User: st.ph.n
st.ph.n • 2.3k
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- Philadelphia, PA
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- 2 days, 7 hours ago
- Joined:
- 4 years, 6 months ago
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- t*******@temple.edu
Posts by st.ph.n
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... You can make any fasta into a blast database with `makeblastdb` ...
written 6 weeks ago by
st.ph.n • 2.3k
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2
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207
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2
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Comment:
C: tab to fasta file conversion
... *Try something*-there are multiple solutions. If you get stuck, post your efforts and errors. ...
written 7 weeks ago by
st.ph.n • 2.3k
1
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139
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... > Since i am new to perl. Can anybody help me out with that?
If you post what you've tried, someone knowledgeable in Perl (if you *need* to use Perl) can help you figure out what might be wrong with your code. ...
written 7 weeks ago by
st.ph.n • 2.3k
1
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3
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244
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3
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... yes, i'm still writing 2.7 syntax. ...
written 8 weeks ago by
st.ph.n • 2.3k
1
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244
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3
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... the `for` statement should be on a new line from the import statement. Looks like it must not have copied/pasted correctly. I commented out the actually renaming part, so you could test first and review the lines that are printed. ...
written 8 weeks ago by
st.ph.n • 2.3k
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3
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244
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... Quick python solution.
#!/usr/bin/env python
import os, glob
for file in glob.glob("*.fastq.gz"):
# test with print statement
print file, '\t', file.split('_')[0] + '_' + file.split('_')[3] + '_.fastq.gz'
# uncomment to rename
# os.rename(file, file.split('_') ...
written 8 weeks ago by
st.ph.n • 2.3k
2
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4
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224
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4
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Answer:
A: headers from multifasta files
... for file in *.fasta; do grep -e '>' | cut -f 2 -d '>' > "`basename .fasta`.headers.txt"; done
Will take each file with `.fasta` extension in your `cwd` and `grep` for the headers, and cut the headers and take everything after the '>' and place them into a file named with the prefix ...
written 3 months ago by
st.ph.n • 2.3k
1
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answers
250
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... Is this an assignment? Why not just use BLAST, and make on of your FASTA files the db? ...
written 3 months ago by
st.ph.n • 2.3k
2
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0
answers
193
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... look into wrapping your command in `nohup` and `&` ...
written 3 months ago by
st.ph.n • 2.3k
0
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0
answers
108
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0
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Comment:
C: Translating Plant DNA to protein
... BLASTX will only align DNA to protein. If you need to translate sequences, there are command line tools to do so, as well as modules for different programming languages, such as Biopython. Are your sequences in frame? ...
written 4 months ago by
st.ph.n • 2.3k
Latest awards to st.ph.n
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5 weeks ago,
created a question with more than 1,000 views.
For Python - Joining Overlapping DNA sequences
Teacher
8 weeks ago,
created an answer with at least 3 up-votes.
For A: single line fasta to mult line fasta
Scholar
8 weeks ago,
created an answer that has been accepted.
For A: Using Trinity with case/control data
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For A: Using Trinity with case/control data
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6 months ago,
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For A: Using Trinity with case/control data
Good Answer
6 months ago,
created an answer that was upvoted at least 5 times.
For A: perl script for concatenating (multiple fasta sequences in a single file), creat
Appreciated
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created a post with more than 5 votes.
For A: perl script for concatenating (multiple fasta sequences in a single file), creat
Scholar
7 months ago,
created an answer that has been accepted.
For A: Using Trinity with case/control data
Teacher
7 months ago,
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For A: single line fasta to mult line fasta
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9 months ago,
created a question with more than 5,000 views.
For Finding Min Value In List Of Lists -- Python -- Without Numpy
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For Upper Triangular Matrix From Array --Python
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10 months ago,
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For A: Using Trinity with case/control data
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For A: single line fasta to mult line fasta
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For Truncated SAM file - odd characters
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For A: single line fasta to mult line fasta
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For A: Using Trinity with case/control data
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For A: single line fasta to mult line fasta
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11 months ago,
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12 months ago,
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For A: Using Trinity with case/control data
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12 months ago,
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For A: Using Trinity with case/control data
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