kescobo

input = open('rosalind_ini6.txt', 'r')
input = input.read()

words = []
list = {}

for word in input.split(' '):
    words.append(word)

for i in xrange(0, len(words)):

kescobo

import re

#open file to read
with open('test.fasta', 'r') as seqs:

	seqFile = (open('throwaway.txt', 'a+'))

	for line in seqs:
		if re.search('^>[a-zA-Z][a-zA-Z][a-zA-Z][a-zA-Z]', line):
			seqFile.close()

kescobo

import annotated genomes

for genome in genomes:
  write genome to genome_database
    database{
            species_name:
              CDS{
                  annotation:
                  aa sequence:
                  nt sequence:

kescobo

LOCUS       BW77_ACAGTG.R1_(paired)_contig_93          233 bp    DNA     linear   UNK 
DEFINITION  Contig BW77_ACAGTG.R1_(paired)_contig_93 from Arthrobacter sp.
            BW77
ACCESSION   unknown
FEATURES             Location/Qualifiers
     source          1..233
                     /mol_type="genomic DNA"
                     /db_xref="taxon: 6666666"
                     /genome_md5=""
                     /project="bewolfe_6666666"

kescobo

from operator import itemgetter
from itertools import groupby

def gbk_to_faa(some_genbank):
    source = None
    for record in SeqIO.parse(some_genbank, 'gb'):
        if source:
            if record.annotations['source'] != source:
                out_file.close()
                source = sub(r'\W+', "_", sub(r'\W$', "", record.annotations['source']))

kescobo

function jaccarddistance(sketch1::MinHashSketch, sketch2::MinHashSketch)
    d = length(setdiff(sketch1.sketch, sketch2.sketch))
    l = length(sketch1)
    return (l-d) / (l+d)
end

function newjd(sketch1::MinHashSketch, sketch2::MinHashSketch)
    matches = 0
    sketchlen = length(sketch1)
    i = 1

kescobo

b1 = open(FASTAReader,
    "/Users/ksb/computation/science/genomes/kv_input/fasta/Brachybacterium_alimentarium_738_10.fna")

seq1 = dna""

for s in b1
    seq1 = seq1 * s.seq
end
length(seq1) # 4160958

kescobo

               _
   _       _ _(_)_     |  A fresh approach to technical computing
  (_)     | (_) (_)    |  Documentation: https://docs.julialang.org
   _ _   _| |_  __ _   |  Type "?help" for help.
  | | | | | | |/ _` |  |
  | | |_| | | | (_| |  |  Version 0.6.0-rc1.0 (2017-05-07 00:00 UTC)
 _/ |\__'_|_|_|\__'_|  |  
|__/                   |  x86_64-apple-darwin16.5.0

julia> using Plots

kescobo

@HD	VN:1.0	SO:unsorted
@SQ	SN:tig00000001	LN:4311805
@SQ	SN:tig00000002	LN:66004
@SQ	SN:tig00000004	LN:1036550
@SQ	SN:tig00000005	LN:256226
@SQ	SN:tig00000007	LN:150530
@SQ	SN:tig00000008	LN:138168
@PG	ID:bowtie2	PN:bowtie2	VN:2.3.2	CL:"/usr/local/bin/../Cellar/bowtie2/2.3.2/bin/bowtie2-align-s --wrapper basic-0 -x jb418 -S jb418.sam -1 ../../raw_reads/r1.fastq -2 ../../raw_reads/r2.fastq"
HWI-D00742:45:H7W5YBCXX:1:1101:1219:2200	73	tig00000001	3359004	42	100M	=	3359004	0	CCTGNGTGACGAAGACCACCTGGGCGACATGGACTTCAAGGTAGCCGGTACCGCCAAAGGTGTTACCGCGCTGCAGATGGACATCAAGATCNAGGGCATC	DDDD#<<EHHHIIHIIIIIIIIIHHIIIIIIIIIIIIIIIIIHEHIIIIIIIIIIIIIIIHHIIIHIIIIIIIIHIEHIHIIIIIIIIGGH#<<EHFHIH	AS:i:-2	XN:i:0	XM:i:2	XO:i:0	XG:i:0	NM:i:2	MD:Z:4G86A8	YT:Z:UP
HWI-D00742:45:H7W5YBCXX:1:1101:1219:2200	133	tig00000001	3359004	0	*	=	3359004	0	NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN	####################################################################################################

kescobo

using LightGraphs
using MetaGraphs
using BenchmarkTools

function name_lookup(mgraph::MetaGraph, name::String)
    return collect(filter_vertices(mgraph, :name, name))[1]
end

function dict_assign!(mgraph::MetaGraph, spindex::Vector{Int}, meindex::Vector{Int}, weights::Vector{Float64})
    for i in 1:10000