From 77c22769712d1d38bceb9c05862905c537c820ab Mon Sep 17 00:00:00 2001 From: chrisquince Date: Mon, 16 Apr 2018 21:18:30 +0100 Subject: [PATCH] Updated doc --- README.md | 4 ++-- complete_example/README.md | 6 +++--- 2 files changed, 5 insertions(+), 5 deletions(-) diff --git a/README.md b/README.md index 1427c30..cc86714 100644 --- 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 index fef8a70..a5ec252 100644 --- 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: