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mikkun/BioShellGei_01_Answers.txt

Created October 21, 2017 16:41
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「シェル芸勉強会 meets バイオインフォマティクス vol.1」解答例
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BioShellGei_01_Answers.txt
「シェル芸勉強会 meets バイオインフォマティクス vol.1」解答例
資料URL: https://bio-shell.connpass.com/event/66089/presentation/
問題URL: https://www.slideshare.net/EmiHattori1/ss-80854726
A1:
$ echo 'Gorilla gorilla' | perl -nlE 's/ori/a/g;s/a\b/us/g;say'
Gallus gallus
A2:
$ mkdir -p koi/chr{{1..50},MT,Un}
$ ls koi/
chr1 chr12 chr15 chr18 chr20 chr23 chr26 chr29 chr31 chr34 chr37 chr4 chr42 chr45 chr48 chr50 chr8 chrUn
chr10 chr13 chr16 chr19 chr21 chr24 chr27 chr3 chr32 chr35 chr38 chr40 chr43 chr46 chr49 chr6 chr9
chr11 chr14 chr17 chr2 chr22 chr25 chr28 chr30 chr33 chr36 chr39 chr41 chr44 chr47 chr5 chr7 chrMT
A3:
$ awk '!/^#/{if(length($4)<length($5)&&$NF~/1\/1/)print}' merge-test-c.vcf
1 3199812 . G GT . . . GT 1/1
A4:
$ ls | perl -nlE '$s=$_;s/^(.*)\.(fa|mfa|fas|fasta)$/$1.fa/;s/^(.*)\.(fq|fastq)$/$1.fq/;say "mv -f $s $_"' | sh 2>/dev/null
$ ls
fa.fa.fas.fas.fas.fa fas.fas.fastq.fastq.mfa.fa fasta.fasta.fq.fq.fas.fa fastq.fq.fq.fas.fasta.fa fq.fq.fasta.fasta.fa.fa
fa.fa.fas.fas.fastq.fa fas.fasta.fa.fa.fas.fa fasta.fastq.fq.fq.fas.fa fastq.fq.fq.fasta.fasta.fa fq.fq.fasta.fasta.fa.fq
fa.fa.fas.fas.fastq.fq fas.fasta.fa.fa.fq.fa fasta.fastq.fq.fq.fasta.fa fastq.fq.mfa.fasta.fasta.fa fq.fq.mfa.fasta.fasta.fa
fa.fa.mfa.fas.fastq.fq fas.fasta.fa.fa.mfa.fa fasta.fastq.fq.fq.mfa.fa fastq.fq.mfa.fasta.fasta.fq fq.mfa.fasta.fasta.fa.fq
fa.fa.mfa.mfa.fastq.fq fas.fastq.fa.mfa.mfa.fa fasta.fq.fq.fas.fa.fa fastq.mfa.fasta.fastq.fq.fq fq.mfa.fasta.fasta.fq.fq
fa.fas.fas.fastq.fa.fa fas.fastq.fastq.fa.mfa.fa fasta.fq.fq.fas.fas.fa fastq.mfa.mfa.fasta.fasta.fq mfa.fas.fastq.fastq.fq.fa
fa.fas.fas.fastq.fastq.fa fas.fastq.fastq.fq.mfa.fa fasta.fq.fq.fas.fasta.fa fastq.mfa.mfa.fasta.fastq.fq mfa.fas.fastq.fastq.mfa.fa
fa.fq.fas.fa.fa.fa fas.fastq.fastq.mfa.mfa.fa fastq.fa.fa.mfa.fas.fq fq.fas.fas.fa.fa.fa mfa.fasta.fasta.fa.fq.fa
fa.fq.fas.fas.fa.fa fasta.fa.fa.fa.fas.fa fastq.fa.mfa.mfa.fas.fq fq.fas.fas.fasta.fa.fa mfa.fasta.fasta.fq.fq.fa
fa.fq.fas.fas.fastq.fa fasta.fa.fa.fas.fas.fq fastq.fa.mfa.mfa.fastq.fq fq.fas.fas.fastq.fa.fa mfa.fasta.fasta.fq.fq.fq
fa.mfa.mfa.fasta.fastq.fq fasta.fa.fa.mfa.fas.fq fastq.fastq.fastq.mfa.mfa.fa fq.fas.fasta.fa.fa.fa mfa.fasta.fastq.fq.fq.fa
fa.mfa.mfa.fastq.fastq.fq fasta.fa.fq.fas.fas.fa fastq.fastq.fq.fq.fasta.fa fq.fas.fasta.fasta.fa.fq mfa.fastq.fastq.fq.fq.fa
fas.fa.fa.fa.mfa.fa fasta.fa.fq.fas.fas.fq fastq.fastq.fq.mfa.fasta.fa fq.fasta.fasta.fa.fq.fa mfa.fastq.fastq.fq.mfa.fa
fas.fa.fa.mfa.fas.fq fasta.fasta.fa.fa.fas.fa fastq.fastq.mfa.mfa.fasta.fa fq.fq.fas.fas.fa.fa mfa.mfa.fasta.fastq.fq.fq
fas.fas.fa.fa.mfa.fa fasta.fasta.fa.fq.fas.fa fastq.fastq.mfa.mfa.fasta.fq fq.fq.fas.fasta.fa.fa mfa.mfa.fastq.fastq.fq.fa
fas.fas.fastq.fa.mfa.fa fasta.fasta.fastq.fq.fq.fa fastq.fastq.mfa.mfa.mfa.fa fq.fq.fas.fasta.fasta.fa mfa.mfa.fastq.fq.mfa.fa
A5:
$ cat linda.txt | awk '!/^#/' | rev | awk -F, '{print $2}' | rev
Linda annamensis
Linda annulicornis
Linda assamensis
Linda atricornis
Linda bimaculicollis
Linda femorata
Linda fraterna
Linda gracilicornis
Linda javaensis
Linda macilenta
Linda major
Linda nigroscutata
Linda pyritosa
