Moderator: shenwei356
shenwei356 ♦ 5.0k
- Reputation:
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- Location:
- China
- Website:
- http://shenwei.me/
- Twitter:
- shenwei356
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- Last seen:
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- Joined:
- 7 years, 10 months ago
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Posts by shenwei356
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3
votes
7
answers
179
views
7
answers
... Lots of solution from others work, but I'd like to recommend a **safer** solution
of mine ([brename](https://github.com/shenwei356/brename/)),
in case you overwrite files with others by accident, which is common in batch renaming files using regular expression.
brename checks all operations befor ...
written 6 days ago by
shenwei356 ♦ 5.0k
4
votes
1
answer
129
views
1
answers
... [seqkit concat](http://bioinf.shenwei.me/seqkit/usage/#concat)
seqkit concat a.fasta b.fasta > c.fasta ...
written 20 days ago by
shenwei356 ♦ 5.0k
1
vote
3
answers
185
views
3
answers
... `seqkit subseq -r 1:20` is enough. ...
written 10 weeks ago by
shenwei356 ♦ 5.0k
1
vote
1
answer
137
views
1
answers
... ```
# converting to tab-delimited
$ ls *.txt | parallel 'csvtk space2tab {} > {.}.tsv'
# all possible values in 1th column
$ cut -f 1 *.tsv | sort | uniq | tee 0.tsv
# join together
$ csvtk join -H -t -k -t *.tsv --fill -
A 1 3 6
B 2 3 -
C 5 - ...
written 12 weeks ago by
shenwei356 ♦ 5.0k
1
vote
3
answers
304
views
3
answers
... Learn some basic knowledge of SHELL: [I/O Redirection](http://linuxcommand.org/lc3_lts0070.php) ...
written 3 months ago by
shenwei356 ♦ 5.0k
3
votes
3
answers
304
views
3
answers
... A solution using [`parallel`](https://www.biostars.org/p/63816) and [`csvtk`](https://github.com/shenwei356/csvtk):
```
# converting space-delimited to tab-delimited
l$ s *.txt | parallel 'csvtk space2tab {} > {}.tsv'
# retrieving colnames
$ ls *.txt.tsv | parallel 'csvtk headers -t {} | csvtk ...
written 3 months ago by
shenwei356 ♦ 5.0k
0
votes
0
answers
148
views
0
answers
... Try [seqkit translate --clean](https://bioinf.shenwei.me/seqkit/usage/#translate) ...
written 4 months ago by
shenwei356 ♦ 5.0k
1
vote
4
answers
2.2k
views
4
answers
...
--id-regexp '^[^\|]+\|[^\|]+\|([^\|]+)\|' ...
written 4 months ago by
shenwei356 ♦ 5.0k
1
vote
3
answers
251
views
3
answers
... try [brename](https://github.com/shenwei356/brename)
```
# read1
$ brename -f 'R1.+fastq$' -p _L -r '_S{nr}_L' -d
[INFO] checking: [ ok ] 'Tube211-16S_L001_R1_001.fastq' -> 'Tube211-16S_S1_L001_R1_001.fastq'
[INFO] checking: [ ok ] 'Tube212-16S_L001_R1_001.fastq' -> 'Tube212-16S_S2_L001_R1_0 ...
written 5 months ago by
shenwei356 ♦ 5.0k
5
votes
2
answers
255
views
2
answers
... try [seqkit grep](http://bioinf.shenwei.me/seqkit/usage/#grep):
seqkit grep -p '^NNNNNGGG' -d read_1.fq.gz -o out_1.fq.gz
or
seqkit grep -R 6:8 -p GGG read_1.fq.gz -o out_1.fq.gz
...
written 6 months ago by
shenwei356 ♦ 5.0k
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