harryscholes

# Copy SSH keys to remote server for passwordless login
ssh-copy-id <username>@<remote.server>
ssh -XY <username>@<remote.server>

# Additionally add this to ~/.ssh/config file
Host <name>
  User <username_on_remote_server>
  HostName <remote.server>
  proxyCommand ssh -W <remote.server>:22 <username>@<login.server>
  

harryscholes

import pandas as pd

BLAST_output_file = ""  # set to the path of the BLAST output file
df = pd.read_csv(BLAST_output_file,
                 sep="\t",
                 header=None,
                 names=["query_id", "subject_id", "pct_identity", "aln_length", "n_of_mismatches",
                        "gap_openings", "q_start", "q_end", "s_start", "s_end", "e_value", "bit_score"])

harryscholes

codes = ["EXP", "IDA", "IPI", "IMP", "IGI", "IEP",  # experimental
         "ISS", "ISO", "ISA", "ISM", "IGC", "IBA", "IBD", "IKR", "IRD", "RCA", "IC", "TAS",  # curated
         "IEA"]  # automatically-assigned

harryscholes

from scipy import sparse

# generate a random sparse matrix
M = sparse.random(100,100)
M

      # <100x100 sparse matrix of type '<class 'numpy.float64'>'
      #	with 100 stored elements in COOrdinate format>

# create boolean array of the data stord in the sparse matrix

harryscholes

# dependencies: conda, autoenv
# cd into dir containing environment.yml file and run: conda env create
# save this gist to file named .env in the dir
# run: source /usr/local/opt/autoenv/activate.sh

# set to the name of the Anaconda environment contained in environment.yml
venv=


# get the current environment

harryscholes

organism=spo

# Download S. pombe KEGG pathways
wget -O kegg_pathways.tsv http://rest.kegg.jp/list/pathway/${organism}

ids=$(cut -f1 kegg_pathways.tsv)
for id in $ids; do
    wget -O ${id}.json http://togows.dbcls.jp/entry/pathway/${id}/genes.json
done

harryscholes

## e.g. for NetworkX (https://github.com/networkx/networkx/blob/master/CONTRIBUTE.rst)

## set up repo

# fork repo on GitHub
cd ~/git
git clone git@github.com:harryscholes/networkx.git
cd networkx
git remote add upstream git@github.com:networkx/networkx.git
git checkout master

harryscholes

import string, secrets

pool = list(string.ascii_uppercase[:] + str(9))
seed = "".join(secrets.choice(pool) for _ in range(81))

harryscholes

# set these to the name of the markdown file exported from Dropbox Paper and the desired name of the LaTeX file
MARKDOWN_FILE=
LATEX_FILE=

# Dropbox uses '$$' for markdown math, so this must be replaced with '$'
sed -i '' -e 's/\$\$/\$/g' $MARKDOWN_FILE

# convert markdown to LaTeX
pandoc $MARKDOWN_FILE -f markdown -t latex -o $LATEX_FILE --mathjax --top-level-division=chapter --wrap=none

harryscholes

class Meta(type):
    """
    Flexible metaclass for defining useful decorator functions.
    """
    def __new__(cls, clsname, bases, clsdict):
        clsobj = super().__new__(cls, clsname, bases, clsdict)
        return clsobj


class Base(object, metaclass=Meta):