From 6b91d2e61848d264d45534857ca1068ddff41841 Mon Sep 17 00:00:00 2001 From: sarah bastkowski <4249932+sbastkowski@users.noreply.github.com> Date: Thu, 24 Aug 2023 09:07:20 +0100 Subject: [PATCH] Fixing README and initial set of commands in executable (#37) --- README.md | 13 ++++++------- tradis | 3 +++ 2 files changed, 9 insertions(+), 7 deletions(-) diff --git a/README.md b/README.md index 97cc854..0a0b6b0 100644 --- a/README.md +++ b/README.md @@ -201,7 +201,7 @@ and add `:` to the previous command (replacing with whatever version ## Usage -QuaTraDIS creates a single executable tool called `tradis`, all functions are available within this tool and it can be +QuaTraDIS creates a single executable tool called `tradis`, all functions are available within this tool and can therefore be used in many different ways. However, a typical use case maybe be to first convert your TraDIS sequenced reads into transposon insertion site plot files. This can be done with a command line such as this below, which has each fastq file (optionally gzipped) listed in `my_fastq_list.txt`: @@ -214,20 +214,19 @@ The output will be a series of directories for each fastq, containing the plot f along with the aligned reads, and some statistics regarding transposon insertion sites both for each sample, and across all samples. -A set of plot files can then be analysed relation to each other. To do this you must first create an experiment file, which -lists each plot file, whether it is a control, or condition, and whether it is a replicate or not. +A set of plot files can then be analysed in relation to each other using the `tradis pipeline compare` command. For example: ```bash -tradis pipeline analyse --output_dir analysis_output experiment.txt my_annotations.embl +tradis pipeline compare --output_dir analysis_output --annotations my_annotations.embl \ + --condition_files cond1.fq.gz cond2.fq.fz \ + --control_files cont1.fq.gz cont2.fq.gz ``` -Further processing of the insert site table may be done using the R scripts mentioned above to compare or assess for gene essentiality. - The `tradis` tool has multiple functions, as shown below, and can also be found using the tools help message `tradis --help`: * `pipeline` * `create_plots` - Creates transposon insertion site plot files from multiple fastq files. This uses a snakemake pipeline and is capable of distributing work over a cluster, running in parallel where possible. - * `analyse` - Comparative analysis of multiple plot files across controls, conditions and replicates. Predicts impact of inserts on nearby genes. + * `compare` - Comparative analysis of multiple plot files across controls, conditions and replicates. Predicts impact of inserts on nearby genes. * `plot` * `create` * `from_fastq` - From a fastq file and reference, maps the reads to the reference and produces the transposon insertion site plot files. diff --git a/tradis b/tradis index cbbe2c1..a8133b3 100755 --- a/tradis +++ b/tradis @@ -35,6 +35,9 @@ def main(): """This script contains a number of tools for running or supporting TraDIS experiments.""", formatter_class=argparse.RawTextHelpFormatter) + parser.add_argument('--profile', dest='profile', action='store_true', + help='Turn on profiling. Prints out cumulative time in each function to stdout and to an output file (tradis.profile). The profile file can be read by tools such as snakeviz.') + # Version option only available at top level parser.add_argument("-V", "--version", action='store_true', default=False, help="Output the software version")