Moderator: Peter
Peter ♦ 5.7k
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- Scotland, UK
- Website:
- http://blastedbio.blog...
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- Last seen:
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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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... 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 9 weeks ago by
Peter ♦ 5.7k
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... 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 9 weeks ago by
Peter ♦ 5.7k
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... 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 9 weeks ago by
Peter ♦ 5.7k
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... 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 9 weeks ago by
Peter ♦ 5.7k
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... 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 ...
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... 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 10 weeks ago by
Peter ♦ 5.7k
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... 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 10 weeks ago by
Peter ♦ 5.7k
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... 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 10 weeks ago by
Peter ♦ 5.7k
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... 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 4 months ago by
Peter ♦ 5.7k
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... 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 6 months ago by
Peter ♦ 5.7k
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