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Question Bot90
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Fast Interval Intersection Methodologies
... Most genomic annotations are specified as intervals along the genome. Interval trees have been known to provide an efficient datastructure that allows for very fast overlap querying. Nested Containment Lists have been proposed as an even faster alternative Provide code examples in your progra ...
use interval query genomics written 10.6 years ago by Question Bot90 • updated 10.6 years ago by User 82260
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(Closed) Computing The Reverse And Complement Of A Sequence With Pygr
... Computing the reverse complement with the Pygr bioinformatics framework: # # Reverse complement example with pygr # from pygr.sequence import Sequence # needs a separate function to reverse strings def rev(it): "Reverses an interable and returns it as a string" return ''.join(reversed(it) ...
sequence python pygr use written 10.6 years ago by Question Bot90 • updated 10.6 years ago by Jane ♦♦ 0
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Computing The Reverse And Complement Of A Sequence With Biopython
... An example that computes the reverse complement of a sequence with BioPython # # Reverse complement example with BioPython # from Bio.Seq import Seq # a separate function to reverse strings (or other iterables) def rev(it): "Reverses an interable and returns it as a string" return ''.join ...
sequence biopython python written 10.6 years ago by Question Bot90 • updated 10.6 years ago by Wubin Qu0
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Answer: A: How Do I Convert An Illumina Export File To Bed?
... I found a script on another site, Uses perl but I have not checked for correctness: #!/usr/bin/perl use strict; use warnings; use IO::File; my $filename = shift @ARGV; die "Usage\n\tperl sorted2bed.pl s_X_sorted.txt > s_X_sorted.bed\n" unless $filename; chomp $filename; my $fh = new IO::File; ...
written 10.7 years ago by Question Bot90 • updated 10.7 years ago by Wubin Qu0
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Answer: A: Site Use Guidelines
... If you are shy about asking the question on your own behalf submit it to to the Question Bot and it will be posted anonymously. Send email to the Question Bot link at the bottom. ...
written 11.0 years ago by Question Bot90 • updated 11.0 years ago by Jane ♦♦ 0
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16 follow
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How To Generate Multi-Nucleotide Occupancy Counts For Each Coordinate Of My Reads?
... I need to generate nucleotide occupancy counts for each position of a given sequence then summed over each of the input sequences. An example desired output (for di-nucleotide AT): ...
nucleotides written 11.0 years ago by Question Bot90 • updated 11.0 years ago by Jane ♦♦ 0

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