Moderator: a.zielezinski

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a.zielezinski6.2k
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Andrzej Zielezinski

Posts by a.zielezinski

<prev • 211 results • page 1 of 22 • next >
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Comment: C: Extracting fasta sequences with identical header
... I edited my answer. The code you pasted in your question has the problem with indentations (no idents after try: or with:) so it doesn't work at all. I would test my code if you provide some sample lines of your input files. ...
written 2 days ago by a.zielezinski6.2k
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Answer: A: Extracting fasta sequences with identical header
... I didn't test it: #!/usr/bin/env python # -*- coding: utf-8 -*- """Extract sequences from a fasta file if their name is in a 'wanted' file. Wanted file contains one sequence name per line. Usage: %program """ import sys import re try: ...
written 2 days ago by a.zielezinski6.2k
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Answer: A: BLAST against multiple databases and get top hit from each one
... You can get a single top hit for each of your query sequence. In standalone BLAST+, you just need to add the -max_target_seqs 1 parameter when running BLAST. The parameter defines the maximum number of aligned sequences to keep in output. For example: blastp -query yourseqs.fasta -db db1.fasta ...
written 11 days ago by a.zielezinski6.2k
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Comment: C: Progress bar to measure blast running time?
... Very nice idea. By the way, does the `XML/ASN.1` format report query identifiers that don't have any matches in database? I know that `outfmt=6/7` exclude these queries from the output. ...
written 18 days ago by a.zielezinski6.2k
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Answer: A: Creating a dictionary within a class
... If you want your class `FastaFile` to behave like dictionary you just need to overload the builtin method `__getitem__()` inside your class. def __getitem__(self, k): return self._map[k] The instances of your class will then have this behaviour: >>> cff = FastaFile("obs.f ...
written 18 days ago by a.zielezinski6.2k
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Comment: C: Creating a dictionary within a class
... `cff._map` is a dictionary. So `print cff._map["ID001"]` statement will give you `'ACGTA'`. I answered your question below. Is this what you wanted? ...
written 18 days ago by a.zielezinski6.2k
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Answer: A: Virulent strains in S aureus
... I would use [PATRIC database][1] (Bioinformatics Database and Analysis Resource Center). There is a list of all *Staphylococcus aureus* strains (currently: [8863 genomes][4]) [*last update: 30-Jan-2017*]. You can then **filter the list of organisms according to**: 1. Disease (e.g. *pneumonia*, ...
written 4 weeks ago by a.zielezinski6.2k
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Answer: A: miRNA Target database?
... You may want to look at [the list][1] of **70** miRNA target prediction resources. The ranking list includes various information about each database, such as: 1. list of features 2. list of organisms 3. last update 4. citations per year 5. popularity 6. paper & url [1]: http://mirand ...
written 6 weeks ago by a.zielezinski6.2k
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Answer: A: Biopython Emboss Needle gives no output file
... You just created a needle command line object without actually running the program :) To run the command, type: stdout, stderr = needle_cline() print(stdout + stderr) The output file `needle.txt` should be right there for you. For more information, read the whole [6.4.5. section (EMBOSS n ...
written 6 weeks ago by a.zielezinski6.2k
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Comment: C: Finding Conserved Protein Domains
... You can also copy & pase your DNA sequence to [Pfam][1]. A six-frame translation of your DNA will be performed automatically, then each frame will be searched for protein domains. [1]: http://pfam.xfam.org/search#tabview=tab0 ...
written 6 weeks ago by a.zielezinski6.2k

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