Moderator: a.zielezinski

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a.zielezinski7.0k
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Andrzej Zielezinski

Posts by a.zielezinski

<prev • 256 results • page 1 of 26 • next >
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Comment: C: basic problem on loop python
... But what if `cdna` directory is empty or it has only `*.cdna.abinitio.fa.gz` file (not `cdna.all.fa` as @elisheva requested) :P ...
written 6 weeks ago by a.zielezinski7.0k
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Answer: A: basic problem on loop python
... Code: fh = open('Content.txt') oh = open('ftp.txt', 'w') for line in fh: if line.startswith('./'): organism = line.split('/')[1].rstrip(':') if 'cdna.all.fa' in line: oh.write(organism + '\n') fh.close() oh.close() ftp.txt: ano ...
written 6 weeks ago by a.zielezinski7.0k
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Answer: A: Printing features of a specific type only from a Genbank file with Biopython
... Code: from Bio import Entrez from Bio import SeqIO Entrez.email = 'yourmail@mail.com' qid = "NM_001135" handle = Entrez.efetch(db="nucleotide", rettype="gb", retmode="text", id=qid) seq_record = SeqIO.read(handle, "gb") for feat in seq_record.features: if fe ...
written 6 weeks ago by a.zielezinski7.0k
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Comment: C: Tool To Generate Venn Diagrams for 8 data sets?
... Sorry, I couldn't resist. ![enter image description here][1] [1]: http://i65.tinypic.com/s27i29.png ...
written 7 weeks ago by a.zielezinski7.0k
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Comment: C: NCBI vs Ensembl - which one to chose - for downloading protein fasta files
... Uniprot has built a database of reference proteomes for most organisms sequences today: http://www.uniprot.org/proteomes/ ...
written 7 weeks ago by a.zielezinski7.0k
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Answer: A: why only 2 amino acids are used in gene prediction
... Hexamers (6 nt long words) are accepted as the most accurate *k*-mer frequency based measure of coding potential. In 1992, a systematic study of more than twenty compositional properties indicated that hexamer composition gave the best discrimination between coding and non-coding regions ([Fickett & ...
written 7 weeks ago by a.zielezinski7.0k
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Comment: C: OrthoMCL step 12: [mclxReadDimensions] could not parse header
... If Philipp and lu.ne correctly answered your question, please accept their answers by clicking on the check mark beside their posts. Accepting an answer is important as it both rewards posters for solving your problem and informs others that your issue is resolved. If an answer has helped you solve ...
written 8 weeks ago by a.zielezinski7.0k
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Answer: A: Bacterial phylogeny download for a list of species
... [NCBI Taxonomy database][1] provides a feature named [Common Tree][2], where you can provide a list of taxonomy identifiers to create a tree of species you are interested in. The tree will be displayed in your browser and you can save it to a file (in text or Newick format). For example, here is a ...
written 8 weeks ago by a.zielezinski7.0k
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Answer: A: [BioPython] Parse blast tabular output
... A long time ago I wrote a module for handling tabular BLAST output (`-outfmt 6` / `-m8`). Maybe you will find it useful. \gist https://gist.github.com/aziele/e060d1c0d1ef2acb4bd67e2fc0f165a6 **SAMPLE USAGE:** Filename: `test.outfmt6` cgl|CAGL0A00187g ecy|Ecym_8168 31.11 90 49 3 597 676 95 18 ...
written 8 weeks ago by a.zielezinski7.0k
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Comment: C: genomics overlap python error
... Sorry for that, I made a mistake. It should be: `st, en = [cst, cen] if cstr == '+' else [cen, cst]`. I also corrected the answer. If you want start always less than end (regardless of the strand), just change this line to `st, en = cst, cen`. ...
written 9 weeks ago by a.zielezinski7.0k

Latest awards to a.zielezinski

Scholar 6 weeks ago, created an answer that has been accepted. For A: biopython pairwise2 result to a file
Teacher 6 weeks ago, created an answer with at least 3 up-votes. For A: biopython pairwise2 result to a file
Appreciated 7 weeks ago, created a post with more than 5 votes. For A: How To Separate A List Of Genomics Regions Into Several Disjoint Subsets
Commentator 7 weeks ago, created a comment with at least 3 up-votes. For C: 200Bp Long Query Returning 201Bp
Teacher 7 weeks ago, created an answer with at least 3 up-votes. For A: biopython pairwise2 result to a file
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Appreciated 11 weeks ago, created a post with more than 5 votes. For A: How To Separate A List Of Genomics Regions Into Several Disjoint Subsets
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Appreciated 3 months ago, created a post with more than 5 votes. For A: How To Separate A List Of Genomics Regions Into Several Disjoint Subsets
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