User: nhaituan

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nhaituan0
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Posts by nhaituan

<prev • 6 results • page 1 of 1 • next >
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Comment: C: Vcftools: Filtering By Multiple Regions (--Positions Flag?)
... Thank you very much, it works for me. ...
written 10 months ago by nhaituan0
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Answer: A: How can extract nucleotide frequency for position on aligned sequences in clusta
... Following method suggested by Healey, I really like to output the PSSM ouput with frequency in each cell as you mentioned. However, I follow your method above, the method gives me something like: 0 7.0 0 7.0 0 0 0 7.0 in the cells ect ... within the output. It seems to be threshold 70%. But I real ...
written 11 months ago by nhaituan0
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Answer: A: Print gene locations from a .gbk file
... ## Thank you very much, here my modified codes: ## from Bio import SeqIO gbk_filename = "N16961_Ch1.gbk" faa_filename = "N16961_Ch1.faa" output_handle = open(faa_filename, "w") for seq_record in SeqIO.parse(gbk_filename, "genbank") : print "Dealing with GenBank record %s" ...
written 13 months ago by nhaituan0
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Answer: A: Download all SRA of one species
... url = 'http://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi' change to url = 'https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi' Than I can get it works ...
written 17 months ago by nhaituan0
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Download all SRA of one species
... I try to run the code below #!/usr/bin/python2.7 import json, urllib query = '"Vibrio cholerae O1"[Organism]"' params = {'db':'sra', 'term':query, 'usehistory':'y', 'retmode':'json',} url = 'http://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi' stream = urllib.urlopen(url, urllib.urlencode ...
software error written 17 months ago by nhaituan0
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Comment: C: How To Remove The Same Sequences In The Fasta Files?
... Really helpful, thank you Brian Bushnell it solved my desire to get unique sequences in my set ...
written 2.5 years ago by nhaituan0

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