Linda rubescens
Linda semiatra
Linda semivittata
Linda signaticornis
Linda stolata
Linda subannulicornis
Linda zayuensis
A6-1:
$ join -t $'\t' -a 1 -a 2 -o 0 1.2 2.2 -e '-' exp_survivor.txt exp_walker.txt
GeneA 1.1 0.1
GeneB 29.1 0.1
GeneC 0.3 -
GeneD - 500.6
GeneE 4.2 4.2
GeneF 3.9 -
GeneG - 34.7
A6-2:
$ awk '{k[$1]=k[$1]" "$2"@"FILENAME}END{for(v in k){print v,k[v]}}' exp_survivor.txt exp_walker.txt | awk '{if(NF==3){print}else{if($2~/exp_survivor\.txt/){print $1,$2,"-"}else{print $1,"-",$2}}}' | sed 's/@exp_\(survivor\|walker\)\.txt//g' | sed 's/ \+/\t/g' | sort -k1,1
GeneA 1.1 0.1
GeneB 29.1 0.1
GeneC 0.3 -
GeneD - 500.6
GeneE 4.2 4.2
GeneF 3.9 -
GeneG - 34.7
A7:
$ awk 'NR!=1{if($9>=0.9)print $1"\t"$2-1"\t"$2}' tommo_EGFR.txt
chr7 55127783 55127784
chr7 55128206 55128207
chr7 55135472 55135473
chr7 55136396 55136397
chr7 55156418 55156419
chr7 55261341 55261342
chr7 55266416 55266417
chr7 55272825 55272826
chr7 55276009 55276010
chr7 55279279 55279280
chr7 55294240 55294241
chr7 55294677 55294678
chr7 55297655 55297656
chr7 55299233 55299234
chr7 55305315 55305316
chr7 55305750 55305751
chr7 55305823 55305824
chr7 55306471 55306472
chr7 55306624 55306625
chr7 55308929 55308930
chr7 55309731 55309732
chr7 55312339 55312340
A8:
$ jq -c '.results[] | [.accession, .symbol, .definition]' fridayThe13th.json | sed 's/^\["//; s/","/\t/g; s/"\]$//'
NM_001303620 DNASE1L1 Homo sapiens deoxyribonuclease 1 like 1 (DNASE1L1), transcript variant 5, mRNA.
NM_001009934 DNASE1L1 Homo sapiens deoxyribonuclease 1 like 1 (DNASE1L1), transcript variant 4, mRNA.
NM_001009933 DNASE1L1 Homo sapiens deoxyribonuclease 1 like 1 (DNASE1L1), transcript variant 3, mRNA.
NM_006730 DNASE1L1 Homo sapiens deoxyribonuclease 1 like 1 (DNASE1L1), transcript variant 1, mRNA.
NM_001009932 DNASE1L1 Homo sapiens deoxyribonuclease 1 like 1 (DNASE1L1), transcript variant 2, mRNA.
NM_019078 UGT1A5 Homo sapiens UDP glucuronosyltransferase family 1 member A5 (UGT1A5), mRNA.
NM_001144952 SDK2 Homo sapiens sidekick cell adhesion molecule 2 (SDK2), mRNA.
NM_205862 UGT1A6 Homo sapiens UDP glucuronosyltransferase family 1 member A6 (UGT1A6), transcript variant 2, mRNA.
NM_019077 UGT1A7 Homo sapiens UDP glucuronosyltransferase family 1 member A7 (UGT1A7), mRNA.
NM_001072 UGT1A6 Homo sapiens UDP glucuronosyltransferase family 1 member A6 (UGT1A6), transcript variant 1, mRNA.
NM_001079653 SDK1 Homo sapiens sidekick cell adhesion molecule 1 (SDK1), transcript variant 2, mRNA.
NM_019093 UGT1A3 Homo sapiens UDP glucuronosyltransferase family 1 member A3 (UGT1A3), mRNA.
NM_019076 UGT1A8 Homo sapiens UDP glucuronosyltransferase family 1 member A8 (UGT1A8), mRNA.
NM_152744 SDK1 Homo sapiens sidekick cell adhesion molecule 1 (SDK1), transcript variant 1, mRNA.
A9:
$ awk '!/^@/&&$2!=0{times[$1]+=1;lines[$1]=lines[$1]"%NEXT%"$0}END{for(i in times)print times[i],lines[i]}' test_input_1_a.sam | awk '/^2/' | sed 's/^2 %NEXT%//;s/%NEXT%/\n/'
r000 99 insert 50 30 10M = 80 30 ATTTAGCTAC AAAAAAAAAA RG:Z:cow PG:Z:bull
r000 211 insert 80 30 10M = 50 -30 CCCAATCATT AAAAAAAAAA RG:Z:cow PG:Z:bull
r001 163 ref1 7 30 8M4I4M1D3M = 37 39 TTAGATAAAGAGGATACTG * XX:B:S,12561,2,20,112 YY:i:100 RG:Z:fish PG:Z:colt
r001 83 ref1 37 30 9M = 7 -39 CAGCGCCAT * RG:Z:fish PG:Z:colt
A10:
$ clear; echo 'This message will self-destruct in five seconds.'; sleep 5; clear
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