nickloman

import argparse as ap
import sys
import vcf
import yaml

VERSION = 0.1

def filter_variants(yaml_variants):
    variants = []

nickloman

root@6cc3ac9c89c3:/# dpkg -i --ignore-depends=libboost-log1.58.0 ont_guppy_2.3.7-1~xenial_amd64.deb
(Reading database ... 15231 files and directories currently installed.)
Preparing to unpack ont_guppy_2.3.7-1~xenial_amd64.deb ...
Unpacking ont-guppy (2.3.7-1~xenial) over (2.3.7-1~xenial) ...
dpkg: dependency problems prevent configuration of ont-guppy:
 ont-guppy depends on libcurl4-openssl-dev; however:
  Package libcurl4-openssl-dev is not installed.
 ont-guppy depends on libssl-dev; however:
  Package libssl-dev is not installed.

nickloman

in bwa/bwamem.c reduce chunk_size to a smaller value otherwise it will not return for ages:
  
      o->chunk_size = 10000;



import subprocess
import select

p = subprocess.Popen(['bin/bwa/bwa', 'mem', 'ref/NC_018143.fna', '/dev/stdin'], stdin=subprocess.PIPE, stdout=subprocess.PIPE)

nickloman

tar -cf - $dir | tee >(ncftpput -v -F -u USER -p PASS -c HOST ${dir}.tar) | md5sum > ${dir}.md5

nickloman

touch a.fasta
touch b.fasta
touch c.fasta

find . -name "*.fasta" | parallel echo union -sequence {} -sformat fasta -outseq {}.union.fasta -osformat fasta -auto

find . -name "*.fasta" | xargs -L 1 -I '{}' echo union -sequence {} -sformat fasta -outseq {}.union.fasta -osformat fasta -auto

nickloman

import pysam
import sys

samfile = pysam.Samfile(sys.argv[1], "rb")

fields = ['Name', 'QueryLen', 'AlignLen', 'NumMismatches']
print "\t".join(fields)

for read in samfile:
        t = dict(read.tags)

nickloman

import h5py
from Bio import SeqIO
from StringIO import StringIO
import sys

keys = {'template' : '/Analyses/Basecall_2D_000/BaseCalled_template/Fastq',
        'complement' : '/Analyses/Basecall_2D_000/BaseCalled_complement/Fastq',
        'twodirections' : '/Analyses/Basecall_2D_000/BaseCalled_2D/Fastq'}

for fn in sys.argv[1:]:

nickloman

require 'formula'

class Hdf5 < Formula
  homepage 'http://www.hdfgroup.org/HDF5'
  url 'http://www.hdfgroup.org/ftp/HDF5/releases/hdf5-1.8.12/src/hdf5-1.8.12.tar.bz2'
  sha1 '8414ca0e6ff7d08e423955960d641ec5f309a55f'
  version '1.8.12'

  # TODO - warn that these options conflict
  option :universal

nickloman

import sys
from collections import defaultdict
from itertools import izip_longest

def grouper(n, iterable, fillvalue=None):
    args = [iter(iterable)] * n
    return izip_longest(fillvalue=fillvalue, *args)

contigs = defaultdict(dict)

nickloman

#Usage:
#blastall -p blastn -d db -i query -m 8 | python pullblast.py db.fasta

import sys
from Bio import SeqIO

records = SeqIO.to_dict(SeqIO.parse(open(sys.argv[1]), "fasta"))

for ln in sys.stdin:
        cols = ln.rstrip().split("\t")