User: st.ph.n
st.ph.n • 2.2k
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Posts by st.ph.n
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1
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4
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143
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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 7 days ago by
st.ph.n • 2.2k
1
vote
0
answers
167
views
0
answers
... Is this an assignment? Why not just use BLAST, and make on of your FASTA files the db? ...
written 26 days ago by
st.ph.n • 2.2k
2
votes
0
answers
116
views
0
answers
... look into wrapping your command in `nohup` and `&` ...
written 27 days ago by
st.ph.n • 2.2k
0
votes
0
answers
72
views
0
answers
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 28 days ago by
st.ph.n • 2.2k
0
votes
5
answers
228
views
5
answers
Comment:
C: help in converting a table
... I'm more use to 2.X syntax so I wasn't aware. Thanks. ...
written 6 weeks ago by
st.ph.n • 2.2k
2
votes
0
answers
113
views
0
answers
... I would also double check that the sequence is the same. ...
written 6 weeks ago by
st.ph.n • 2.2k
0
votes
5
answers
228
views
5
answers
Comment:
C: help in converting a table
... Sometimes new line characters aren't interpreted properly, depending on how you're opening your file, e.g. notepad. Trying using the command-line, `less output.txt`, or open in Excel if it is not too large. ...
written 6 weeks ago by
st.ph.n • 2.2k
0
votes
5
answers
228
views
5
answers
Comment:
C: help in converting a table
... How many times does `hsa-mir-4649` appear in your input file? This should equal (+1) the number of columns in the output for that gene id.
grep -e 'hsa-mir-4649' | wc -l
How many genes in your input file? How many lines in your output file? These should be identical.
cut -f 1 input.txt | ...
written 6 weeks ago by
st.ph.n • 2.2k
1
vote
5
answers
228
views
5
answers
Answer:
A: help in converting a table
... Here's a quick python solution. I'm assuming your table is tab-delimited, and it will output tab-delimited.
#!/usr/bin/env python
import sys
from collections import defaultdict
with open(sys.argv[1], 'r') as f:
genes = defaultdict(list)
for line in f:
genes[lin ...
written 6 weeks ago by
st.ph.n • 2.2k
2
votes
1
answer
272
views
1
answers
... Try something. If you get stuck, or get an error - post the output and error message. ...
written 9 weeks ago by
st.ph.n • 2.2k
Latest awards to st.ph.n
Scholar
5 weeks ago,
created an answer that has been accepted.
For A: Using Trinity with case/control data
Scholar
3 months ago,
created an answer that has been accepted.
For A: Using Trinity with case/control data
Appreciated
3 months ago,
created a post with more than 5 votes.
For A: perl script for concatenating (multiple fasta sequences in a single file), creat
Good Answer
3 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
Scholar
4 months ago,
created an answer that has been accepted.
For A: Using Trinity with case/control data
Teacher
4 months ago,
created an answer with at least 3 up-votes.
For A: single line fasta to mult line fasta
Great Question
6 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
Teacher
7 months ago,
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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 Python- Find ORF in sequence, compound return statement
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For A: Using Trinity with case/control data
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For A: conditional replacing rows with 9
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For A: single line fasta to mult line fasta
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8 months ago,
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For A: Using Trinity with case/control data
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8 months ago,
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For A: single line fasta to mult line fasta
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8 months ago,
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For A: Using Trinity with case/control data
Teacher
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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9 months ago,
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For A: Using Trinity with case/control data
Scholar
9 months ago,
created an answer that has been accepted.
For A: Using Trinity with case/control data
Scholar
9 months ago,
created an answer that has been accepted.
For A: Using Trinity with case/control data
Scholar
9 months ago,
created an answer that has been accepted.
For A: Using Trinity with case/control data
Scholar
9 months ago,
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For A: Using Trinity with case/control data
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