Moderator: shenwei356
shenwei356 ♦ 4.0k
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- http://shenwei.me/
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- Last seen:
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Posts by shenwei356
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7
votes
5
answers
390
views
5
answers
... https://www.biostars.org/p/63816/
But I think you should write a script to avoid read the data file thousands times. ...
written 11 days ago by
shenwei356 ♦ 4.0k
0
votes
3
answers
85
views
3
answers
... oh, you can google it ...
written 17 days ago by
shenwei356 ♦ 4.0k
1
vote
3
answers
85
views
3
answers
... $ seqkit replace -p '^(.+?) (.+)' -r '${1}_{nr} $2' --nr-width 9 -w 0 seq.fa
>NZ_CP00000.1_000000001 volvox complete genome
AAAAAAAATGTGCTCCGGCCTCCGCGAAATTCGCGACGCCGGCCGCGTGGGCATGCACGTC
>NZ_CP00000.1_000000002 volvox complete genome
GGCCGTTACCTGGAGCCAGCGGGACTCGAAGGATGCCCCAC ...
written 17 days ago by
shenwei356 ♦ 4.0k
1
vote
4
answers
189
views
4
answers
... Well, just for fun. Here's a long one-liner using [csvtk](https://github.com/shenwei356/csvtk) and [rush](https://github.com/shenwei356/rush) (can be replaced with [GNU parallel](https://www.gnu.org/software/parallel/)). You can run this in Windows if you install the windows version !
csvtk xls ...
written 18 days ago by
shenwei356 ♦ 4.0k
0
votes
2
answers
785
views
2
answers
... For you
seqkit grep -n -f ids.txt seqs.fa -o result.fa
`[ERRO] fastx: stdin not detected` means no input file provided and stdin not detected.
...
written 20 days ago by
shenwei356 ♦ 4.0k
1
vote
3
answers
199
views
3
answers
... thanks for pointing out, if you have ran with the old command, you can run 'brename -u' to undo. ...
written 26 days ago by
shenwei356 ♦ 4.0k
4
votes
3
answers
199
views
3
answers
... Try safe-batch-rename tool `brename` ( https://github.com/shenwei356/brename )
brename -p '^(\w+?)_.+_(R[12])_.+' -r '${1}_$2.fq.gz' # updated
# original answer
# brename -p '^(\w+)_.+_(R[12])_.+' -r '${1}_$2.fq.gz'
# if you have ran this, you can run 'brename -u' to undo.
...
written 26 days ago by
shenwei356 ♦ 4.0k
5
votes
4
answers
250
views
4
answers
... simple with https://github.com/shenwei356/csvtk
csvtk grep -H -t -f 4 -P file1 file2 > result ...
written 27 days ago by
shenwei356 ♦ 4.0k
0
votes
0
answers
186
views
0
answers
... Why not show counting the first column? ...
written 29 days ago by
shenwei356 ♦ 4.0k
1
vote
4
answers
199
views
4
answers
... inner join.
inner join. ...
written 5 weeks ago by
shenwei356 ♦ 4.0k
Latest awards to shenwei356
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11 days ago,
created a post with more than 5 votes.
For C: Inserting delim between numbers and strings in bash
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For C: single line fasta to mult line fasta
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21 days ago,
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For C: Inserting delim between numbers and strings in bash
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21 days ago,
created an answer with at least 3 up-votes.
For A: single line fasta to mult line fasta
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21 days ago,
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For A: looking for 16S RNA sequence consensus
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26 days ago,
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For A: single line fasta to mult line fasta
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For A: looking for 16S RNA sequence consensus
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For A: single line fasta to mult line fasta
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6 weeks ago,
created an answer with at least 3 up-votes.
For A: single line fasta to mult line fasta
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9 weeks ago,
created an answer that has been accepted.
For A: looking for 16S RNA sequence consensus
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9 weeks ago,
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For A: single line fasta to mult line fasta
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created an answer that has been accepted.
For A: looking for 16S RNA sequence consensus
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Teacher
11 weeks ago,
created an answer with at least 3 up-votes.
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5 months ago,
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For A: looking for 16S RNA sequence consensus
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5 months ago,
created a question with more than 1,000 views.
For csvtk - a cross-platform, efficient, practical and pretty CSV/TSV toolkit
Appreciated
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created a post with more than 5 votes.
For C: Inserting delim between numbers and strings in bash
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8 months ago,
created an answer with at least 3 up-votes.
For A: single line fasta to mult line fasta
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created a question with more than 1,000 views.
For SeqKit: a cross-platform and ultrafast toolkit for FASTA/Q file manipulation in Golang
Scholar
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For A: looking for 16S RNA sequence consensus
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For A: looking for 16S RNA sequence consensus
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13 months ago,
created an answer with at least 3 up-votes.
For A: single line fasta to mult line fasta
Scholar
13 months ago,
created an answer that has been accepted.
For A: looking for 16S RNA sequence consensus
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