#!/usr/bin/env python
# coding: utf-8

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get_ipython().run_cell_magic('bash', '', 'date\n')


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get_ipython().run_cell_magic('bash', '', 'system_profiler SPSoftwareDataType\n')


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get_ipython().run_cell_magic('bash', '', '#Uses grep to exclude lines that display serial number and hardware UUID\nsystem_profiler SPHardwareDataType | grep -v [SH][ea]\n')


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get_ipython().run_cell_magic('bash', '', 'time cp /Volumes/web/nightingales/O_lurida/20160223_gbs/160123_I132_FCH3YHMBBXX_L4_OYSzenG1AAD96FAAPEI-109_*.gz /Users/Sam/oly_gbs_bgi/\n')


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pwd


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cd


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cd oly_gbs_bgi/


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ls


# ### Rename FASTQ files to match R1 and R2 requirements for pyrad demultiplexing

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mv 160123_I132_FCH3YHMBBXX_L4_OYSzenG1AAD96FAAPEI-109_1.fq.gz 160123_I132_FCH3YHMBBXX_L4_OYSzenG1AAD96FAAPEI-109_R1.fq.gz


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mv 160123_I132_FCH3YHMBBXX_L4_OYSzenG1AAD96FAAPEI-109_2.fq.gz 160123_I132_FCH3YHMBBXX_L4_OYSzenG1AAD96FAAPEI-109_R2.fq.gz


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ls


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mv params.txt 20160525_pyrad/params.txt


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cd 20160525_pyrad/


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ls


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get_ipython().run_cell_magic('bash', '', 'cat params.txt\n')


# ### Edited line 11 (Datatype) to reflect paired-end GBS data

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get_ipython().run_cell_magic('bash', '', 'cat params.txt\n')


# ### Step 1: De-multiplex reads

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get_ipython().run_cell_magic('bash', '', 'time pyrad -p params.txt -s 1\n')


# #### Rename fastq files again, based on error message above

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get_ipython().run_cell_magic('bash', '', 'mv /Users/Sam/oly_gbs_bgi/160123_I132_FCH3YHMBBXX_L4_OYSzenG1AAD96FAAPEI-109_R1.fq.gz \\\n/Users/Sam/oly_gbs_bgi/160123_I132_FCH3YHMBBXX_L4_OYSzenG1AAD96FAAPEI-109_R1_.fq.gz\n')


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get_ipython().run_cell_magic('bash', '', 'mv /Users/Sam/oly_gbs_bgi/160123_I132_FCH3YHMBBXX_L4_OYSzenG1AAD96FAAPEI-109_R2.fq.gz \\\n/Users/Sam/oly_gbs_bgi/160123_I132_FCH3YHMBBXX_L4_OYSzenG1AAD96FAAPEI-109_R2_.fq.gz\n')


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ls ../


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get_ipython().run_cell_magic('bash', '', 'time pyrad -p params.txt -s 1\n')


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