finswimmer

Hello Python Discord

finswimmer

[tool.poetry]
name = "issue"
version = "0.1.0"
description = ""
authors = ["Fin Swimmer"]
exclude = ["issue/exclude_me.py"]

[tool.poetry.dependencies]
python = "^3.6"

finswimmer

rule target:
    input:
        bam = "SRR7526729_realigned.bam",
        index = "SRR7526729_realigned.bam.bai"

rule umi_extract:
    input:
        R1 = "../{sample}_1.fastq.gz",
        R2 = "../{sample}_2.fastq.gz"
    output:

finswimmer

finswimmer

#!/usr/bin/env python
# -*- coding: utf-8 -*-
from __future__ import print_function
import sys
from argparse import ArgumentParser


def main():
    args = get_args()

finswimmer

configfile:
    "config.json"

SAMPLES, = glob_wildcards(config['data']+"/{id}_L001_R1_001.fastq.gz")

rule move:
    input:
        bam = expand("{sample}.final.bam", sample=SAMPLES),
        bai = expand("{sample}.final.bai", sample=SAMPLES)
    params:

finswimmer

configfile:
    "config.json"

SAMPLES, = glob_wildcards(config['data']+"/{id}_L001_R1_001.fastq.gz")

rule move:
    input:
        bam = expand("{sample}.final.bam", sample=SAMPLES),
        bai = expand("{sample}.final.bai", sample=SAMPLES)
    params:

finswimmer

from Bio import AlignIO


def column(alignment):
    '''Generator for getting list of characters in each column in the alignment'''
    for i in range(alignment.get_alignment_length()):
        c = []

        for record in alignment:
            c.append(record.seq[i])

finswimmer

ENSPFO	Poecilia formosa (Amazon molly)
ENSJJA	Jaculus jaculus (Lesser Egyptian jerboa)
ENSPCO	Propithecus coquereli (Coquerel's sifaka)
ENSNGA	Nannospalax galili (Upper Galilee mountains blind mole rat)
ENSMFA	Macaca fascicularis (Crab-eating macaque)
ENSMIC	Microcebus murinus (Mouse Lemur)
MGP_CAROLIEiJ_	Mus caroli (Ryukyu mouse)
ENSFAL	Ficedula albicollis (Flycatcher)
ENSCLA	Chinchilla lanigera (Long-tailed chinchilla)
ENSPEM	Peromyscus maniculatus bairdii (Northern American deer mouse)

finswimmer

import sys
from Bio import SeqIO


def mismatch(seq1, seq2):
    index = []

    for i, (s1, s2) in enumerate(zip(seq1, seq2)):
        if s1 != s2:
            index.append(i)