User: mobiusklein

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mobiusklein160
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Posts by mobiusklein

<prev • 16 results • page 1 of 2 • next >
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Comment: C: Writing Genbank files
... The entity denoted `self` in the code being debugged here was an instance of a class OP's created. I don't think it is 1:1 with `SeqRecord`. If you're trying to write a `SeqRecord` in GenBank format, I think you'd just pass your `SeqRecord` through `SeqIO.write(records, handle, "genbank")`. I'm not ...
written 23 months ago by mobiusklein160
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Answer: A: Is there no way to bypass the Windows requirement for working with Thermo RAW fi
... Thermo has released a new version of their RAW file reader written for `.NET` [http://planetorbitrap.com/rawfilereader#.W9R8oZNKiUk][1]. This is only a library, so you'll need to use a tool written on top of it like [https://github.com/compomics/ThermoRawFileParser][2] in order to convert a RAW file ...
written 23 months ago by mobiusklein160
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Answer: A: How to merge mgf files?
... If none of the MGF files have parameters set at the top of the file, merging MGF files is as simple as concatenating two text files. #!/usr/bin/python with open("output.mgf", 'w') as fh: fh.write(open("a.mgf", 'r').read()) fh.write("\n") fh.write(open("b.mgf", 'r').read ...
written 2.1 years ago by mobiusklein160
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Comment: C: mass spectrometry and bioinformatics
... `pyteomics` will give you access to the information about each spectrum, though it might be difficult to access the total number of spectra acquired directly. Of course, `sum(1 for scan in mzml.read("path/to/file.mzML"))` will work for that. The unassigned question could be solved using the `mzid`, ...
written 2.7 years ago by mobiusklein160
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Answer: A: proteomics and mass spectrometry
... The total number of scans should be listed in the `count` attribute of the `` element of an mzML file. A shell approach to finding this is to run `grep " ...
written 2.7 years ago by mobiusklein160
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Answer: A: Retrieve qualifiers plasmid and pathovar
... If you would like your script to run to completion even when that information is not present, you can wrap each access to `seq_feature.qualifiers` in a `try-except` block catching `KeyError` and `IndexError`: import sys from Bio import SeqIO from Bio import GenBank input_file ...
written 2.8 years ago by mobiusklein160
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Comment: C: Plotting contig length after a MIRA run / iteration
... Have you tried running the program without `plt.show` or `plt.pause`? Both of these functions may cause the program to block until some GUI action is taken. Similarly, have you checked that the conditions in the while loop are not satisfied? ...
written 2.8 years ago by mobiusklein160
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Comment: C: How do I go from UniProt ID to retrieving the gene name?
... The code I posted [here][1] could solve your problem as well, once you add the necessary input and output logic you're looking for. [1]: https://www.biostars.org/p/283313/#283337 ...
written 2.8 years ago by mobiusklein160
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Answer: A: UniProt references to SwissProt references?
... Uniprot's HTTP API is very accommodating about translating identifiers. Requesting `http://www.uniprot.org/uniprot/SYDND_PSEFS` will be redirected to `http://www.uniprot.org/uniprot/C3JYT1`. If you're comfortable with Python, you could use the following approach: from lxml import etree ...
written 2.8 years ago by mobiusklein160
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Answer: A: Writing Genbank files
... It looks like a parenthesis problem. Solution: loc = SeqFeature(FeatureLocation(self.get_start(),self.get_stop()), type="CDS",strand=self.get_strand()) You wrote loc = SeqFeature(FeatureLocation( (self.get_start(),self.get_stop()), t ...
written 2.9 years ago by mobiusklein160

Latest awards to mobiusklein

Great Question 8 months ago, created a question with more than 5,000 views. For Genbank Flat File (.Gb) Proper Usage
Appreciated 2.1 years ago, created a post with more than 5 votes. For A: Writing Genbank files
Scholar 2.8 years ago, created an answer that has been accepted. For A: Writing Genbank files
Teacher 2.8 years ago, created an answer with at least 3 up-votes. For A: Writing Genbank files
Scholar 2.9 years ago, created an answer that has been accepted. For A: Writing Genbank files
Teacher 2.9 years ago, created an answer with at least 3 up-votes. For A: Writing Genbank files
Popular Question 5.3 years ago, created a question with more than 1,000 views. For Genbank Flat File (.Gb) Proper Usage

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