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finswimmer / discord
Created August 12, 2020 16:41
Hello Python Discord
@finswimmer
finswimmer / pyproject.toml
Created September 18, 2019 06:44
[tool.poetry]
name = "issue"
version = "0.1.0"
description = ""
authors = ["Fin Swimmer"]
exclude = ["issue/exclude_me.py"]
[tool.poetry.dependencies]
python = "^3.6"
@finswimmer
finswimmer / Snakefile_UMI
Created August 16, 2019 05:34
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 / triplets_hg38.tsv
Last active June 18, 2019 03:51
kmer count
AAA 72422544
AAC 43498931
AAG 58395299
AAT 72538809
ACA 54592537
ACC 33744272
ACG 7570315
ACT 47439444
AGA 60011989
@finswimmer
finswimmer / default.py
Last active December 22, 2018 13:53
boilerplate to create new scripts, that can read and write from stream and/or filename
#!/usr/bin/env python
# -*- coding: utf-8 -*-
from __future__ import print_function
import sys
from argparse import ArgumentParser
def main():
args = get_args()
@finswimmer
finswimmer / Snakefile_advanced
Created September 3, 2018 13:12
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
finswimmer / Snakefile_basic
Created September 3, 2018 13:10
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
finswimmer / phylip.py
Created July 12, 2018 09:02
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
finswimmer / prefixes.txt
Created June 30, 2018 05:35
Ensembl stable ID species prefixes
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
finswimmer / compare_v2.py
Created June 18, 2018 12:37
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)