Kmer experiment with --confid-step arg

Vagrantfile

@@ -0,0 +1,110 @@
+# -*- mode: ruby -*-
+# vi: set ft=ruby :
+
+# All Vagrant configuration is done below. The "2" in Vagrant.configure
+# configures the configuration version (we support older styles for
+# backwards compatibility). Please don't change it unless you know what
+# you're doing.
+Vagrant.configure("2") do |config|
+  # The most common configuration options are documented and commented below.
+  # For a complete reference, please see the online documentation at
+  # https://docs.vagrantup.com.
+
+  # Every Vagrant development environment requires a box. You can search for
+  # boxes at https://atlas.hashicorp.com/search.
+  config.vm.box = "bento/ubuntu-14.04"
+
+  # Disable automatic box update checking. If you disable this, then
+  # boxes will only be checked for updates when the user runs
+  # `vagrant box outdated`. This is not recommended.
+  # config.vm.box_check_update = false
+
+  # Create a forwarded port mapping which allows access to a specific port
+  # within the machine from a port on the host machine. In the example below,
+  # accessing "localhost:8080" will access port 80 on the guest machine.
+  # config.vm.network "forwarded_port", guest: 80, host: 8080
+
+  # Create a private network, which allows host-only access to the machine
+  # using a specific IP.
+  # config.vm.network "private_network", ip: "192.168.33.10"
+
+  # Create a public network, which generally matched to bridged network.
+  # Bridged networks make the machine appear as another physical device on
+  # your network.
+  # config.vm.network "public_network"
+
+  # Share an additional folder to the guest VM. The first argument is
+  # the path on the host to the actual folder. The second argument is
+  # the path on the guest to mount the folder. And the optional third
+  # argument is a set of non-required options.
+  # config.vm.synced_folder "../data", "/vagrant_data"
+
+  # Provider-specific configuration so you can fine-tune various
+  # backing providers for Vagrant. These expose provider-specific options.
+  # Example for VirtualBox:
+  #
+  config.vm.provider "virtualbox" do |vb|
+    # Display the VirtualBox GUI when booting the machine
+    # vb.gui = true
+
+    # Customize the amount of memory on the VM:
+    vb.memory = "8192" # 8GB
+    vb.cpus = 2
+  end
+  #
+  # View the documentation for the provider you are using for more
+  # information on available options.
+
+  # Define a Vagrant Push strategy for pushing to Atlas. Other push strategies
+  # such as FTP and Heroku are also available. See the documentation at
+  # https://docs.vagrantup.com/v2/push/atlas.html for more information.
+  # config.push.define "atlas" do |push|
+  #   push.app = "YOUR_ATLAS_USERNAME/YOUR_APPLICATION_NAME"
+  # end
+
+  # Enable provisioning with a shell script. Additional provisioners such as
+  # Puppet, Chef, Ansible, Salt, and Docker are also available. Please see the
+  # documentation for more information about their specific syntax and use.
+  config.vm.provision "shell", inline: <<-SHELL
+    sudo apt-get update
+    sudo apt-get install -y g++ libncurses5-dev python-dev python3-dev emacs cmake
+    cd
+    # Stampy
+    curl -O http://www.well.ox.ac.uk/~gerton/software/Stampy/stampy-latest.tgz
+    tar xfz stampy-latest.tgz
+    cd stampy
+    make
+    cd ..
+    # VCFTools
+    wget https://downloads.sourceforge.net/project/vcftools/vcftools_0.1.13.tar.gz
+    tar xfz vcftools_0.1.13.tar.gz
+    cd vcftools_0.1.13
+    make
+    cd ..
+    # Cortex
+    git clone --recursive https://github.com/iqbal-lab/cortex.git
+    cd cortex
+    bash install.sh
+    for k in 31 63 95 127; do
+      for ncol in 1 2 3 9 10 11; do
+        make cortex_var MAXK=$k NCOLS=$ncol
+      done
+    done
+    echo 'export PERL5LIB="${HOME}/cortex/scripts/analyse_variants/bioinf-perl/lib/:${HOME}/cortex/scripts/calling/:${PERL5LIB}"' >> .profile
+    echo 'export PATH="${HOME}/cortex/scripts/analyse_variants/needleman_wunsch/:${PATH}"' >> .profile
+    cd ..
+    # McCortex
+    git clone --recursive -b develop https://github.com/mcveanlab/mccortex.git
+    cd mccortex
+    cd libs && make all && cd ..
+    for k in 31 63 95 127; do
+      make all test MAXK=31
+    done
+    cd ..
+    # Freebayes
+    git clone --recursive https://github.com/ekg/freebayes.git
+    cd freebayes
+    make
+    cd ..
+  SHELL
+end

results/kmer_size_experiment/results/20170211sat_chr22_28M_confidstep/README.md

@@ -0,0 +1,2 @@
+
+human `chr22:28,000,000-28,999,999`, contigs assembled with `--no-missing-check --confid-step 0.8` argument.

