kronopt / fastaparser Goto Github PK

Is your feature request related to a problem?
Sometimes warnings are unnecessary.

Describe the solution you'd like
Implement a way to disable warnings without having to implicitly import the warnings package outside of FastaParser.
Maybe add a new parameter to all classes specifying if warnings should be disabled or not (defaulting to 'No')

conda build is failing to build FastaParser v1.1 because it can't find the docs/history.md file when running setup.py.
Because it installs the package directly from pypi instead of the local package, I would have to release a new version of FastaParser without the use of history.md for it to build properly...

Unless there's another solution, which I haven't found yet.

Is your feature request related to a problem?
FastaSequence.id should provide more information on the id.
Most FASTA id's are standard and should, therefore, be easy to parse.

Sources:
https://en.wikipedia.org/wiki/FASTA_format#NCBI_identifiers
https://ncbi.github.io/cxx-toolkit/pages/ch_demo#ch_demo.id1_fetch.html_ref_fasta

Describe the solution you'd like
Implement a new class FastaId which should describe a certain FASTA id.
Instances of FastaId should be returned when calling FastaSequence.id

Is your feature request related to a problem?
FASTQ is as popular as FASTA.
FASTQ has a specification, as described here:
https://en.wikipedia.org/wiki/FASTQ_format
http://maq.sourceforge.net/fastq.shtml

Describe the solution you'd like
Implement a FASTQ parser/writer

Is your feature request related to a problem?
FastaParser's id and description properties are read only.

Describe the solution you'd like
It might make sense to implement a setter for both properties.
A user might want to make changes to the id or description.

Is your feature request related to a problem?
Right now warnings are only shown when calling complement (FastaSequence and LetterCode), at_gc_ratio or gc_content (FastaSequence) methods.
No warning is shown when a sequence has characters not defined in the FASTA specification.

Describe the solution you'd like
It might make sense to show a warning if a sequence has at least a single character not defined in the FASTA specification.