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توضیحات

I/O and utilities for the Consensus Multiple Alignment (CMA) file format.

ویژگی	مقدار
سیستم عامل	-
نام فایل	biocma-0.2.1
نام	biocma
نسخه کتابخانه	0.2.1
نگهدارنده	[]
ایمیل نگهدارنده	[]
نویسنده	Eric Talevich
ایمیل نویسنده	eric.talevich@gmail.com
آدرس صفحه اصلی	http://github.com/etal/biocma
آدرس اینترنتی	https://pypi.org/project/biocma/
مجوز	UNKNOWN

BioCMA ====== Consensus Multiple Alignment format, using Biopython alignments. I/O support and relevant functionality for the Consensus Alignment Format (CMA). This format represents protein sequence alignments. It is used by a few tools by Dr. Andrew F. Neuwald, notably CHAIN_ and MAPGAPS_. .. _CHAIN: http://chain.igs.umaryland.edu/ .. _MAPGAPS: http://mapgaps.igs.umaryland.edu/ Biopython objects and conventions are used where possible. Installation ------------ This is an ordinary Python package. You can install it from source with the setup.py script:: python setup.py build python setup.py install Stable releases are uploaded to PyPI as well, so you can install BioFrills with Python package managers:: pip install biofrills Or:: easy_install biofrills Some scripts that I find useful are in the scripts/ directory. By default these are not installed, but you can include them by uncommenting the line in setup.py that starts with ``scripts=glob``... Alternatively, you can just copy those scripts into another directory in your ``$PATH``. What can the CMA format do for me? ---------------------------------- - Like the A2M and Stockholm formats, alignments are shown with insertions as lowercase characters and deletions are dashes - Like the A3M format, alignments are pairwise versus a profile (or "consensus" sequence), which also dictates which sites are indels. By compressing the insert columns, a large of alignment of many divergent (but related) sequences can be shown without filling it will mostly gap characters, as Stockholm can. - Like Stockholm, but unlike A2M and A3M, more than one alignment can be contained in a single file. - Typically, an ungapped consensus sequence will be included as the first sequence. - A FASTA-like header contains additional, optional fields for the number of leading and trailing sites and NBCI taxonomy codes Who uses CMA? ------------- The CMA format appears to have been invented by Dr. Andrew Neuwald at the University of Maryland, and is used in these programs: - MAPGAPS: http://mapgaps.igs.umaryland.edu/ - CHAIN: http://chain.igs.umaryland.edu/ Should I use CMA in my own work? -------------------------------- Unless you're working with MAPGAPS or CHAIN, no.

نحوه نصب

نصب پکیج whl biocma-0.2.1:

pip install biocma-0.2.1.whl

نصب پکیج tar.gz biocma-0.2.1:

pip install biocma-0.2.1.tar.gz