results/kmer_size_experiment/results/20170211sat_chr22_28M_confidstep/bad.edges.csv

@@ -0,0 +1,12 @@
+# The number of sequencing errors that would add a new edge between two
+# existing kmers. Note: there are 3*reflen possible mutations
+kmer,reflen,nkmers,nedges,nerror_edges,cov,err_rate,est_bad_edges
+21,1000000,955450,959133,3627,100,0.005,604
+31,1000000,980343,981744,838,100,0.005,139
+41,1000000,990014,990588,183,100,0.005,30
+51,1000000,993938,994179,44,100,0.005,7
+61,1000000,995750,995879,15,100,0.005,2
+71,1000000,996793,996870,7,100,0.005,1
+81,1000000,997395,997442,2,100,0.005,0
+91,1000000,997789,997822,5,100,0.005,0
+99,1000000,998029,998055,4,100,0.005,0

results/kmer_size_experiment/results/20170211sat_chr22_28M_confidstep/cleaning.corr.table.csv

@@ -0,0 +1,13 @@
+# Number of kmers in the perfect, raw and cleaned graphs
+# _nreal is the number of real kmers in the raw/cleaned graph
+# raw_errs, clean_errs are the fraction of error kmers in each graph
+# frac_remove_errs is the fraction of kmers removed that were seqn errs
+kmer,nkmers,raw_nkmers,raw_nreal,clean_nkmers,clean_nreal,raw_errs,clean_errs,frac_remove_errs
+21,943524,1041105,943524,943614,943524,0.09373,0.00010,1.00000
+31,973199,1184735,973199,973203,973199,0.17855,0.00000,1.00000
+41,985939,1265236,985939,985939,985939,0.22075,0.00000,1.00000
+51,991526,1292210,991526,991526,991526,0.23269,0.00000,1.00000
+61,994205,1284937,994205,994205,994205,0.22626,0.00000,1.00000
+71,995708,1249759,995708,995708,995708,0.20328,0.00000,1.00000
+81,996639,1188147,996639,996638,996638,0.16118,0.00000,0.99999
+91,997273,1102712,997215,994901,994896,0.09567,0.00001,0.97849

results/kmer_size_experiment/results/20170211sat_chr22_28M_confidstep/cleaning.table.csv

@@ -0,0 +1,13 @@
+# Number of kmers in the perfect, raw and cleaned graphs
+# _nreal is the number of real kmers in the raw/cleaned graph
+# raw_errs, clean_errs are the fraction of error kmers in each graph
+# frac_remove_errs is the fraction of kmers removed that were seqn errs
+kmer,nkmers,raw_nkmers,raw_nreal,clean_nkmers,clean_nreal,raw_errs,clean_errs,frac_remove_errs
+21,943524,8281513,943524,944420,943506,0.88607,0.00097,1.00000
+31,973199,10505480,973199,973255,973151,0.90736,0.00011,0.99999
+41,985939,11685959,985939,985901,985901,0.91563,0.00000,1.00000
+51,991526,11925083,991526,991494,991494,0.91685,0.00000,1.00000
+61,994205,11290786,994205,994174,994174,0.91195,0.00000,1.00000
+71,995708,9832665,995706,995658,995658,0.89873,0.00000,0.99999
+81,996639,7598955,996636,995784,995784,0.86885,0.00000,0.99987
+91,997273,4637375,995584,409278,409248,0.78531,0.00007,0.86132

results/kmer_size_experiment/results/20170211sat_chr22_28M_confidstep/perfect.links.csv

@@ -0,0 +1,9 @@
+K,NG50,AssemblyErrors
+21,94392,0
+31,94392,0
+41,94392,0
+51,94392,0
+61,94392,0
+71,94392,0
+81,94392,0
+91,94392,0

results/kmer_size_experiment/results/20170211sat_chr22_28M_confidstep/perfect.pe.csv

@@ -0,0 +1,9 @@
+K,NG50,AssemblyErrors
+21,22583,7
+31,52417,9
+41,76714,6
+51,85267,8
+61,125711,8
+71,125711,7
+81,125659,2
+91,123940,1

results/kmer_size_experiment/results/20170211sat_chr22_28M_confidstep/perfect.plain.csv

@@ -0,0 +1,9 @@
+K,NG50,AssemblyErrors
+21,1920,0
+31,3161,0
+41,5928,0
+51,12729,0
+61,27317,0
+71,71586,0
+81,75608,0
+91,94391,0

results/kmer_size_experiment/results/20170211sat_chr22_28M_confidstep/stoch.links.csv

@@ -0,0 +1,9 @@
+K,NG50,AssemblyErrors
+21,94392,5
+31,94392,4
+41,94391,3
+51,94391,2
+61,94391,2
+71,94391,1
+81,94391,1
+91,17625,0

results/kmer_size_experiment/results/20170211sat_chr22_28M_confidstep/stoch.pe.csv

