Tasks

OpenVariant is a package that can perform different functionalities with multiple files as an input. In this section we will describe the tasks that can be executed with this library. If you want a more practical demo or some possible use of cases, check Examples section.

Find files

From a base path (directory or file) it will generate an iterator that will throw all the input files and its corresponding annotation file that matches the pattern parameter.

This is can be useful to make sure which annotation file can correspond on each input file and then each file can be parsed through Variant task. Check Find files examples for more cases.

# Example
from openvariant import find_files

for file, annotation in find_files("datasets/"):
    print(f"File path: {file} - Annotation object: {annotation}")

Variant

Allow us to parse an input file through the annotation file. It will generate an object which you can apply different functionalities. Here, there is an example, but for further details and more in-depth understanding of each functionality, check Variant examples.

# Example
from openvariant import Annotation, Variant

file_path = "./indexes.tsv"
annotation = Annotation("./metadata.yaml")
result = Variant(file_path, annotation)
for line in result.read():
    print(f"Line in a dict: {line}")

Cat

It will show on the stdout (standard out) the whole parsed output. This task can be also executed with Command-line interface (CLI). Check, Cat examples in Tasks examples for more cases.

# Example
from openvariant.tasks import cat

file_path = "./indexes.tsv"
annotation_path = "./metadata.yaml"

cat(file_path, annotation_path)

Group by

It will generate an iterator that will throw three variables: group_key (the value of each group), group_result (a list of all rows that pertain to each group) and command (if it uses the script parameter or not). It will group the parsed result for each different value of the specified key_by. For further details, check out the Group by examples in Tasks examples.

# Example
from openvariant.tasks import group_by

file_path = "./indexes.tsv"
annotation_path = "./metadata.yaml"

for group_key, group_result, command in group_by(file_path, annotation_path, script=None, key_by='COUNTRY'):
    for r in group_result:
        print(f"{group_key}\t{r}")

Count

It returns the number of rows that matches a specific conditions. You can see more examples in this section: Count examples in Tasks examples.

# Example
from openvariant.tasks import count

file_path = "./indexes.tsv"
annotation_path = "./metadata.yaml"

result = count(file_path, annotation_path)
print(result)

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Annotation structure

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Command-line interface (CLI)