Running BSMAP with different version of Genome

In [4]:

    

%%bash
date
system_profiler SPSoftwareDataType


    

    




Sat Oct 29 16:56:40 PDT 2016
Software:

    System Software Overview:

      System Version: macOS 10.12 (16A323)
      Kernel Version: Darwin 16.0.0
      Boot Volume: Macintosh HD
      Boot Mode: Normal
      Computer Name: genefish
      User Name: Steven Roberts (Steven)
      Secure Virtual Memory: Enabled
      System Integrity Protection: Enabled
      Time since boot: 12 days 4:04

In [5]:

    

bsmaploc="/Users/Shared/Apps/bsmap-2.74/"


    

In [8]:

    

cd /Volumes/web/halfshell/working-directory/


    

    




/Volumes/web/halfshell/working-directory

In [9]:

    

!ls -lh


    

    




total 0
drwxrwxrwx  1 Steven  staff   1.7K Jan 27  2016 16-01-271
drwxrwxrwx  1 Steven  staff   1.7K Jan 27  2016 16-01-27b
drwxrwxrwx  1 Steven  staff   264B Apr  1  2016 16-04-01
drwxrwxrwx  1 Steven  staff   264B Apr  4  2016 16-04-01c
drwxrwxrwx  1 Steven  staff   264B Apr  4  2016 16-04-04
drwxrwxrwx  1 Steven  staff   264B Apr  4  2016 16-04-04b
drwxrwxrwx  1 Steven  staff   1.4K Apr  5  2016 16-04-04c
drwxrwxrwx  1 Steven  staff   264B Apr  4  2016 16-04-04d
drwxrwxrwx  1 Steven  staff   1.1K Apr  5  2016 16-04-05
drwxrwxrwx  1 Steven  staff   3.0K Apr 12  2016 16-04-11
drwxrwxrwx  1 Steven  staff   264B Apr 11  2016 16-04-11-hum-a
drwxrwxrwx  1 Steven  staff   3.0K Apr 13  2016 16-04-12
drwxrwxrwx  1 Steven  staff   2.4K Apr 14  2016 16-04-13
drwxrwxrwx  1 Steven  staff   264B Apr 13  2016 16-04-13b
drwxrwxrwx  1 Steven  staff   6.5K Apr 15  2016 16-04-15
drwxrwxrwx  1 Steven  staff   466B Apr 17  2016 16-04-15b
drwxrwxrwx  1 Steven  staff   264B Apr 15  2016 16-04-15c
drwxrwxrwx  1 Steven  staff   264B Apr 18  2016 16-04-17
drwxrwxrwx  1 Steven  staff   670B May 13 07:41 16-05-05
drwxrwxrwx  1 Steven  staff   264B May 12 15:43 16-05-12
drwxrwxrwx  1 Steven  staff   432B May 13 13:02 16-05-13
drwxrwxrwx  1 Steven  staff   466B May 25 10:43 16-05-17
drwxrwxrwx  1 Steven  staff   264B May 17 08:47 16-05-17b
drwxrwxrwx  1 Steven  staff   264B May 17 09:19 16-05-17c
drwxrwxrwx  1 Steven  staff   432B May 30 14:29 16-05-27
drwxrwxrwx  1 Steven  staff   364B Sep 19 09:53 16-09-19
drwxrwxrwx  1 Steven  staff   568B Oct 22 02:44 16-10-17
drwxrwxrwx  1 Steven  staff   264B Oct 19 07:50 16-10-19
drwxrwxrwx  1 Steven  staff   264B Oct 24 16:05 16-10-24
drwxrwxrwx  1 Steven  staff   772B Oct 25 07:32 16-10-25
drwxrwxrwx  1 Steven  staff   1.8K Jan 27  2016 16-27-01
drwxrwxrwx  1 Steven  staff   264B Jan 27  2016 scripts

In [10]:

    

mkdir 16-10-29


    

In [11]:

    

cd 16-10-29


    

    




/Volumes/web/halfshell/working-directory/16-10-29

In [3]:

    

# Genome


    

In [3]:

    

cd ../data


    

    




/Volumes/caviar/wd/data

In [12]:

    

!curl -O http://owl.fish.washington.edu/halfshell/working-directory/16-10-24/Ostrea_lurida-Scaff-10k.fa


    

    




  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed
100  125M  100  125M    0     0  11.1M      0  0:00:11  0:00:11 --:--:-- 12.8M

In [13]:

    

!ls


    

    




Ostrea_lurida-Scaff-10k.fa

In [19]:

    

!curl -O http://owl.fish.washington.edu/nightingales/O_lurida/4_TGACCA_L001_R1_001.fastq.gz


    

    




  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed
100  619M  100  619M    0     0  4372k      0  0:02:25  0:02:25 --:--:--  9.8M

In [23]:

    

!mv 4_TGACCA_L001_R1_001.fastq.gz ../16-10-17/4_TGACCA_L001_R1_001.fastq.gz


    

In [25]:

    

!ls ../16-10-17/*gz


    

    




../16-10-17/1_ATCACG_L001_R1_001.fastq.gz
../16-10-17/2_CGATGT_L001_R1_001.fastq.gz
../16-10-17/3_TTAGGC_L001_R1_001.fastq.gz
../16-10-17/4_TGACCA_L001_R1_001.fastq.gz
../16-10-17/5_ACAGTG_L001_R1_001.fastq.gz
../16-10-17/6_GCCAAT_L001_R1_001.fastq.gz
../16-10-17/7_CAGATC_L001_R1_001.fastq.gz
../16-10-17/8_ACTTGA_L001_R1_001.fastq.gz

In [26]:

    

pwd


    

    
Out[26]:





u'/Volumes/web/halfshell/working-directory/16-10-29'

In [ ]:

    

for i in ("1_ATCACG","2_CGATGT","3_TTAGGC","5_ACAGTG","4_TGACCA", "6_GCCAAT", "7_CAGATC", "8_ACTTGA"):
    !{bsmaploc}bsmap \
-a ../16-10-17/{i}_L001_R1_001.fastq.gz \
-d Ostrea_lurida-Scaff-10k.fa \
-o bsmap_out_{i}.sam \
-p 8 \
2> bsmap_out_{i}.stderr


    

In [ ]:

    

!date


    

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!ls bsmap


    

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!tail *err


    

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