Colelyman

#!/bin/sh

TEMP_BIB_PATH=".mybib.bib"
TEMP_MD_PATH=".mybib.md"
TEMP_CITATION_PATH=".mycitation.md"

clean() {
    rm -rf $TEMP_BIB_PATH $TEMP_MD_PATH $TEMP_CITATION_PATH
}

Colelyman

"""Discover an Eulerian Cycle from a graph."""

import argparse
from typing import Dict, List


def construct_graph_from_adjacency(
    graph_file_path: str,
) -> Dict[str, List[str]]:
    """Construct a graph from an adjacency list in `graph_file_path`.

Colelyman

"""Discover an Eulerian Path from a graph."""

import argparse
from collections import Counter
from typing import Dict, List, Optional


def construct_graph_from_adjacency(
    graph_file_path: str,
) -> Dict[str, List[str]]:

Colelyman

import random

simulate_deletion_lens = range(30) #deletions to simulate - here, 0 to 30bp deletions. The longer the deletion, the more adapter will be included in the read
simulate_mismatch_counts = range(3) #number of mismatches to simulate - her, 0, 1, and 2 mismatches between r1 and r2. The higher the number of mismatches, the less likely the read will be merged.
read_len = 210 #length of reads to generate

read        = '                                 CGGATGTTCCAATCAGTACGCAGAGAGTCGCCGTCTCCAAGGTGAAAGCGGAAGTAGGGCCTTCGCGCACCTCATGGAATCCCTTCTGCAGCACCTGGATCGCTTTTCCGAGCTTCTGGCGGTCTCAAGCACTACCTACGTCAGCACCTGGGACCCCGCCACCGTGCGCCGGGCCTTGCAGTGGGCGCGCTACCTGCGCCACATCCATCGGCGCTTTGGTCGG                                 '
readthrough = 'ACACTCTTTCCCTACACGACGCTCTTCCGATCTCGGATGTTCCAATCAGTACGCAGAGAGTCGCCGTCTCCAAGGTGAAAGCGGAAGTAGGGCCTTCGCGCACCTCATGGAATCCCTTCTGCAGCACCTGGATCGCTTTTCCGAGCTTCTGGCGGTCTCAAGCACTACCTACGTCAGCACCTGGGACCCCGCCACCGTGCGCCGGGCCTTGCAGTGGGCGCGCTACCTGCGCCACATCCATCGGCGCTTTGGTCGGAGATCGGAAGAGCACACGTCTGAACTCCAGTC

Colelyman

"""Report the quantification window indexes used from a CRISPResso run.

The script expects to be adjacent to any number of CRISPResso runs, it will
search among the runs and extract each CRISPResso2_info.json file and print
out the quantification windows for each amplicon.
"""
import glob
import json

Colelyman

Pi Coding Agent Extensions

Custom extensions for pi, a CLI coding agent.

Directory Structure

Place these files in ~/.pi/agent/extensions/:

~/.pi/agent/extensions/