Robert Syme robsyme
robsyme
/ Bioruby_neil.rb
Created
June 4, 2009 11:07
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| require "rubygems" | |
| require "bio" | |
| filepath = '/media/Store/data/sn15_genes/080611_sn15_aagi_gene.fas' | |
| Bio::FlatFile.open(filepath) do |flatfile| | |
| flatfile.each do |entry| | |
| puts entry.entry_id | |
| puts entry.seq | |
| puts entry.seq.reverse_complement |
robsyme
/ gist:144288
Created
July 10, 2009 07:10
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| #!/bin/bash | |
| echo "Starting script now..." | |
| sleep 5m | |
| vlc ~/Music/im_going_to_kill_you.mp3 --volume 1024 | |
| echo "Script done" |
robsyme
/ gist:157825
Created
July 29, 2009 02:15
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| %-3.fa: %-1.fa | |
| awk '/^>/ { getline s; if ($$3/($$2-$k+1)>=$c) \ | |
| { print $$0 "\n" s } }' $< \ | |
| |ABYSS $v -k$k -l$l -e0 -o $@ - |
robsyme
/ Blastout_example.xml
Created
November 6, 2009 06:51
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| <BlastOutput> | |
| <BlastOutput_iterations> | |
| <Iteration> | |
| <Iteration_query-def>10000_g</Iteration_query-def> | |
| <Iteration_hits> | |
| <Hit> | |
| <Hit_def>hypothetical protein SNOG_01615</Hit_def> | |
| <Hit_hsps> | |
| <Hsp> | |
| <Hsp_score>1420</Hsp_score> |
robsyme
/ xmltest.rb
Created
November 6, 2009 06:55
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| #!/usr/bin/ruby | |
| require "xml/libxml" | |
| a = XML::Reader.file(ARGV.shift) | |
| while a.read | |
| node = a.node | |
| if node.name == "Iteration" | |
| iteration = XML::Document.string(node.to_s) |
robsyme
/ Renaming getorf files.sh
Created
November 17, 2009 09:28
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| # We start with something like | |
| # >1_1 [17 - 52] 53 8 | |
| # We want to end up with something like | |
| # >Pmm_orf_00001_00001|Pmm_orf_00001_00001 17-52 [Phoma medicaginis var. medicaginis] | |
| # Get rid of the length and coverage info (the '55 8' in the example above) | |
| awk '/^>/ {print $1, $2, $3, $4} /^[^>]/ {print}' OMT5_6frame.fa > nojunk.fasta | |
| # Remove the brackets and underscore | |
| sed -e 's/\[\|\]//g' -e 's/_/ /g' nojunk.fasta > minimal.fasta |
robsyme
/ genemark output renamer.awk
Created
November 18, 2009 04:37
Genemark produces genes with names such as "10000_g". This little awk script pads the id with zeroes and gives a sensible name. Run awk -f scriptname filename
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| BEGIN {FS="_"} | |
| /^>/ {printf ">PmpT_%05d.1|PmpT_%05d hypothetical protein [Phoma medicaginis var. medicaginis]\n", substr($1,2), substr($1,2)} | |
| /^[^>]/ {print} |
robsyme
/ abyss_renamer.awk
Created
November 18, 2009 06:16
Renames fasta files from the abyss assembler
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| /^>/ {printf ">foxy19911_scaf_%05d_length_%d\n", substr($1,2), $2} | |
| /^[^>]/ {print} | |
| # See explanation here: http://picasaweb.google.com/lh/photo/iwAxZYVX1J4yuckbjBCGyg?feat=directlink |
robsyme
/ Bioruby blast to tiny table
Created
November 27, 2009 06:18
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| #!/usr/bin/ruby | |
| require 'rubygems' | |
| require 'bio' | |
| Bio::Blast.reports(ARGF) do |report| | |
| query_name = report.query_def | |
| top_hit = report.hits.max {|one,two| one.bit_score <=> two.bit_score } | |
| puts "#{query_name}\t#{top_hit.target_def}\t#{top_hit.evalue}\t#{top_hit.bit_score}" |
robsyme
/ lcd_test.processing
Created
December 14, 2009 07:17
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| #include <LiquidCrystal.h> // include the LiquidCrystal library | |
| // definitions of program states | |
| #define READY 0 | |
| #define ACTIVE 1 | |
| #define FINISHED 2 | |
| int progState = 0; | |
| // variable declaration |
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