User: st.ph.n

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st.ph.n2.1k
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Posts by st.ph.n

<prev • 533 results • page 1 of 54 • next >
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Comment: C: blast using python
... If there is no particular reason to run BLAST through Biopython with XML output, I typically will run the blast command if I have downstream python code, using `suprocess()`, with tab-delimited output which is easier to parse IMO after with python. ...
written 6 days ago by st.ph.n2.1k
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Comment: C: Any ideas on converting IUPAC ambiguity codes in a fasta file
... It appears as though you want a new sequence for each ambiguity code encountered. See edited post for reference. Otherwise if you want a new sequence and ALL codes changed at once, it will be slightly different. ...
written 7 days ago by st.ph.n2.1k
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Answer: A: Any ideas on converting IUPAC ambiguity codes in a fasta file
... This python code should work if you FASTA is single-line. If not you can [linearize][1] it. #!/usr/bin/env python import sys with open(sys.argv[1], 'r') as f: with open(sys.argv[2], 'w') as out: for line in f: if line.startswith(">"): header = line.strip() ...
written 7 days ago by st.ph.n2.1k
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Comment: C: Rename FASTA files according to FASTA file header
... Ok, so how do you want the files named according to these headers? ...
written 12 days ago by st.ph.n2.1k
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Comment: C: Rename FASTA files according to FASTA file header
... What does `cat *.fasta | grep -e '>' | head -n 10` give you? It would be helpful to see the structure of the sequence headers, in order to provide a proper solution. ...
written 14 days ago by st.ph.n2.1k
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Comment: C: split seq in fasta file in groups according to seq similarity?
... `awk` or `grep` will also work with FASTA. It is not the format of your data, it is the quantity, and efficiency of your script. Do you know the average length of your sequences? Again, do you have a multi-line or single-line FASTA? This will help in the efficacy of reading the file. ...
written 19 days ago by st.ph.n2.1k
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Comment: C: Comparing 2 Columns at once
... You're skipping a cpl of cols in your output example. Did you try any code in R? If so, show it along with any errors. If not, try something and come back with it. ...
written 21 days ago by st.ph.n2.1k
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Comment: C: split seq in fasta file in groups according to seq similarity?
... Do you have a multi-line or single line fasta? What is the output of `grep -c '>' example2.fas`? ...
written 21 days ago by st.ph.n2.1k
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Comment: C: How to rename multiple file name
... `for file in *.fastq; do mv -v $file ${file/_/_R}; done` should be sufficient. ...
written 23 days ago by st.ph.n2.1k
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Comment: C: hey, can someone help me with python?
... > can someone solve this for me? Show some code and errors, if any. The OP sounds like an assignment, and you should show something you've attempted. ...
written 5 weeks ago by st.ph.n2.1k

Latest awards to st.ph.n

Scholar 6 days ago, created an answer that has been accepted. For A: Using Trinity with case/control data
Good Answer 21 days 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 6 weeks ago, created an answer that has been accepted. For A: Using Trinity with case/control data
Teacher 6 weeks ago, created an answer with at least 3 up-votes. For A: single line fasta to mult line fasta
Great Question 3 months ago, created a question with more than 5,000 views. For Finding Min Value In List Of Lists -- Python -- Without Numpy
Great Question 4 months ago, created a question with more than 5,000 views. For Upper Triangular Matrix From Array --Python
Teacher 4 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: Using Trinity with case/control data
Student 4 months ago, asked a question with at least 3 up-votes. For Truncated SAM file - odd characters
Great Question 4 months ago, created a question with more than 5,000 views. For Python- Find ORF in sequence, compound return statement
Scholar 4 months ago, created an answer that has been accepted. For A: Using Trinity with case/control data
Scholar 4 months ago, created an answer that has been accepted. For A: conditional replacing rows with 9
Scholar 4 months ago, created an answer that has been accepted. For A: Using Trinity with case/control data
Scholar 5 months ago, created an answer that has been accepted. For A: Using Trinity with case/control data
Teacher 5 months ago, created an answer with at least 3 up-votes. For A: single line fasta to mult line fasta
Teacher 5 months ago, created an answer with at least 3 up-votes. For A: single line fasta to mult line fasta
Scholar 5 months ago, created an answer that has been accepted. For A: Using Trinity with case/control data
Teacher 5 months ago, created an answer with at least 3 up-votes. For A: single line fasta to mult line fasta
Scholar 6 months ago, created an answer that has been accepted. For A: Using Trinity with case/control data
Scholar 6 months ago, created an answer that has been accepted. For A: Using Trinity with case/control data
Scholar 6 months ago, created an answer that has been accepted. For A: Using Trinity with case/control data
Scholar 6 months ago, created an answer that has been accepted. For A: Using Trinity with case/control data
Scholar 7 months ago, created an answer that has been accepted. For A: Using Trinity with case/control data
Scholar 7 months ago, created an answer that has been accepted. For A: Using Trinity with case/control data

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