User: atapee

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atapee10
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10
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New User
Location:
Germany
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3 years, 8 months ago
Joined:
6 years, 6 months ago
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a*****@gmail.com

about me

Posts by atapee

<prev • 12 results • page 1 of 2 • next >
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Is it possible to get local blast output directly in Biopython, without making and reading an XML file?
... Hi I am currently filtering through a large amount of reads from a 454 machine. I would like to blast every read against a local blast database and check if the sequence is indeed from a targeted genus/species and not a contaminant. For that i would like to get a direct output to python, so i can r ...
biopython blast written 4.7 years ago by atapee10 • updated 4.7 years ago by Peter5.8k
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Comment: C: Biopython: qBLAST only retrieving 50 hits, inserting "hitlist_size=100" does not
... Thank you, that did the trick! Is everything else quoted properly?  ...
written 4.9 years ago by atapee10
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Biopython: qBLAST only retrieving 50 hits, inserting "hitlist_size=100" does not change it.
... I've been wanting to retrieve the first 100 hits from my blast, but it always produces only the first 50 hits (as set by default) and I am unable to change it.   save_file = open("C:/Users/.../my_blast.xml", "w") result_handle = NCBIWWW.qblast("blastp", "nr", "4504191", "hitlist_size=100", entrez ...
biopython blast written 4.9 years ago by atapee10 • updated 4.9 years ago by David W4.7k
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Answer: C: BioPython: CodeML FileNotFoundError: [WinError 2]
... I think i have found the problem...  this is the control file that CodeML produces:  seqfile = kodonskaporavnava.fasta outfile = results.out treefile = novodrevo1.nwk kappa = 4.54006 cleandata = 1 RateAncestor = 0 seqtype = 1 model = 0 noisy = 0 verbose = 0 fix_alpha = 1 NSsites = 0 1 2 CodonFreq ...
written 5.0 years ago by atapee10
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Comment: C: BioPython: CodeML FileNotFoundError: [WinError 2]
... It has been deleted...  ...
written 5.0 years ago by atapee10
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Comment: C: BioPython: CodeML FileNotFoundError: [WinError 2]
... from Bio.Phylo.PAML import codeml Well all the old errors are back, it had a random flash previously  ...
written 5.0 years ago by atapee10
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Comment: C: BioPython: CodeML FileNotFoundError: [WinError 2]
... It could be the Environmental varibles, but it would be strange since other biopython tools work.  I have been using these files with other Biopython tools, they are probably not the cause of the problem.  I have been able to reduce the errors to only one: File "C:/Python34/standalone.py", line 2 ...
written 5.0 years ago by atapee10
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[solved] BioPython: CodeML FileNotFoundError: [WinError 2]
... I have been trying to run a basic codeML wraper, that I got from the Biopython cookbook, but it doesn't seem to be working. I have been getting the error "FileNotFoundError: [WinError 2]". This is what the piece of code looks like: def codeML(outfile):     cml = codeml.Codeml()     cml.alignment ...
paml python biopython codeml winerror written 5.0 years ago by atapee10 • updated 5.0 years ago by RamRS25k
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Comment: C: BioPython: collapsing nodes on tree if node in list.
... Well, not directly, but replacing  newtree.collapse(name) with  newtree.prune(targe=name) fixed everything, thank you very much! :)  ...
written 5.0 years ago by atapee10
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BioPython: collapsing nodes on tree if node in list.
... I have phylogenetic tree in newick format and I would like to remove all species from it that are on a specific list This is the tree:  ((((((((('Capra hircus', 'Ovis aries'), 'Pantholops hodgsonii'), ('Bubalus bubalis', ('Bison bison bison', ('Bos mutus', ('Bos primigenius', 'Bos taurus'))))), 'M ...
phylogenetics biopython phyllo written 5.0 years ago by atapee10

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Popular Question 4.7 years ago, created a question with more than 1,000 views. For Software For Aligning Cdna Onto Reference Genomic Sequences To Retrieve Introns

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