Metadata-Version: 2.1
Name: simplebitk
Version: 0.0.1a0
Summary: A bioinformatics tools kit
Home-page: https://github.com/btrspg/simplebitk/tree/master/
Author: Yuelong CHEN
Author-email: yuelong.chen.btr@gmail.com
License: Apache Software License 2.0
Description: # BioInformatics Tools kit
        > Summarized some useful tools in it.
        
        
        BITK will help us manipulate data in different formats.
        
        ## Install
        
        `pip install bitk`
        
        ## How to use
        
        ### dedim.py
        
        
        
        ```bash
        usage: dedim.py [-h] [--sep SEP] [--dedimensions-method DEDIMENSIONS_METHOD]
                        [--cluster-method CLUSTER_METHOD]
                        [--assess-method ASSESS_METHOD] [--dimensions DIMENSIONS]
                        [--cluster-number CLUSTER_NUMBER] [-r] [--no-row-feature]
                        [--annotation ANNOTATION] [--size SIZE] [--style STYLE]
                        [-t TITLE] [-f FIG] [--version]
                        matrix prefix
        
        positional arguments:
          matrix                matrix table, if row represents feature, please note to add '--row-feature' option
          prefix                output prefix
        
        optional arguments:
          -h, --help            show this help message and exit
          --sep SEP             separation
                                (default: 	)
          --dedimensions-method DEDIMENSIONS_METHOD
                                de-dimensions method
                                (default: PCA)
          --cluster-method CLUSTER_METHOD
                                cluster method
                                (default: MiniBatchKMeans)
          --assess-method ASSESS_METHOD
                                assess methods for best cluster number
                                (default: silhouette_score)
          --dimensions DIMENSIONS
                                reduce to n dimensions
                                (default: 3)
          --cluster-number CLUSTER_NUMBER
                                cluster number, if not specific it, it will be the best cluster number infered
                                (default: None)
          -r, --row-feature     row in the matrix represents feature
                                (default: True)
          --no-row-feature
          --annotation ANNOTATION
                                annotation file, sep should be ','
                                (default: None)
          --size SIZE           size column in annotation file
                                (default: None)
          --style STYLE         style column in annotation file
                                (default: None)
          -t TITLE, --title TITLE
                                figure title
                                (default: None)
          -f FIG, --fig FIG     png/pdf
                                (default: png)
          --version             show program's version number and exit
        ```
        
        
        
        #### example
        
        ```bash
        dedim.py tests/test.csv tests/test_result \
                --sep , --dimensions 2 \
                --no-row-feature --annotation tests/test_anno.csv \
                --style targets --title 'test PCA' \
                --dedimensions-method TSNE --fig png
        ```
        
        ![pca](tests/test_result_TSNE.png)
        
        ### fc_rename.py
        
        ```
        usage: fc_rename.py [-h] [-s SAMPLE_TITLE] [-b BAM_TITLE] [-c COUNT_TITLE]
                            [--version]
                            featurecounts clinical prefix
        
        featurecounts will use the bamfile name as the sample name. This script rename the featurecounts by the given table.
        
        positional arguments:
          featurecounts         featurecounts table file
          clinical              clinical table file with header
          prefix                output prefix, there will be two outputs, one is count output (prefix_count.txt), and the other one is the rename featurecounts (prefix_fc.txt)
        
        optional arguments:
          -h, --help            show this help message and exit
          -s SAMPLE_TITLE, --sample-title SAMPLE_TITLE
                                the column name of the sample name
                                (default: sample)
          -b BAM_TITLE, --bam-title BAM_TITLE
                                the column name of the bamfile name
                                (default: bam)
          -c COUNT_TITLE, --count-title COUNT_TITLE
                                the column name used as identity in count data
                                (default: Geneid)
          --version             show program's version number and exit
        ```
        
Keywords: biology bioinformatics
Platform: UNKNOWN
Classifier: Development Status :: 2 - Pre-Alpha
Classifier: Intended Audience :: Developers
Classifier: License :: OSI Approved :: Apache Software License
Classifier: Natural Language :: English
Classifier: Programming Language :: Python :: 3.6
Classifier: Programming Language :: Python :: 3.7
Classifier: Programming Language :: Python :: 3.8
Requires-Python: >=3.6
Description-Content-Type: text/markdown
