https://github.com/mfcovington/cosopt-assembly-line
Format expression data for COSOPT analysis, run COSOPT, and format the results.
https://github.com/mfcovington/cosopt-assembly-line
Last synced: 6 days ago
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Format expression data for COSOPT analysis, run COSOPT, and format the results.
- Host: GitHub
- URL: https://github.com/mfcovington/cosopt-assembly-line
- Owner: mfcovington
- Created: 2015-08-24T23:04:07.000Z (almost 11 years ago)
- Default Branch: develop
- Last Pushed: 2016-02-24T00:49:37.000Z (over 10 years ago)
- Last Synced: 2025-04-08T18:55:45.007Z (over 1 year ago)
- Language: Perl
- Homepage:
- Size: 411 KB
- Stars: 1
- Watchers: 2
- Forks: 0
- Open Issues: 0
-
Metadata Files:
- Readme: README.md
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README
# COSOPT Assembly Line
The COSOPT Assembly Line does the following:
- Converts expression data into COSOPT input files
- Runs COSOPT
- Converts COSOPT output into a more user-friendly format
## COSOPT Requires Wine or Windows
Although [COSOPT was written by Marty Straume](http://www.ncbi.nlm.nih.gov/pubmed/15063650) to run on Microsoft Windows, it can be run on OS X, Linux, etc. using [Wine](https://wiki.winehq.org/Main_Page). To install Wine on OS X, I recommend [David Baumgold's Wine installation tutorial](http://www.davidbaumgold.com/tutorials/wine-mac/).
## Input File Format
The input file for COSOPT Assembly Line should be tab-delimited and have gene expression counts organized as in the [sample input file](sample-run/counts.tsv).
## How To Run COSOPT Assembly Line
To get the COSOPT Assembly Line up and running, set the parameters and run the following code on the command line.
```sh
# When setting these variables, do not use blank spaces (e.g., OUT_DIR=my-output-directory)
OUT_DIR= # Path to the output directory
COUNT_FILE_IN= # Path to the tab-delimited counts file to be used for input
COSOPT_OUT_FILE= # Output path and filename (will be tab-delimited)
BIN_DIR= # Path to 'cosopt-formatter.pl' (e.g., BIN_DIR=COSOPT-Assembly-Line/bin)
$BIN_DIR/cosopt-formatter.pl -o $OUT_DIR $COUNT_FILE_IN
cd $OUT_DIR
wine cmd /c doit.bat > cosopt.log 2> cosopt.err
$BIN_DIR/cosopt-deformatter.pl session.op4 $COSOPT_OUT_FILE
```
For improved reproducibility and workflow documentation, you can save the above (with variables defined) to a file and run the commands directly from that file in the command line using `source`. For example:
```sh
source my-cosopt-run.2016-02-23
```
*Note: COSOPT is not the fastest program; on my laptop, it took me nearly 6 hours to analyze data from 42,128 genes with 23 timepoints in triplicate.*
## Custom Period Length Parameters
By default, `cosopt-formatter.pl` looks for rhythmic gene expression with periods from 20 to 28 hours at 0.1 hour increments. These parameters can be customized. For example, the following would be used to identify for genes with periods from 22 to 26 hours at 0.5 hour increments:
```sh
perl cosopt-formatter.pl --period_min 22 --period_max 26 --period_inc 0.5 -o $OUT_DIR $COUNT_FILE_IN
```