In [1]:

    

workDir = '/home/nick/notebook/SIPSim/dev/Ecoli/'
SIPSimExe = '/home/nick/notebook/SIPSim/SIPSim'


    

In [2]:

    

import os,sys
import numpy as np
import pandas as pd
from ggplot import *
import matplotlib.pyplot as plt


    

In [3]:

    

%load_ext rpy2.ipython
%matplotlib inline


    

In [4]:

    

if not os.path.isdir(workDir):
    os.mkdir(workDir)


    

In [9]:

    

genomeDir = os.path.join(workDir, 'genomes')
if not os.path.isdir(genomeDir):
    os.mkdir(genomeDir)


    

In [10]:

    

!cd $genomeDir; \
    seqDB_tools accession-GI2fasta < ../accession.txt > Ecoli_O157H7.fna


    

    




Starting batch: 1
Starting trial: 1

--------------------- WARNING ---------------------
MSG: No whitespace allowed in FASTA ID [AE005174|Escherichia coli O157:H7 EDL933, complete genome.]
---------------------------------------------------

--------------------- WARNING ---------------------
MSG: No whitespace allowed in FASTA ID [AE005174|Escherichia coli O157:H7 EDL933, complete genome.]
---------------------------------------------------

In [12]:

    

!cd $genomeDir; \
    seq_tools fasta_info --tl --tgc --header Ecoli_O157H7.fna


    

    




total_seq_length	total_GC
5528445	50.38

In [13]:

    

# list of all genomes files and their associated names
!cd $genomeDir; \
    find . -name "*fna" | \
    perl -pe 's/.+\///' | \
    perl -pe 's/(.+)(\.[^.]+)/\$1\t\$1\$2/' > genome_index.txt


    

In [ ]:

    

!cd $genomeDir; \
    $SIPSimExe indexGenomes genome_index.txt --fp .


    

    




Indexing: "Ecoli_O157H7"
0
0: 1.81%, 0:00:00.885690
0: 3.62%, 0:00:01.596740
0: 5.43%, 0:00:02.329085

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