Moderator: 5heikki

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5heikki6.9k
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Posts by 5heikki

<prev • 978 results • page 1 of 98 • next >
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Answer: A: Fasta header trimming for multiple delimiters
... awk 'BEGIN{FS="|"}{if(/^>/){print ">"$2}else{print $0}}' input > output ...
written 3 days ago by 5heikki6.9k
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Comment: C: Survey/Vote: If you could double the speed of any three commandline tools, which
... I think with large files the main bottle neck is IO ...
written 14 days ago by 5heikki6.9k
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7
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526
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7
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Answer: A: Survey/Vote: If you could double the speed of any three commandline tools, which
... In my pipelines, more often than not, `GNU sort` is the bottle neck. ...
written 15 days ago by 5heikki6.9k
1
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1
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148
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Comment: C: awk command in shell script
... Alternatively for i in $(seq 2 4); do ..; done or for i in 2 3 4; do ..; done OP is probably using Ubuntu so his sh points to dash instead of bash ...
written 20 days ago by 5heikki6.9k
1
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1
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148
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Comment: C: awk command in shell script
... Since you're using my answer from your other thread, could you please go mark it as the accepted answer? ...
written 20 days ago by 5heikki6.9k
1
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3
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Answer: A: Uncollapsing FASTA file
... Another awk solution (assuming no linebreaks in sequences): awk 'BEGIN{FS="_x"}{if(/^>/){x=$1;y=$2;z=getline}{for(i=1;i<=y;i++){print x"\n"$z}}}' file ...
written 21 days ago by 5heikki6.9k
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2
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Answer: A: extracting blast hit whith the highest bit score
... export LANG=C; sort -t $'\t' -k1,1 -k12,12gr tabularBlastOutput | sort -t $'\t' -uk1,1 ...
written 21 days ago by 5heikki6.9k
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181
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Answer: A: save the file_name according to the column headers
... for((i=2;i<5;i++)); do awk -v i=$i 'BEGIN{OFS=FS="\t"}NR==1{n=$i}{print $1,$i > n".txt"}' file; done ...
written 21 days ago by 5heikki6.9k
2
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2
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169
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Answer: A: Has anyone tried to run SNPEff, Bedtools or Prokka with GNU parallel or a simila
... #!/bin/bash function doSomething(){ program "$1" } export -f doSomething find /place/with/input/files -name "*.txt" \ | parallel -j 32 doSomething {} GNU parallel is great for embarrassingly parallel problems.. ...
written 22 days ago by 5heikki6.9k
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170
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Answer: A: How to retrieve rows from OTU table
... Assuming tab separated files join -1 1 -2 1 -t $'\t' <(sort -t $'\t' -k1,1 otutable) <(sort -t $'\t' -k1,1 listfile) ...
written 23 days ago by 5heikki6.9k

Latest awards to 5heikki

Commentator 13 days ago, created a comment with at least 3 up-votes. For C: Finding a sequence in a fasta file
Teacher 14 days ago, created an answer with at least 3 up-votes. For A: If you have a chance to ask questions to the CEO of Illumina, what would you do?
Scholar 16 days ago, created an answer that has been accepted. For A: Rfam, cmsearch and cmscan
Scholar 21 days ago, created an answer that has been accepted. For A: The best way to share scientific findings with community
Great Question 29 days ago, created a question with more than 5,000 views. For Best tools for circular genome visualization?
Scholar 6 weeks ago, created an answer that has been accepted. For A: The best way to share scientific findings with community
Scholar 8 weeks ago, created an answer that has been accepted. For A: Rfam, cmsearch and cmscan
Teacher 8 weeks ago, created an answer with at least 3 up-votes. For A: If you have a chance to ask questions to the CEO of Illumina, what would you do?
Scholar 8 weeks ago, created an answer that has been accepted. For A: Rfam, cmsearch and cmscan
Teacher 3 months ago, created an answer with at least 3 up-votes. For A: If you have a chance to ask questions to the CEO of Illumina, what would you do?
Popular Question 3 months ago, created a question with more than 1,000 views. For Bootsrapped tree from a distance matrix
Good Answer 3 months ago, created an answer that was upvoted at least 5 times. For A: fasta header with leading zeros
Teacher 4 months ago, created an answer with at least 3 up-votes. For A: If you have a chance to ask questions to the CEO of Illumina, what would you do?
Scholar 4 months ago, created an answer that has been accepted. For A: Rfam, cmsearch and cmscan
Teacher 5 months ago, created an answer with at least 3 up-votes. For A: If you have a chance to ask questions to the CEO of Illumina, what would you do?
Scholar 5 months ago, created an answer that has been accepted. For A: Rfam, cmsearch and cmscan
Scholar 5 months ago, created an answer that has been accepted. For A: Rfam, cmsearch and cmscan
Scholar 5 months ago, created an answer that has been accepted. For A: Rfam, cmsearch and cmscan
Teacher 5 months ago, created an answer with at least 3 up-votes. For A: If you have a chance to ask questions to the CEO of Illumina, what would you do?
Teacher 7 months ago, created an answer with at least 3 up-votes. For A: If you have a chance to ask questions to the CEO of Illumina, what would you do?
Teacher 7 months ago, created an answer with at least 3 up-votes. For A: If you have a chance to ask questions to the CEO of Illumina, what would you do?
Scholar 7 months ago, created an answer that has been accepted. For A: Rfam, cmsearch and cmscan
Commentator 7 months ago, created a comment with at least 3 up-votes. For C: Finding a sequence in a fasta file

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