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توضیحات

A package to count the number of repeats in a Short Tandem Repeat Expansion from long reads.

ویژگی	مقدار
سیستم عامل	OS Independent
نام فایل	STRcount-0.1.1
نام	STRcount
نسخه کتابخانه	0.1.1
نگهدارنده	[]
ایمیل نگهدارنده	[]
نویسنده	Sabiq Chaudhary
ایمیل نویسنده	<sabiq.work@gmail.com>
آدرس صفحه اصلی	-
آدرس اینترنتی	https://pypi.org/project/STRcount/
مجوز	-

# STRcount Software tool to analyse STR loci from long read data. STRcount can count the number of repeats in a repeat expansion and give you the count in a tabular format for further downstream analysis. ## Release notes * 0.1.0: Initial release with tools updated on Pypi and ready to use. ## Dependencies Developed and tested on Python 3.7.10. Dependencies include: * [GraphAligner](https://github.com/maickrau/GraphAligner) * [Pysam](https://github.com/pysam-developers/pysam) ## Installation instructions ### Install GraphAligner STRcount requires and uses GraphAligner as it's alignment tool. To install this you could either install it using Anaconda: * Install miniconda https://conda.io/projects/conda/en/latest/user-guide/install/index.html * ```conda install -c bioconda graphaligner``` Or you could install it from source using the instructions [here](https://github.com/maickrau/GraphAligner#compilation) ### Installation using pip Use the following command to install STRcount and all dependencies: ``` pip install STRcount ``` ### Installation from source ``` git clone https://github.com/sabiqali/strcount.git cd strcount python setup.py install ``` ### Installation to develop To develop using STRcount, you will need to create a conda environment or python virtual environment, then perform the following steps: ``` git clone https://github.com/sabiqali/strcount.git cd strcount python -m pip install -r requirements.txt python src/STRcount/STRcount.py -h ``` ## Config file format The config file should be in the following format: | chr | begin | end | name | repeat | prefix | suffix | | --- | --- | --- | --- | --- | --- | --- | | chr9 | 27573527 | 27573544 | c9orf72 | GGCCCC | <150bp_left_flank> | <150bp_right_flank> | ## Usage If installed using pip or from source, you will be able to use it using ```STRcount``` else if you have installed to develop, you will be able to use it using ```python src/STRcount/STRcount.py``` ``` STRcount [-h] --reference REFERENCE --fastq FASTQ --config CONFIG --output OUTPUT [--min-identity MIN_IDENTITY] [--min-aligned-fraction MIN_ALIGNED_FRACTION] [--write-non-spanned] [--repeat_orientation REPEAT_ORIENTATION] [--prefix_orientation PREFIX_ORIENTATION] [--suffix_orientation SUFFIX_ORIENTATION] [--cleanup CLEANUP] [--output_directory OUTPUT_DIRECTORY] [--multiseed-DP MULTISEED_DP] [--precise-clipping PRECISE_CLIPPING] optional arguments: -h, --help show this help message and exit --reference REFERENCE the reference from which the STR Graph will be generated --fastq FASTQ the baseaclled reads in fastq format --config CONFIG the config file --output OUTPUT the output file --min-identity MIN_IDENTITY only use reads with identity greater than this --min-aligned-fraction MIN_ALIGNED_FRACTION require alignments cover this proportion of the query sequence --write-non-spanned do not require the reads to span the prefix/suffix region --repeat_orientation REPEAT_ORIENTATION the orientation of the repeat string. + or - --prefix_orientation PREFIX_ORIENTATION the orientation of the prefix, + or - --suffix_orientation SUFFIX_ORIENTATION the orientation of the suffix, + or - --cleanup CLEANUP do you want to clean up the temporary file? --output_directory OUTPUT_DIRECTORY the output directory for all output and temporary files --multiseed-DP MULTISEED_DP Aligner option --precise-clipping PRECISE_CLIPPING Aligner option: use arg as the identity threshold for a valid alignment. ``` ## Output The output is in a ```.tsv``` format that will look something like this: | read_name | strand | spanned | count | align_score | identity | query_aligned_fraction | | --- | --- | --- | --- | --- | --- | --- | * read_name: The name of the read that is currently being proccessed * strand: The strand on which the primary alignment has been detected * spanned: If set to 1, it means that the read spanned the repeat locus and the flanking sequence * count: The number of repeat motifs detected at the locus for that particular read * align_score: The alignment score as given by GraphAligner * identity: The percentage identity as given by GraphAligner * query_aligned_fraction: This signifies how much of the query sequence is covered by the alignment ## Contact [Sabiq Chaudhary](mailto:schaudhary@oicr.on.ca) ## License ```MIT```

نیازمندی

مقدار	نام
-	pysam

نحوه نصب

نصب پکیج whl STRcount-0.1.1:

pip install STRcount-0.1.1.whl

نصب پکیج tar.gz STRcount-0.1.1:

pip install STRcount-0.1.1.tar.gz