User: shenwei356
shenwei356 • 3.1k
- Reputation:
- 3,140
- Status:
- Trusted
- Location:
- China
- Website:
- http://shenwei.me/
- Twitter:
- shenwei356
- Scholar ID:
- Google Scholar Page
- Last seen:
- 9 hours ago
- Joined:
- 5 years, 3 months ago
- Email:
- s*********@gmail.com
Wei Shen is a PhD student of Microbiology studying Bioinformatic algorithm and gut metagenomics at Third Military University, China.
He develops and shares many reusable open-source tools on Bioinformatics and data manipulations on Github (http://bioinf.shenwei.me). And he also likes writing posts on software development and scientific research.
Learn more: Google Scholar | ResearchGate | ORCID, Github.
Posts by shenwei356
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3
votes
4
answers
823
views
4
answers
... [Table 1: Comparison of Nextflow with other workflow management systems](https://www.nature.com/nbt/journal/v35/n4/fig_tab/nbt.3820_T1.html)
Workflow
Nextflow
Galaxy
Toil
Snakemake
Bpipe
Platforma
Groovy/JVM
Python
Python
Python
Groovy/JVM
Native task supportb
Yes (any)
No
No
Yes (BASH only) ...
written 4 weeks ago by
shenwei356 • 3.1k
0
votes
2
answers
170
views
2
answers
Answer:
A: Column Regex Find And Replace
... [csvtk](https://github.com/shenwei356/csvtk/), supporting Windows/Linux/Mac OS X
csvtk replace -H -t -f 2 -p "gi\|(\d+).+" -r "\$1" data.tsv ...
written 4 weeks ago by
shenwei356 • 3.1k
0
votes
3
answers
1.9k
views
3
answers
... Thanks for your explanation. ...
written 5 weeks ago by
shenwei356 • 3.1k
2
votes
0
answers
121
views
0
answers
... Steps:
1. read the positions as list
1. iterate FASTA records:
for seq_record in SeqIO.parse(query_file, "fasta"):
for x in positions:
# get the base at position x
seq_record.seq[x-1]
...
written 6 weeks ago by
shenwei356 • 3.1k
1
vote
1
answer
105
views
1
answers
... [MultiQC](http://multiqc.info/) - Aggregate results from bioinformatics analyses across many samples into a single report ...
written 6 weeks ago by
shenwei356 • 3.1k
2
votes
1
answer
112
views
1
answers
... [Manipulation on NCBI refseq bacterial assembly summary](http://blog.shenwei.me/manipulation-on-ncbi-refseq-bacterial-assembly-summary/) ...
written 6 weeks ago by
shenwei356 • 3.1k
0
votes
1
answer
454
views
1
answers
Comment:
C: fasta file to tab delimited file
... [seqkit](https://github.com/shenwei356/seqkit)
seqkit tab2fx xxx.tab > xxx.fasta ...
written 7 weeks ago by
shenwei356 • 3.1k
3
votes
2
answers
132
views
2
answers
... For locating motifs, try `locate` command ([usage](http://bioinf.shenwei.me/seqkit/usage/#locate)) of [SeqKit](https://github.com/shenwei356/seqkit).
For some motifs:
$ cat motifs.txt
ACTNGCT
GCTGRTCGAAC
Convert to FASTA format which seqkit wants:
$ awk '{print ">"$1"\n"$1}' ...
written 7 weeks ago by
shenwei356 • 3.1k
3
votes
3
answers
159
views
3
answers
Answer:
A: Pattren counter in fasta file
... You can also try [SeqKit](https://github.com/shenwei356/seqkit).
$ seqkit locate -p CAGAT seqs.fa | column -t
seqID patternName pattern strand start end matched
chr1 CAGAT CAGAT + 6 10 CAGAT
chr1 CAGAT CAGAT + 24 28 CAGAT
ch ...
written 7 weeks ago by
shenwei356 • 3.1k
2
votes
2
answers
153
views
2
answers
... try [taxonkit](https://github.com/shenwei356/taxonkit), providing single binary files for Windows/Linux. It's really fast.
$ cat names.txt
Homo sapiens
Akkermansia muciniphila ATCC BAA-835
Akkermansia muciniphila
Mouse Intracisternal A-particle
Wei Shen
uncultured murin ...
written 7 weeks ago by
shenwei356 • 3.1k
Latest awards to shenwei356
Teacher
4 weeks ago,
created an answer with at least 3 up-votes.
For A: single line fasta to mult line fasta
Scholar
5 weeks ago,
created an answer that has been accepted.
For A: looking for 16S RNA sequence consensus
Scholar
6 weeks ago,
created an answer that has been accepted.
For A: looking for 16S RNA sequence consensus
Teacher
7 weeks ago,
created an answer with at least 3 up-votes.
For A: single line fasta to mult line fasta
Teacher
7 weeks ago,
created an answer with at least 3 up-votes.
For A: single line fasta to mult line fasta
Scholar
9 weeks ago,
created an answer that has been accepted.
For A: looking for 16S RNA sequence consensus
Scholar
9 weeks ago,
created an answer that has been accepted.
For A: looking for 16S RNA sequence consensus
Teacher
9 weeks ago,
created an answer with at least 3 up-votes.
For A: single line fasta to mult line fasta
Scholar
10 weeks ago,
created an answer that has been accepted.
For A: looking for 16S RNA sequence consensus
Scholar
11 weeks ago,
created an answer that has been accepted.
For A: looking for 16S RNA sequence consensus
Scholar
11 weeks ago,
created an answer that has been accepted.
For A: looking for 16S RNA sequence consensus
Scholar
3 months ago,
created an answer that has been accepted.
For A: looking for 16S RNA sequence consensus
Teacher
3 months ago,
created an answer with at least 3 up-votes.
For A: single line fasta to mult line fasta
Scholar
3 months ago,
created an answer that has been accepted.
For A: looking for 16S RNA sequence consensus
Good Answer
3 months ago,
created an answer that was upvoted at least 5 times.
For A: Bioinformatics software distribution
Scholar
3 months ago,
created an answer that has been accepted.
For A: looking for 16S RNA sequence consensus
Teacher
3 months ago,
created an answer with at least 3 up-votes.
For A: single line fasta to mult line fasta
Scholar
3 months ago,
created an answer that has been accepted.
For A: looking for 16S RNA sequence consensus
Teacher
3 months ago,
created an answer with at least 3 up-votes.
For A: single line fasta to mult line fasta
Scholar
4 months ago,
created an answer that has been accepted.
For A: looking for 16S RNA sequence consensus
Scholar
4 months ago,
created an answer that has been accepted.
For A: looking for 16S RNA sequence consensus
Scholar
4 months ago,
created an answer that has been accepted.
For A: looking for 16S RNA sequence consensus
Teacher
4 months ago,
created an answer with at least 3 up-votes.
For A: single line fasta to mult line fasta
Commentator
4 months ago,
created a comment with at least 3 up-votes.
For C: single line fasta to mult line fasta
Appreciated
4 months ago,
created a post with more than 5 votes.
For C: Inserting delim between numbers and strings in bash
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