- Project components:
hybkit toolkit of command-line utilities for manipulating, analyzing, and plotting hyb-format data.
The hybkit python API, an extendable documented codebase for creation of custom analyses of hyb-format data.
Example analysis pipelines for analysis of publicly available qCLASH hybrid sequence data implemented either with toolkit scripts or the hybkit Python API.
- Hybkit Toolkit:
The hybkit toolkit includes several command-line utilities for manipulation of “.hyb” format data:
Parse a hyb file and check for errors
Evaluate hyb records to identify segment types and miRNAs
Filter a hyb file to a specific subset of sequences
Perform a type, miRNA, summary, or target analysis on a hyb file
Filter a fold file using an exclusion table created by hyb_filter
Perform a fold analysis on a hyb and a RNA secondary structure (fold) file in “.vienna” or “.ct” format on a hyb file
These scripts are used on the command line with hyb files. For example, to filter a hyb file to contain only hybrids with a sequence identifier containing the string “kshv”
$ hyb_filter -i my_hyb_file.hyb --filter any_seg_contains kshv
- Hybkit API:
Hybkit provides a Python3 module with a documented API for interacting with records in hyb files. This capability was inspired by the BioPython Project. The primary utility is provided by classes for hyb records (HybRecord), classes for fold records (FoldRecord, DynamicFoldRecord), and file-iterator classes (HybFile, ViennaFile, CTFile). Record attributes can be analyzed, set, and evaluated using included class methods.
For example, a workflow to print the identifiers of only sequences within a “.hyb” file that contain a miRNA can be performed as such:
#!/usr/bin/env python3 import hybkit in_file = '/path/to/my_hyb_file.hyb' # Open a hyb file as a HybFile Object: with hybkit.HybFile.open(in_file, 'r') as hyb_file: # Return each line in a hyb file as a HybRecord object for hyb_record in hyb_file: # Analyze each record to assign segment types hyb_record.eval_types() # If the record contains a long noncoding RNA type, print the record identifier. if hyb_record.has_prop('any_seg_type_contains', 'lncRNA') print(hyb_record.id)
Hybkit provides several example pipelines for analysis of “hyb” data using the utilities provided in the toolkit. These include:
Quantify the sequence and miRNA types in a hyb file
Analyze targets of a set of miRNAs from a single experiment
Grouped Target Analysis
Analyze and plot targets of a set of miRNAs from pooled experimental replicates
Analyze and plot predicted miRNA folding patterns in miRNA-containing hybrids
These pipelines provide analysis results in both tabular and graph form. As an illustration, the example summary analysis includes the return of the contained hybrid sequence types as both a csv table and as a pie chart:
$ pip install hybkit
Acquisition of the package can also be performed by cloning the project’s Github repository:
$ git clone git://github.com/RenneLab/hybkit
Or by downloading the zipped package:
$ curl -OL https://github.com/dstrib/hybkit/archive/master.zip $ unzip master.zip
Followed by installation using python’s setuptools:
$ python setup.py install
Further documentation on hybkit usage can be found in this documentation.
- hybkit is a free, sharable, open-source project.All source code and executable scripts contained within this package are considered part of the “hybkit” project and are distributed without any warranty or implied warranty under the GNU General Public License v3.0 or any later version, described in the “LICENSE” file.
- hybkit Hyb File Specification
- hybkit Toolkit
- Example Pipelines
- hybkit API