Moderator: Peter

gravatar for Peter
Peter5.7k
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5,700
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Location:
Scotland, UK
Website:
http://blastedbio.blog...
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Google Scholar Page
Last seen:
4 days ago
Joined:
8 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

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Comment: C: (solved) I couldn't reproduce the problem of max_target_seqs
... I checked too, before simply asking - the reason there is a cache on archive.org from 2 November is because I requested the snapshot ;) ...
written 12 days ago by Peter5.7k
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Comment: C: Using STDIN with BioPython's PDB methods
... Strange but perhaps you are right and something happens inside argparse? I would suggest setting the defaults to the string ``"-"`` (minus sign) in the command line API, and when you come to call ``get_structure`` use: if args.input == "-": structure = PDB.get_structure("File from stdi ...
written 12 days ago by Peter5.7k
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Comment: C: Using STDIN with BioPython's PDB methods
... I can see from the code you care about the peptide fragments as inferred from the structural data (breaking at discontinuities), otherwise it would be one line to get the PDB sequence out as FASTA format: $ python -c "import sys; from Bio import SeqIO; SeqIO.convert(sys.stdin, 'pdb-atom', sys.s ...
written 12 days ago by Peter5.7k
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Comment: C: Using STDIN with BioPython's PDB methods
... You have forgotten to say what version of Biopython, Python, etc you are using. Also could you simplify your example? Does this work for you - I was using Python 2.7.10 or Python 3.7.0rc1 with Biopython 1.73dev0 (i.e. a prerelease of 1.73 from git) and things seem fine? $ python -c "import sy ...
written 12 days ago by Peter5.7k
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Comment: C: (solved) I couldn't reproduce the problem of max_target_seqs
... I asked by email and https://www.ncbi.nlm.nih.gov/books/NBK279684/#_appendices_Outline_of_the_BLAST_process_ was added in October 2018 (which I mentioned when I linked to it in https://blastedbio.blogspot.com/2018/11/blast-max-alignment-limits-repartee-two.html ), but they weren't sure where the las ...
written 13 days ago by Peter5.7k • updated 13 days ago by genomax58k
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Comment: C: BLAST options: max_target_seqs and num_alignments
... See https://blastedbio.blogspot.com/2018/11/blast-max-alignment-limits-repartee-one.html and https://blastedbio.blogspot.com/2018/11/blast-max-alignment-limits-repartee-two.html for more details - all of ``-max_target_seqs``, ``-num_descriptions`` and ``-num_alignments`` set an internal limit during ...
written 16 days ago by Peter5.7k
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Answer: A: (solved) I couldn't reproduce the problem of max_target_seqs
... It took me a while to publish this on GitHub, but I made a self-contained test case very close to the original 2015 NR example using current hits including ``WP_042303394.1`` and ``KRX89030.1`` but not the tardigrade sequences which were added after 2015: * https://github.com/peterjc/blast_max_tar ...
written 17 days ago by Peter5.7k
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Comment: C: (solved) I couldn't reproduce the problem of max_target_seqs
... Yes, e-value is also used as a filter before the final step - this was also noted in the comment from Harm Nijveen on 3 Dec 2015 on the original max_target_seqs report from Sujai (I would link to it but BioStars insists on embedding the entire gist) ...
written 17 days ago by Peter5.7k
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Comment: C: Trimming TruSeq Universal Adapter (Trimmomatic)
... I was just looking at this for a sample where FASTQC reported lots of the Illumina Universal Adapter present. Looking in the files included with FASTQC, this is defined in Configuration/adapter_list.txt (under the conda opt folder if you use conda), and says: Illumina Universal Adapter AGAT ...
written 12 weeks ago by Peter5.7k
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Comment: C: Arrow Assembly polishing Error "KeyError: 'BASECALLERVERSION'"
... It seems you can't use a BAM file made by mapping a FASTA file in this way as it is missing PacBio meta-data which is expected (e.g. the ``BASECALLERVERSION`` information). You should be able to map the raw unaligned PacBio BAM file, or use the ``*.subreadset.xml`` file which also has metadata. ...
written 4 months ago by Peter5.7k

Latest awards to Peter

Appreciated 13 days ago, created a post with more than 5 votes. For A: Speed Of Efetch In Biopython
Teacher 17 days 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 11 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?
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Scholar 17 months ago, created an answer that has been accepted. For A: The Longest Chromosome > Sizeof(Int32)
Appreciated 19 months ago, created a post with more than 5 votes. For A: Speed Of Efetch In Biopython
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Appreciated 20 months ago, created a post with more than 5 votes. For A: Speed Of Efetch In Biopython
Teacher 20 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 2.3 years ago, created a post with more than 5 votes. For A: Speed Of Efetch In Biopython
Teacher 2.3 years 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
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Epic Question 2.5 years ago, created a question with more than 10,000 views. For Bash $@ (Dollar At Variable) Loses Quote Characters
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Scholar 2.7 years ago, created an answer that has been accepted. For A: The Longest Chromosome > Sizeof(Int32)
Good Answer 2.9 years ago, created an answer that was upvoted at least 5 times. For A: Biopython Embl Parser Only Reads One Entry
Teacher 2.9 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 2.9 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 2.9 years ago, created an answer that has been accepted. For A: The Longest Chromosome > Sizeof(Int32)
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Appreciated 3.5 years ago, created a post with more than 5 votes. For A: Biopython Embl Parser Only Reads One Entry
Scholar 3.5 years ago, created an answer that has been accepted. For A: The Longest Chromosome > Sizeof(Int32)
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Scholar 3.6 years ago, created an answer that has been accepted. For A: BioPython: convert fasta to fastq without quality score input file

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