apcamargo

#!/usr/bin/env python

"""
This script processes SAM (Sequence Alignment/Map format) inputs from standard
input and extracts alignment information that is then provided in a tab-separated
table. The following fields are produced: query, target, query_length, query_start,
query_end, target_start, target_end, alignment_length, alignment_identity.

This script was designed for use with SAM files produced by minimap2. However,
it will work with any SAM data that:

apcamargo

from pathlib import Path
from typing import Iterator, Optional, Union

import polars as pl
from needletail import parse_fastx_file
from polars.io.plugins import register_io_source


def scan_fastx(fastx_file: Union[str, Path]) -> pl.LazyFrame:
    schema = pl.Schema(

apcamargo

#!/usr/bin/env python

import json
import re
import sys
from typing import Generator, Dict, Any, Optional

import requests
from tqdm import tqdm

apcamargo

duckdb -c "
INSTALL httpfs;
LOAD httpfs;
INSTALL parquet;
LOAD parquet;
COPY (
  SELECT *
  FROM read_parquet('s3://sra-pub-metadata-us-east-1/sra/metadata/*')
) TO STDOUT WITH (FORMAT CSV, DELIMITER E'\t', HEADER);"

apcamargo

from typing import Sequence
import math


def find_cutoff(values: Sequence[float]) -> float:
    """
    Determine the cutoff point in a biphasic distribution curve by identifying
    the "bending point" where the curve transitions from slowly growing values 
    to rapidly growing values, using the maximum perpendicular distance method.

apcamargo

#!/usr/bin/env python

import shutil
from pathlib import Path
from typing import Literal

import pyarrow as pa
import pyarrow.parquet as pq