ggirelli / fastx-barber Goto Github PK

Describe the bug
Running e.g., time fbarber extract input.test.fastq test.trimmed.fastq.gz will write uncompressed output to test.trimmed.fastq.gz, as the input (input.test.fastq) is not gzipped. The output should be correctly compressed instead or the .gz extension should be dropped.

For all scripts.

Related to #38.

SAMtags specs: https://raw.githubusercontent.com/samtools/hts-specs/master/SAMtags.pdf
SAMv1 specs: https://raw.githubusercontent.com/samtools/hts-specs/master/SAMv1.pdf

To speed up in cases in which no perfect match is needed and the flag length is fixed, use a pattern format constituting of single-char flag names and flag lengths, e.g., "U8B8C4", indicating a "U" flag of 8, a "B" flag of 8, and a "C" flag of 4 chars, respectively, with the pattern placed at the start of the sequence.

Modes: extract, extract & trim, trim, none

Description

An abstract class with abc.ABCMeta as metaclass has abstract methods and is instantiated. This will result in a TypeError as Python can't instantiate abstract class with abstract methods.

Occurrences

There are 3 occurrences of this issue in the repository.

See all occurrences on DeepSource → deepsource.io/gh/ggirelli/fastx-barber/issue/PYL-E0110/occurrences/

Description

An unused variable takes up space in the code, and can lead to confusion, and it should be removed. If this variable is necessary, name the variable _ to indicate that it will be unused, or start the name with unused or _unused.

Occurrences

There are 33 occurrences of this issue in the repository.

See all occurrences on DeepSource → deepsource.io/gh/ggirelli/fastx-barber/issue/PYL-W0612/occurrences/

In fqdedup style

Is your feature request related to a problem? Please describe.
Generate summary of extracted flag values (frequency). Also make separate script that runs on fastx files with extracted flag values.

Description

A private attribute defined in the class should be only accessible inside the class. The names of attributes which are supposed to be public should not start with _ or __.

Occurrences

There is 1 occurrence of this issue in the repository.

See all occurrences on DeepSource → deepsource.io/gh/ggirelli/fastx-barber/issue/PTC-W0037/occurrences/

Description

Do not use a mutable like list or dictionary as a default value to an argument. Python’s default arguments are evaluated once when the function is defined. Using a mutable default argument and mutating it will mutate that object for all future calls to the function as well.

Occurrences

There is 1 occurrence of this issue in the repository.

See all occurrences on DeepSource → deepsource.io/gh/ggirelli/fastx-barber/issue/PYL-W0102/occurrences/

https://github.com/willmcgugan/rich
https://rich.readthedocs.io/en/latest/logging.html

Allow to split output based on the value of selected flags.

Description

It is customary for instance or class methods to take self or cls, respectively, as their first arguments, a method that uses either of these names but is found to be a static method may have been defined incorrectly. Choose names other than self or cls for arguments to avoid …

Occurrences

There is 1 occurrence of this issue in the repository.

See all occurrences on DeepSource → deepsource.io/gh/ggirelli/fastx-barber/issue/PYL-W0211/occurrences/

Is your feature request related to a problem? Please describe.
A clear and concise description of what the problem is. Ex. I'm always frustrated when [...]

Describe the solution you'd like
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Describe alternatives you've considered
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Additional context
Add any other context or screenshots about the feature request here.

Evaluate flag value to identify the most represented one(s) and suggest value(s) and mismatch filter.

Basically, use the flag (barcode) value frequency and the expected N number of flag values, to select the top N barcodes and suggest also a number of allowed mismatches.

Should we require also a minimum edit distance between the original sequences or expected minimum distance?

Both as a separate script, and natively with the extractcommand.

I have a bunch of Bioinformatics students looking to get involved, I remember in the past people were trying stuff here but with the new rules of projects having to opt in I am not sure if fastx-barber was flagged for people to help out

Description

An unused argument can lead to confusions. It should be removed. If this variable is necessary, name the variable _ or start the name with unused or _unused.

Occurrences

There are 5 occurrences of this issue in the repository.

See all occurrences on DeepSource → deepsource.io/gh/ggirelli/fastx-barber/issue/PYL-W0613/occurrences/

For all scripts.

Description

It is recommended to name the first argument of a classmethod as cls so that it's easy to differentiate them from regular instance methods.

Occurrences

There are 2 occurrences of this issue in the repository.

See all occurrences on DeepSource → deepsource.io/gh/ggirelli/fastx-barber/issue/PYL-C0202/occurrences/

Address the following:

./fastx_barber/scripts/extract.py:133:1: C901 'run_chunk' is too complex (7)
./fastx_barber/scripts/common.py:177:14: F541 f-string is missing placeholders
./fastx_barber/scripts/common.py:187:14: F541 f-string is missing placeholders

Writing unit tests after the code is a pain, but I guess this is what lazy asses deserve... 😢

The current approach of saving quality flag string portions by appending a "q" prefix to the flag name is prone to flag name conflicts. Instead, the qual string could be saved as a third flag value by moving from key/value to key/value[/qual] format and updating the FlagReader class accordingly.