terrycojones

$ echo $i

$ set i aaaxy
$ echo $i
untrackedfiles
$ echo $FISH_VERSION
2.7.1-1829-g742fde0d

# Whereas:

terrycojones

from gor4 import GOR4

_GOR4 = None

def predictions(sequence):
  global _GOR4
  if _GOR4 is None:
    _GOR4 = GOR4()
  return _GOR4.predict(sequence)['predictions']

terrycojones

"My dear fellow," Burlingame said caustically, "we sit on a blind rock
careening through space; we are all of us rushing headlong to the
grave. Think you the worms will care, when anon they make a meal of
you, whether you spent your moment sighing wigless in your chamber, or
sacked the golden towns of Montezuma? Lookee, the day's nigh spent;
'tis gone careening into time forever. Not a tale's length since we
lined our bowels with dinner, and already they growl for more. We are
dying men Ebenezer: i'faith, there's time for nought but bold
resolves!"

terrycojones

ls summary-proteins-* | \
proteins-to-pathogens.py \
    --format fastq \
    --html \
    --minProteinFraction 0.1 \
    --pathogenType bacterial \
    --proteinFastaFilename $HOME/rdsbt/root/share/ncbi/bacterial-refseq/20180609-bacteria.nonredundant_protein.fasta.gz \
    --pathogenPanelFilename bacteria.png \
    --sampleIndexFilename samples.index \
    --pathogenIndexFilename pathogens.index \

terrycojones

from sklearn.metrics import mutual_info_score
from sklearn.metrics.cluster import entropy

def normalized_information_distance(c1, c2):
    """
    Calculate Normalized Information Distance

    Taken from Vinh, Epps, and Bailey, (2010). Information Theoretic Measures
    for Clusterings Comparison: Variants, Properties, Normalization and
    Correction for Chance, JMLR

terrycojones

[color]
  ui = auto
[color "branch"]
  current = yellow reverse
  local = yellow
  remote = green
[color "diff"]
  meta = yellow bold
  frag = magenta bold
  old = red bold

terrycojones

$ locale
LANG=en_GB.UTF-8
LC_CTYPE="en_GB.UTF-8"
LC_NUMERIC=de_DE.UTF-8
LC_TIME=de_DE.UTF-8
LC_COLLATE="en_GB.UTF-8"
LC_MONETARY=de_DE.UTF-8
LC_MESSAGES="en_GB.UTF-8"
LC_PAPER=de_DE.UTF-8
LC_NAME=de_DE.UTF-8

terrycojones

ExifTool Version Number         : 8.98
File Name                       : tcr6.jpg
Directory                       : /Users/terry/Downloads
File Size                       : 40 kB
File Modification Date/Time     : 2018:01:12 02:41:28+00:00
File Permissions                : rw-rw-rw-
File Type                       : JPEG
MIME Type                       : image/jpeg
JFIF Version                    : 1.02
Resolution Unit                 : None

terrycojones

If you use rsync to synchronize your notebook to the server (or for anything else), you might want to switch to unison.

My notebook dir has 2166 files in it. rsync took 111 seconds the last time I ran it (no files had changed). With unison:

$ time unison output ssh://ac/dark-matter/generated-notebook
Contacting server...
Connected [//Terrys-MacBook-Pro.local//Users/terry/dark-matter/www/output -> //i19//syn/WebSites/Protected/terry]
Looking for changes
  Waiting for changes from server
Reconciling changes

terrycojones

#!/usr/bin/env python

from __future__ import print_function

from ete3 import Tree
import sys
import re

numeric_prefix = re.compile('^\d+_')
numeric = re.compile('^\d+$')