Moderator: Peter
Peter ♦ 5.5k
- Reputation:
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- Trusted
- Location:
- Scotland, UK
- Website:
- http://blastedbio.blog...
- Scholar ID:
- Google Scholar Page
- Last seen:
- 2 days, 2 hours ago
- Joined:
- 7 years, 6 months ago
- Email:
- p*********@googlemail.com
I contribute to a number of open source bioinformatics projects, including Biopython and Galaxy. I have written a number of Galaxy tools & wrappers, co-ordinate the Galaxy BLAST+ wrappers, and currently serve on the Intergalactic Utilities Commission (aka the Galaxy ToolShed Police).
Posts by Peter
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... Unfortunately, I think you might have to list all the child taxon identifiers explicitly - but try exploring the web interface for building an advanced query first in case that shows a better solution. ...
written 2 days ago by
Peter ♦ 5.5k
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Comment:
C: Refseq Proteins For A Given Taxid
... It might be best to email the NCBI Entrez team with the full details - it sounds like something on their server is failing. ...
written 2 days ago by
Peter ♦ 5.5k
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... Does you FASTA file have one sequence in it, or many?
If one, you only need to open the FASTA file once, and you should use ``SeqIO.read`` for that.
If many, you need to know which sequence each of the values `x` refers to. Perhaps ``SeqIO.index`` would be useful here for loading the relevant reco ...
written 5 weeks ago by
Peter ♦ 5.5k
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... Did you open this on the Galaxy Q&A site? Could you add the link here please. ...
written 5 weeks ago by
Peter ♦ 5.5k
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Answer:
A: Galaxy local update
... You most likely need to run `git fetch origin` first to ensure git has a local copy of all the changes in the master repository at GitHub. That would explain why your local git repository has no matches to ``release_17.05``. ...
written 5 weeks ago by
Peter ♦ 5.5k
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... If I have understood your question, yes - if you are trying to get the matched sequence from the reference, it would need reverse complementing. ...
written 5 weeks ago by
Peter ♦ 5.5k
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... As per the comments, there was a bug in the user script not explicitly closing the output handles before trying to parse the same file. This can result in data "missing" as it has not yet been flushed to disk.
Python introduced the ``with`` statement to help with automating closing handles, since f ...
written 7 weeks ago by
Peter ♦ 5.5k
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... The current release is Biopython 1.70, but please do try upgrading since the pairwise code was rewritten in Biopython 1.68 ...
written 7 weeks ago by
Peter ♦ 5.5k
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2
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382
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... Please say which version of Biopython you are using, since the pairwise code was rewritten in Biopython 1.68 ...
written 7 weeks ago by
Peter ♦ 5.5k
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... The ``if "locus_tag" in f.qualifiers:`` condition should avoid the ``KeyError``, see also https://www.biostars.org/p/258744/ ...
written 3 months ago by
Peter ♦ 5.5k
Latest awards to Peter
Scholar
3 months ago,
created an answer that has been accepted.
For A: The Longest Chromosome > Sizeof(Int32)
Appreciated
5 months ago,
created a post with more than 5 votes.
For A: Speed Of Efetch In Biopython
Teacher
6 months ago,
created an answer with at least 3 up-votes.
For A: Is There A Way To Sort A Biopython Alignment By A Feature Other Then Id?
Appreciated
6 months ago,
created a post with more than 5 votes.
For A: Speed Of Efetch In Biopython
Good Answer
6 months ago,
created an answer that was upvoted at least 5 times.
For A: Speed Of Efetch In Biopython
Teacher
13 months ago,
created an answer with at least 3 up-votes.
For A: How To Have Only Id And Sequence Printed In Output After Parse Sequences From A
Teacher
13 months ago,
created an answer with at least 3 up-votes.
For A: Is There A Way To Sort A Biopython Alignment By A Feature Other Then Id?
Appreciated
13 months ago,
created a post with more than 5 votes.
For A: Speed Of Efetch In Biopython
Epic Question
16 months ago,
created a question with more than 10,000 views.
For Bash $@ (Dollar At Variable) Loses Quote Characters
Teacher
16 months ago,
created an answer with at least 3 up-votes.
For A: Is There A Way To Sort A Biopython Alignment By A Feature Other Then Id?
Scholar
18 months ago,
created an answer that has been accepted.
For A: The Longest Chromosome > Sizeof(Int32)
Good Answer
20 months ago,
created an answer that was upvoted at least 5 times.
For A: Biopython Embl Parser Only Reads One Entry
Teacher
21 months ago,
created an answer with at least 3 up-votes.
For A: Is There A Way To Sort A Biopython Alignment By A Feature Other Then Id?
Teacher
21 months ago,
created an answer with at least 3 up-votes.
For A: Is There A Way To Sort A Biopython Alignment By A Feature Other Then Id?
Scholar
21 months ago,
created an answer that has been accepted.
For A: The Longest Chromosome > Sizeof(Int32)
Teacher
2.0 years ago,
created an answer with at least 3 up-votes.
For A: Is There A Way To Sort A Biopython Alignment By A Feature Other Then Id?
Teacher
2.2 years ago,
created an answer with at least 3 up-votes.
For A: Is There A Way To Sort A Biopython Alignment By A Feature Other Then Id?
Appreciated
2.4 years ago,
created a post with more than 5 votes.
For A: Biopython Embl Parser Only Reads One Entry
Scholar
2.4 years ago,
created an answer that has been accepted.
For A: The Longest Chromosome > Sizeof(Int32)
Teacher
2.4 years ago,
created an answer with at least 3 up-votes.
For A: Is There A Way To Sort A Biopython Alignment By A Feature Other Then Id?
Scholar
2.4 years ago,
created an answer that has been accepted.
For A: BioPython: convert fasta to fastq without quality score input file
Scholar
2.4 years ago,
created an answer that has been accepted.
For A: BioPython: convert fasta to fastq without quality score input file
Scholar
2.5 years ago,
created an answer that has been accepted.
For A: BioPython: convert fasta to fastq without quality score input file
Teacher
2.5 years ago,
created an answer with at least 3 up-votes.
For A: Is There A Way To Sort A Biopython Alignment By A Feature Other Then Id?
Commentator
2.5 years ago,
created a comment with at least 3 up-votes.
For C: Biopython Seqio - Why Is It Repeating Deflines?
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