<jupyter_start><jupyter_text>Running BSMAP with different version of Genome10k cuttoff<jupyter_code>%%bash
date
system_profiler SPSoftwareDataType<jupyter_output>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: <NAME> (Steven)
      Secure Virtual Memory: Enabled
      System Integrity Protection: Enabled
      Time since boot: 12 days 4:04<jupyter_text><jupyter_code>bsmaploc="/Users/Shared/Apps/bsmap-2.74/"

cd /Volumes/web/halfshell/working-directory/
!ls -lh 
mkdir 16-10-29
cd 16-10-29<jupyter_output>/Volumes/web/halfshell/working-directory/16-10-29<jupyter_text><jupyter_code># Genome
cd ../data
!curl -O http://owl.fish.washington.edu/halfshell/working-directory/16-10-24/Ostrea_lurida-Scaff-10k.fa
!ls
!curl -O http://owl.fish.washington.edu/nightingales/O_lurida/4_TGACCA_L001_R1_001.fastq.gz
!mv 4_TGACCA_L001_R1_001.fastq.gz ../16-10-17/4_TGACCA_L001_R1_001.fastq.gz
!ls ../16-10-17/*gz

pwd
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
!date
!ls bsmap
!tail *err<jupyter_output><empty_output>
{'fraction_non_alphanumeric': 0.13652357494722026, 'fraction_numerical': 0.08585503166783955, 'mean_word_length': 4.208791208791209, 'pattern_counts': {'":': 0, '<': 12, '<?xml version=': 0, '>': 13, 'https://': 0, 'lorem ipsum': 0, 'www.': 0, 'xml': 0}, 'pii_count': 0, 'substrings_counts': 0, 'word_list_counts': {'cursed_substrings.json': 0, 'profanity_word_list.json': 0, 'sexual_word_list.json': 0, 'zh_pornsignals.json': 0}}
{'chain_length': '3', 'dir': 'jupyter-structured-clean-dedup', 'id': '94598', 'license': 'MIT', 'n_tokens_mistral': 695, 'n_tokens_neox': 604, 'n_words': 104, 'path': 'jupyter/Olurida/.ipynb_checkpoints/Fidalgo-Siblings-BS-genefish-10k-checkpoint.ipynb', 'repo_name': 'sr320/ocattau.github.io', 'size': '1429'}