@@ -0,0 +1,9 @@
+K,NG50,AssemblyErrors
+21,24439,8
+31,50982,19
+41,76714,12
+51,91821,18
+61,125711,16
+71,125711,14
+81,125659,5
+91,19076,3

results/kmer_size_experiment/results/20170211sat_chr22_28M_confidstep/stoch.plain.csv

@@ -0,0 +1,9 @@
+K,NG50,AssemblyErrors
+21,1920,0
+31,3161,0
+41,5928,0
+51,12729,0
+61,27317,0
+71,71586,0
+81,75608,0
+91,16878,0

results/kmer_size_experiment/results/20170211sat_chr22_28M_confidstep/stocherr.links.csv

@@ -0,0 +1,9 @@
+K,NG50,AssemblyErrors
+21,5555,737
+31,6687,548
+41,18591,182
+51,44614,73
+61,67584,41
+71,75599,14
+81,14421,9
+91,139,4

results/kmer_size_experiment/results/20170211sat_chr22_28M_confidstep/stocherr.pe.csv

@@ -0,0 +1,9 @@
+K,NG50,AssemblyErrors
+21,6155,763
+31,7638,540
+41,25027,225
+51,74994,77
+61,75074,52
+71,72574,17
+81,14494,10
+91,139,4

results/kmer_size_experiment/results/20170211sat_chr22_28M_confidstep/stocherr.plain.csv

@@ -0,0 +1,9 @@
+K,NG50,AssemblyErrors
+21,1866,15
+31,3126,6
+41,5928,0
+51,12729,0
+61,27317,0
+71,60471,0
+81,14272,0
+91,139,4

results/kmer_size_experiment/results/20170211sat_chr22_28M_confidstep/stocherr.sga.csv

@@ -0,0 +1,9 @@
+K,NG50,AssemblyErrors
+21,2010,344
+31,3232,357
+41,4706,345
+51,7206,226
+61,12176,108
+71,38131,21
+81,93964,5
+91,16165,5

results/kmer_size_experiment/results/20170211sat_chr22_28M_confidstep/stocherrcorr.links.csv

@@ -0,0 +1,9 @@
+K,NG50,AssemblyErrors
+21,6630,558
+31,6976,586
+41,27260,147
+51,50329,84
+61,74915,45
+71,93763,16
+81,94391,5
+91,13390,5

results/kmer_size_experiment/results/20170211sat_chr22_28M_confidstep/stocherrcorr.pe.csv

@@ -0,0 +1,9 @@
+K,NG50,AssemblyErrors
+21,7439,560
+31,8287,518
+41,30490,168
+51,75065,90
+61,75501,44
+71,94643,17
+81,100768,18
+91,13644,13

results/kmer_size_experiment/results/20170211sat_chr22_28M_confidstep/stocherrcorr.plain.csv

@@ -0,0 +1,9 @@
+K,NG50,AssemblyErrors
+21,1920,11
+31,3126,0
+41,5928,0
+51,12729,0
+61,27317,0
+71,71586,0
+81,75608,0
+91,13382,5

results/kmer_size_experiment/results/20170211sat_chr22_28M_confidstep/stocherrcorr.sga.csv

@@ -0,0 +1,9 @@
+K,NG50,AssemblyErrors
+21,2010,736
+31,3176,765
+41,4032,735
+51,5845,357
+61,10533,137
+71,30368,24
+81,93964,7
+91,16165,4

results/kmer_size_experiment/results/generate-results.sh

@@ -6,7 +6,7 @@ for d in perfect_cov stoch_cov stocherr_cov stocherr_corr
 do
   if [ -d ../$d/k99 ]
   then
-    mv ../$d/k99 ../$d/99_hidden
+    mv ../$d/k99 ../$d/hidden_k99
   fi
 done
 
@@ -93,8 +93,8 @@ echo "-- Making cleaning tables"
 # unhide k99 files
 for d in perfect_cov stoch_cov stocherr_cov stocherr_corr
 do
-  if [ -d ../$d/k99_hidden ]
+  if [ -d ../$d/hidden_k99 ]
   then
-    mv ../$d/k99_hidden ../$d/k99
+    mv ../$d/hidden_k99 ../$d/k99
   fi
 done

results/kmer_size_experiment/runk.mk

@@ -32,7 +32,7 @@ PYSTATS=python $(CTXDIR)/scripts/python/break-contigs-vs-truth.py
 
 DIR=$(NAME)/k$(K)
 MEM=1G
-CONTIGS_ARGS=--no-missing-check
+CONTIGS_ARGS=--no-missing-check --confid-step 0.8
 
 RAWGRAPH=$(DIR)/graph.k$(K).raw.ctx
 CLEANGRAPH=$(DIR)/graph.k$(K).clean.ctx