Moderator: Peter

gravatar for Peter
Peter5.6k
Reputation:
5,570
Status:
Trusted
Location:
Scotland, UK
Website:
http://blastedbio.blog...
Scholar ID:
Google Scholar Page
Last seen:
1 week, 6 days ago
Joined:
7 years, 8 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 • 611 results • page 1 of 62 • next >
1
vote
1
answer
146
views
1
answers
Answer: A: Is the order of descriptions and alignments identical while iterating over the B
... In the legacy human readable plain text BLAST output, there was a summary table which is where the descriptions came from, followed by pairwise alignments. You could control the max number of entries to show in each at the BLAST command line. So, it made sense to parse them separately. In the BLAST ...
written 13 days ago by Peter5.6k
0
votes
2
answers
170
views
2
answers
Comment: C: Parsing fasta file using seqIO
... BioPerl's SeqIO? Biopython's SeqIO? Some other seqIO? (Only clear from the tags you've added) ...
written 13 days ago by Peter5.6k
0
votes
1
answer
96
views
1
answers
Answer: A: Blast-XML and Biopython: extract query-anchored results (i.e. MSA)
... There is indeed a ``.multiple_alignment`` attribute in the BLAST record object, and there is code in ``Bio.Blast.NCBIStandalone`` (the plain text BLAST parser) which should populate it. There is an example of sorts in one test within ``Tests/test_NCBITextParser.py`` which might be useful. As a self ...
written 13 days ago by Peter5.6k
0
votes
0
answers
139
views
0
answers
Comment: C: AttributeError: 'Hit' object has no attribute 'sacc_ver'
... What version of Biopython do you have? If updating does not fix this you might want to report this at https://github.com/biopython/biopython/issues ...
written 6 weeks ago by Peter5.6k
0
votes
1
answer
152
views
1
answers
Comment: C: biopython esearch not giving all children taxIDs
... Oh good. I should have tried the example myself really to confirm my hunch. Thanks! ...
written 8 weeks ago by Peter5.6k
0
votes
1
answer
152
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 8 weeks ago by Peter5.6k
0
votes
3
answers
6.3k
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 8 weeks ago by Peter5.6k
0
votes
0
answers
247
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 3 months ago by Peter5.6k
1
vote
1
answer
256
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 3 months ago by Peter5.6k
1
vote
1
answer
243
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 3 months ago by Peter5.6k

Latest awards to Peter

Commentator 8 weeks ago, created a comment with at least 3 up-votes. For C: Is There A Way To Sort A Biopython Alignment By A Feature Other Then Id?
Scholar 5 months ago, created an answer that has been accepted. For A: The Longest Chromosome > Sizeof(Int32)
Appreciated 7 months ago, created a post with more than 5 votes. For A: Speed Of Efetch In Biopython
Good Answer 8 months ago, created an answer that was upvoted at least 5 times. For A: Speed Of Efetch In Biopython
Appreciated 8 months ago, created a post with more than 5 votes. For A: Speed Of Efetch In Biopython
Teacher 8 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 15 months ago, created a post with more than 5 votes. For A: Speed Of Efetch In Biopython
Teacher 15 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 15 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?
Epic Question 18 months ago, created a question with more than 10,000 views. For Bash $@ (Dollar At Variable) Loses Quote Characters
Teacher 18 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 20 months ago, created an answer that has been accepted. For A: The Longest Chromosome > Sizeof(Int32)
Good Answer 22 months ago, created an answer that was upvoted at least 5 times. For A: Biopython Embl Parser Only Reads One Entry
Teacher 23 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 23 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 23 months ago, created an answer that has been accepted. For A: The Longest Chromosome > Sizeof(Int32)
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?
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?
Appreciated 2.5 years ago, created a post with more than 5 votes. For A: Biopython Embl Parser Only Reads One Entry
Scholar 2.5 years ago, created an answer that has been accepted. For A: The Longest Chromosome > Sizeof(Int32)
Teacher 2.6 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 2.6 years ago, created an answer that has been accepted. For A: BioPython: convert fasta to fastq without quality score input file
Scholar 2.6 years ago, created an answer that has been accepted. For A: BioPython: convert fasta to fastq without quality score input file
Scholar 2.7 years ago, created an answer that has been accepted. For A: BioPython: convert fasta to fastq without quality score input file
Teacher 2.7 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?

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1068 users visited in the last hour