidingWindow/seq small/8800_8999.fasta
diff --git a/...s/slidingWindow/seq small/8900_9099.fasta → ...s/slidingWindow/seq small/8900_9099.fasta b/...s/slidingWindow/seq small/8900_9099.fasta → ...s/slidingWindow/seq small/8900_9099.fasta
diff --git a/...s/slidingWindow/seq small/9000_9199.fasta → ...s/slidingWindow/seq small/9000_9199.fasta b/...s/slidingWindow/seq small/9000_9199.fasta → ...s/slidingWindow/seq small/9000_9199.fasta
diff --git a/...es/slidingWindow/seq small/900_1099.fasta → ...es/slidingWindow/seq small/900_1099.fasta b/...es/slidingWindow/seq small/900_1099.fasta → ...es/slidingWindow/seq small/900_1099.fasta
diff --git a/...s/slidingWindow/seq small/9100_9299.fasta → ...s/slidingWindow/seq small/9100_9299.fasta b/...s/slidingWindow/seq small/9100_9299.fasta → ...s/slidingWindow/seq small/9100_9299.fasta
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diff --git a/...s/slidingWindow/seq small/9400_9599.fasta → ...s/slidingWindow/seq small/9400_9599.fasta b/...s/slidingWindow/seq small/9400_9599.fasta → ...s/slidingWindow/seq small/9400_9599.fasta
diff --git a/...s/slidingWindow/seq small/9500_9699.fasta → ...s/slidingWindow/seq small/9500_9699.fasta b/...s/slidingWindow/seq small/9500_9699.fasta → ...s/slidingWindow/seq small/9500_9699.fasta
diff --git a/...s/slidingWindow/seq small/9600_9799.fasta → ...s/slidingWindow/seq small/9600_9799.fasta b/...s/slidingWindow/seq small/9600_9799.fasta → ...s/slidingWindow/seq small/9600_9799.fasta
diff --git a/...s/slidingWindow/seq small/9700_9899.fasta → ...s/slidingWindow/seq small/9700_9899.fasta b/...s/slidingWindow/seq small/9700_9899.fasta → ...s/slidingWindow/seq small/9700_9899.fasta
diff --git a/...s/slidingWindow/seq small/9800_9999.fasta → ...s/slidingWindow/seq small/9800_9999.fasta b/...s/slidingWindow/seq small/9800_9999.fasta → ...s/slidingWindow/seq small/9800_9999.fasta
diff --git a/.../slidingWindow/seq small/9900_10099.fasta → .../slidingWindow/seq small/9900_10099.fasta b/.../slidingWindow/seq small/9900_10099.fasta → .../slidingWindow/seq small/9900_10099.fasta
diff --git a/.../slidingWindow/seq very small/0_199.fasta → .../slidingWindow/seq very small/0_199.fasta b/.../slidingWindow/seq very small/0_199.fasta → .../slidingWindow/seq very small/0_199.fasta
diff --git a/...dingWindow/seq very small/1000_1199.fasta → ...dingWindow/seq very small/1000_1199.fasta b/...dingWindow/seq very small/1000_1199.fasta → ...dingWindow/seq very small/1000_1199.fasta
diff --git a/...lidingWindow/seq very small/100_299.fasta → ...lidingWindow/seq very small/100_299.fasta b/...lidingWindow/seq very small/100_299.fasta → ...lidingWindow/seq very small/100_299.fasta
diff --git a/...dingWindow/seq very small/1100_1299.fasta → ...dingWindow/seq very small/1100_1299.fasta b/...dingWindow/seq very small/1100_1299.fasta → ...dingWindow/seq very small/1100_1299.fasta
diff --git a/...dingWindow/seq very small/1200_1328.fasta → ...dingWindow/seq very small/1200_1328.fasta b/...dingWindow/seq very small/1200_1328.fasta → ...dingWindow/seq very small/1200_1328.fasta
diff --git a/...dingWindow/seq very small/1300_1328.fasta → ...dingWindow/seq very small/1300_1328.fasta b/...dingWindow/seq very small/1300_1328.fasta → ...dingWindow/seq very small/1300_1328.fasta
diff --git a/...lidingWindow/seq very small/200_399.fasta → ...lidingWindow/seq very small/200_399.fasta b/...lidingWindow/seq very small/200_399.fasta → ...lidingWindow/seq very small/200_399.fasta
diff --git a/...lidingWindow/seq very small/300_499.fasta → ...lidingWindow/seq very small/300_499.fasta b/...lidingWindow/seq very small/300_499.fasta → ...lidingWindow/seq very small/300_499.fasta
diff --git a/...lidingWindow/seq very small/400_599.fasta → ...lidingWindow/seq very small/400_599.fasta b/...lidingWindow/seq very small/400_599.fasta → ...lidingWindow/seq very small/400_599.fasta
diff --git a/...lidingWindow/seq very small/500_699.fasta → ...lidingWindow/seq very small/500_699.fasta b/...lidingWindow/seq very small/500_699.fasta → ...lidingWindow/seq very small/500_699.fasta
diff --git a/...lidingWindow/seq very small/600_799.fasta → ...lidingWindow/seq very small/600_799.fasta b/...lidingWindow/seq very small/600_799.fasta → ...lidingWindow/seq very small/600_799.fasta
diff --git a/...lidingWindow/seq very small/700_899.fasta → ...lidingWindow/seq very small/700_899.fasta b/...lidingWindow/seq very small/700_899.fasta → ...lidingWindow/seq very small/700_899.fasta