Create simulated HIV drug resistance testing data.
Turns a set of susceptible and a set of resistant HIV pol sequences into simulated sample data, as input to a drug resistance testing platform. Produces a folder containing hashed filenames, and a manifest containing a legend to decode the files.
Example input can be found in the data folder.
Uses the ART sequence simulator and the sierra HIV drug resistance database.
From root:
python setup.py build
sudo python setup.py install
virtualenv env
env/bin/pip install .
The install script may suggest a number of external software packages which must be in your build system for seq2simulate to work. These include art_454/art_illumina.
Java is also required, and can be installed via a package manager or from Oracle.
Create a Roche/454 simulation from Seq6 at 1% prevalence:
simulate --prevalence 1 --susceptible data/split/Seq6_Sus --resistant data/split/Seq6_Res --out temp_roche --platform roche
Create an Illumina simulation from all sequences, with randomized errors, at all prevalences:
simulate --susceptible data/SusceptibleSeqs_all.fasta --resistant data/ResistantSeqs_all.fasta --out temp_out --platform illumina --paired-end --randomize
Create a Roche/454 simulation from Seq6 at 1% prevalence with APOBEC proviral hypermutation:
simulate --prevalence 1 --susceptible data/split/Seq6_Sus --resistant data/split/Seq6_Res --out temp_roche --platform roche --proviral
--susceptible PATH Path to a FASTA file of susceptible
sequence(s).
--resistant PATH Path to a FASTA file of resistant
sequence(s).
--out PATH Path to the desired output folder (will be
created).
--platform [illumina|ion|roche]
Sequencing platform to simulate.
--working-dir PATH Returns a specific working directory
location. Defaults to a randomly generated
uuid in an appropriate data folder.
--prevalence INTEGER Select a prevalence to run at. Default is
to generate 10prevalences: 0.5, 1, 2, 5, 10,
15, 20, 30, 50, 100
--diversity-only Leaves the working directory at a point
where diversity, but not sequencing error,
has been simulated.
--error-only When used with --working-dir, generates
sequencing error from the given working
directory, which should already have been
created using --evolve-only.
--prevalence-only When used with --working-dir, creates the
final output from already --error-only
simulated reads in the given working
directory
--pcr-error Include a false PCR error in this
simulation.
--env-error Include some DNA from HIV ENV in this
simulation.
--human-error Include some human DNA in this simulation.
--remove-rt Remove the piece of RT covering K103N
entirely.
--randomize For multiple sequences. Shuffle and
randomly assign error types.
--paired-end Paired-end sequencing. Only valid with
illumina data.
--proviral After evolving sequences, apply APOBEC
hypermutation to mimic proviral DNA.
--help Show this message and exit.