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Instruction manual

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Installation

Clone the project from GitHub. Create and launch a virtual environment for python

python3 -m venv venv
source venv/bin/activate

and install dependencies

pip install -r requirements.txt

Running application

The application is run with the following command

python3 src/compana.py <arguments>

The application accepts the following CLI arguments:

Short Long Description
g gffcompare_gtf provide full path for gtf file produced by gffcompare.
r reference_gtf provide full path for reference gtf file used to create the gffcompare gtf-file.
i isoquant_gtf provide full path for IsoQuant transcript_model.gtf file
a reference_fasta provide full path for reference FASTA-file (e.g. fa)
b reads_bam provide full path for reads provided to IsoQuant
t reads_tsv provide full path for model_reads.tsv generated by IsoQuant
f force force re-creation of sqlite3 database. By default a new database is not created if one already exists to improve efficiency.
s stats output statistics on class codes.
c class-code specify one or several class codes for which to generate offset data.
o offset provide a closed range of offsets to be extracted from comparison results. Provide one or two values. If one value is given, the range will be set to (0, max(0, given value))
j json provide a filename for a json-file containing arguments. Example below.
w window_size window from which indels are to be searched
e extended_debugging enable extended debug output, to create more log-files
m min_reads_for_graph threshold for the n of cases for creating images
n no_canonicals canonical splice sites are not considered. Enables more aggressive error prediction and correction.
v very_conservative canonical splice sites are considered, threshold must exceed, there must be a consentration of deletions

The suggested way to run the application is to provide arguments in a json-format. An example template is provided in the root directory. For input files the best practice is to use absolute path.

{
    "reads_bam": "<file.bam>",
    "reads_tsv": "<file.tsv>",
    "reference_gtf": "<file.gtf>",
    "reference_fasta": "<file.fa>",
    "gffcompare_gtf": "<file.gtf>",
    "isoquant_gtf": "<file.gtf>",
    "offset": [0, 6],
    "class_code": "j c k s x",
    "window_size": 8,
    "min_reads_for_graph": 100,
    "force": false,
    "extended_debugging": false,
    "no_canonicals": false,
    "very_conservative": false
}

Examples

The following insruction extracts arguments from a given json file

python3 src/compana.py -j <arguments.json>

The following CLI-instruction contains the minimum arguments needed to run compAna:

python3 src/compana.py \
--gffcompare_gtf=gffcompare-file.gtf \
--reference_gtf=ref-file.gtf  \
--reference_fasta=file.fa \
--reads_bam=file.bam \
--reads_tsv=file.tsv \
--offset="0 6"