Tiny FASTA package, without dependencies, for processing biological sequence files.
TinyFasta is a Python package for parsing biological sequences from FASTA files.
There are already several Python packages available for parsing FASTA files. However, many of these packages do much more than just parse FASTA files and as such have dependencies on NumPy and SciPy . These are quite heavy weight dependencies if all you want to do is a little bit of text processing. This is where TinyFasta fits in. It is a lightweight Python package with no dependencies outside of the Python standard library.
To install the TinyFasta package:
sudo pip install tinyfasta
To parse a FASTA file:
>>> from tinyfasta import FastaParser >>> for fasta_record in FastaParser("tests/data/dummy.fasta"): ... if fasta_record.description.contains('seq1'): ... print(fasta_record) ... >seq1|contains 2x78 A's AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
To create a FASTA record:
>>> from tinyfasta import FastaRecord >>> sequence = "C" * 100 >>> fasta_record = FastaRecord.create("My Sequence", sequence) >>> print(fasta_record) >My Sequence CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC CCCCCCCCCCCCCCCCCCCC
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