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バイオシェル芸勉強会 2017/10/18

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October 18, 2017

バイオシェル芸勉強会 2017/10/18

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carushi

October 18, 2017
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  1. • ਓଟ͗͢Ͱ͸ʂʁ Śŕ ƅЧƅ㲇ƅЧƅ)ŵŢƄ? • ͱ͍͏͔ϓϩͷํʑͷલͰԿΛ͠Ό΂Ζ͏ʂʂʁ:(ʀƄƅ’Тƅ'): ࡉ๔ϨϕϧͰ࿀γΣϧܳͯ͠Δʁ γΣϧܳͱͷೃΕॳΊΛ͔ͨΓ·͢(✿◕ ‿◕ฺ)φ →

    ؾ߹͍ೖΕͯbashͷίʔυͷಡΈ௚͠ΛਐΊ͖ͯͨ • Bashͷmailcheck + cronɾat • ࣗ෼ͷਪ͔͠Β͍ͭ΋Ԡԉϝʔϧ͕͘ΔγεςϜͱ͔ • ͪΐͬͱؾ࣋ͪѱ͍
  2. ͋Γ͕ͪͳಥવͷཪ੾Γ ύΠϓύΠϓύΠϓ….. seq 0 5 | xargs -I{} echo "samtools

    view -F 16 {}.bam | grep -v \”XS: \” | awk 'BEGIN{OFS='\t'}{if(length(\$10) >= 15) { print }}' | cut -f6,6 | grep \"^[0-9]*S\" | cut -f1,1 -d\"S\" | sort -n | uniq -c > {}_local.txt " | bash…
  3. ࣮ྫʣBam/Samͷॲཧ 11 # github/carushi/RT_end_count/ࢀর samtools view -F 16 temp.bam \

    | gawk 'BEGIN{OFS="\t"}{if (NF == 3) {;} else if ($6 ~ / ^[0-9]*M/){ print 0 } else if ($6 ~ /^[0-9]*S/){print gensub(/ ^([0-9]*)S.*\$/, "\\1", "1", $6)} else {print "Error", $6}}'" • samtoolsͰ+࠯ʢਖ਼ํ޲ʣͷϦʔυͷΈΛऔΓग़͢ • gawkͰ • 1. ϔομʔ৘ใ͸ແࢹ • 2. ࠷ॳ͕਺ࣈͱϚονͰ࢝·͍ͬͯͨΒ0ϕʔεΛग़ྗ • 3. ࠷ॳ͕਺ࣈͱιϑτΫϦοϓͰ࢝·͍ͬͯͨΒɺ1൪໨ʹݟ͔ͭͬͨจࣈྻΛஔ ׵ͯ͠਺ࣈ෦෼ͷΈΛग़ྗ͢Δ • 4. ͦΕҎ֎͸Τϥʔใࠂ
  4. Ұ൪࢖͏γΣϧίϚϯυ LC_ALL=C tr '|' ‘\n' < ~/.zshistory | sed 's/^

    //g' | cut -f1 -d” “ \ | grep -v "=" | sort | uniq -c | sort -n (-r) ӫ͑͋ΔୈҐ͸ʜʂʁ
  5. ༨ஊɿ࠷ۙͷγΣϧ؀ڥ • command line filtering: zsh+tmux+peco+ghq -> fzf΋ྑ͍… • unco:

    ਲͬ෷ͬͯ࡞ۀ͢Δͱ͖͸࢖͏΂͖ͩͳͱ਎ʹ͠Έͨ • pbpaste/pbcopy • Control + TʢControl + a, h, d, k, e, …ʣ • લޙͷจࣈΛೖΕସ͑Δʢtransposeʣ • sl -> lsʂ • macͰ͸ίϚϯυ࣮ߦதʹԡ͢ͱsnapshot ʢࠓͳΜͷίϚϯ υ͕࣮ߦ͞Ε͍ͯΔ͔ʣΛදࣔ͢Δ͜ͱ͕Ͱ͖Δ