Updated doc

chrisquince · Apr 16, 2018 · 77c2276 · 77c2276
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diff --git a/README.md b/README.md
@@ -101,11 +101,11 @@ Then run the example data file which corresponds to a single COG from the mock c
 described in the manuscript. This COG0015 has 933 variant positions. The input file is in the data 
 folder. We run the variant filtering as follows:
 
-    python3 ../desman/Variant_Filter.py ../data/contig_6or16_genesL_scgCOG0015.freq -o COG0015_out -p
+    Variant_Filter.py ../data/contig_6or16_genesL_scgCOG0015.freq -o COG0015_out -p
 
 The variant filtering has a number of optional parameters to see them run:
 
-    python3 ../desman/Variant_Filter.py -h
+    Variant_Filter.py -h
     
 They should all be fairly self explanatory. We recommend always using the 
 the '-p' flag for one dimenisonal optimisition of individual base frequencies if it is not 

diff --git a/complete_example/README.md b/complete_example/README.md
@@ -599,7 +599,7 @@ Now lets use Desman to find the variant positions on these core cogs:
 mkdir Variants
 cd Variants/
 mv ../Cluster_esc3_scgs.freq .
-python3 $DESMAN/desman/Variant_Filter.py Cluster_esc3_scgs.freq
+Variant_Filter.py Cluster_esc3_scgs.freq
 cd ..
 ```
 
@@ -746,7 +746,7 @@ The _-g_ flag here tells the script to expect gene positions in a slightly diffe
 mkdir VariantsAll
 cd VariantsAll
 mv ../Cluster_esc3.freq .
-python3 $DESMAN/desman/Variant_Filter.py Cluster_esc3.freq -m 0.0 -v 0.03
+Variant_Filter.py Cluster_esc3.freq -m 0.0 -v 0.03
 cd ..
 ```
 
@@ -798,7 +798,7 @@ This should generate the following output files.
 We will now compare predictions with known assignments to reference genomes. First we 
 use the mapping files to determine number of reads from each genome mapping to each gene.
 ```
-python3 $DESMAN/scripts/gene_read_count_per_genome.py ../contigs/final_contigs_c10K.fa ../AnnotateEC/ClusterEC.genes ../AssignGenome/Mock1_20genomes.fasta  ../Map/*mapped.sorted.bam > ClusterEC_gene_counts.tsv
+python3 $DESMAN/scripts/gene_read_count_per_genome.py ../AnnotateEC/ClusterEC.genes ../AssignGenome/Mock1_20genomes.fasta  ../Map/*mapped.sorted.bam > ClusterEC_gene_counts.tsv
 ```
 
 As above we will rename the header file to be a bit more presentable: