Moderator: Peter

gravatar for Peter
Peter5.5k
Reputation:
5,540
Status:
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

<prev • 606 results • page 1 of 61 • next >
0
votes
1
answer
81
views
1
answers
Comment: C: biopython esearch not giving all children taxIDs
... 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 Peter5.5k
0
votes
3
answers
6.1k
views
3
answers
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 Peter5.5k
0
votes
0
answers
193
views
0
answers
Comment: C: extract list of positions from fasta file biopython
... 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 Peter5.5k
1
vote
1
answer
195
views
1
answers
Comment: C: tool_dependencies.xml Not Working - Why?
... Did you open this on the Galaxy Q&A site? Could you add the link here please. ...
written 5 weeks ago by Peter5.5k
1
vote
1
answer
196
views
1
answers
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 Peter5.5k
0
votes
1
answer
226
views
1
answers
Comment: C: s. start and s.end in tabular BLAST output are the wrong way around?
... 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 Peter5.5k
1
vote
1
answer
197
views
1
answers
Answer: A: SeqIO.parse reading a 200bp FASTA sequence as 132bp
... 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 Peter5.5k
1
vote
2
answers
382
views
2
answers
Comment: C: How to display mismatched sequences from alignment when using Biopython
... 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 Peter5.5k
0
votes
2
answers
382
views
2
answers
Comment: C: How to display mismatched sequences from alignment when using Biopython
... Please say which version of Biopython you are using, since the pairwise code was rewritten in Biopython 1.68 ...
written 7 weeks ago by Peter5.5k
0
votes
1
answer
1.8k
views
1
answers
Comment: C: How to pull gene identifier from genbank file in Biopython
... 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 Peter5.5k

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?

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 691 users visited in the last hour