mdshw5

<?xml version="1.0" encoding="utf-8"?>
<style xmlns="http://purl.org/net/xbiblio/csl" class="in-text" version="1.0" default-locale="en-US">
  <info>
    <title>Human Mutation</title>
    <link href="http://onlinelibrary.wiley.com/journal/10.1002/(ISSN)1098-1004/homepage/ForAuthors.html" rel="documentation"/>
    <id>http://www.zotero.org/styles/human-mutation</id>
    <link href="http://www.zotero.org/styles/human-mutation" rel="self"/>
    <updated>2012-07-06T16:31:32+00:00</updated>
    <author>
      <name>Matthew Shirley</name>

mdshw5

<?xml version="1.0" encoding="utf-8"?>
<style xmlns="http://purl.org/net/xbiblio/csl" class="in-text" version="1.0">
  <info>
    <title>F1000 Research</title>
    <id>http://www.zotero.org/styles/f1000-research</id>
    <link href="http://www.zotero.org/styles/vancouver" rel="independent-parent"/>
    <link href="http://f1000research.com/author-guidelines/" rel="documentation"/>
    <author>
      <name>Courtney Shirley</name>
      <email>[email protected]</email>

mdshw5

#!/bin/bash

# per-directory history
shopt -s histappend  # always append to history, don't replace
export PROMPT_COMMAND="builtin history -a;$PROMPT_COMMAND" # write to history file at every new prompt
export HISTTIMEFORMAT="%m/%d/%y %T "
alias cd='cd_with_local_history'
alias history='cat $HOME/.bash_history'
export HISTFILE="$PWD/.bash_cwd_history_$USER"
function cd_with_local_history()

mdshw5

Python 2.7.5 (default, Oct  9 2013, 20:09:30) 
[GCC 4.2.1 Compatible Apple LLVM 5.0 (clang-500.2.78)] on darwin
>>> x = range(100)
>>> random.seed(1)
>>> print([random.choice(x) for i in range(10)])
[13, 84, 76, 25, 49, 44, 65, 78, 9, 2]

>>> random.seed(1)
>>> print([choice(x) for i in range(10)])
[13, 84, 76, 25, 49, 44, 65, 78, 9, 2]

mdshw5

def choice(self, seq):
    """Choose a random element from a non-empty sequence.""" 
    return seq[int(self.random() * len(seq))]  # raises IndexError 

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import random

def choice(seq): 
     """Choose a random element from a non-empty sequence.
      This function produces consistent results from Python2.7 to 3.3
      in contrast to random.choice(). """ 
     return seq[int(random.random() * len(seq))]

mdshw5

rule sam_to_bam:
    input: "{dataset}.sam"
    output: "{dataset}.bam"
    shell: "module load sharedapps samtools; samtools view -@ 8 -bSo {output} {input}"
 
rule bam_index:
    input: "{dataset}.bam"
    output: "{dataset}.bam.bai"
    shell: "module load sharedapps samtools; samtools index {input} {output}"

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    import urllib2
    from bs4 import BeautifulSoup
    from icalendar import Calendar, Event
    import pytz
    from datetime import datetime, timedelta
    def scrape_scical():
        data = urllib2.urlopen('http://www.hopkinsmedicine.org/scical/').read()
        soup = BeautifulSoup(data)
        cal = Calendar()
        cal.add('prodid', '-//Hopkins Science Calendar//mattshirley.com/scical//')

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prefix=/home/matt/.local
exec_prefix=${prefix}
includedir=${prefix}/include
libdir=${exec_prefix}/lib

Name: freetype2
Description: The freetype2 library
Version: 2.5.3
Cflags: -I${includedir}/freetype2
Libs: -L${libdir} -lfreetype

mdshw5

from pyfaidx import Fasta

with open("regions.txt") as regions, Fasta("sequence.fasta") as fasta:
  for line in regions:
    fields = line.rstrip().split()
    rname, start, end = fields[4:7]
    repeat = ' '.join(fields[9:11])
    seq = fasta[rname][int(start)-1:int(end)-1]
    print(seq.name + repeat)
    print(seq.seq)