gedankenstuecke

(gdb) run
Starting program: /home/bastian/bin/Metassembler/bin/mateAn -m 5000 -s 500 -p ./MIRA/CEstat/MIRA.ce/MIRA -e 0 -z 3 -q 20 -N 1 -f 6 -c 0.05 -n 30 -a ./MIRA/CEstat/BWTaln/MIRA.mtp.sam
---------- Parameters:
----------------------
-a : ./MIRA/CEstat/BWTaln/MIRA.mtp.sam
-m : 5000
-s : 500
-p : ./MIRA/CEstat/MIRA.ce/MIRA
-e : 0
-z : 3

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[global]

#Mate-pair mapping parameters:
bowtie2_threads=1
bowtie2_read1=clad9_ast1_matepair1.fq
bowtie2_read2=clad9_ast1_matepair2.fq
bowtie2_maxins=5500
bowtie2_minins=4500

#CE-stat computation parameters:

gedankenstuecke

	# this one works, plink is in cwd + conversion to BED files works flawlessly
	
for f in usable_files:
	# gid is the genotype-ID
	gid = f.split("/")[-1].split("_")[1].replace("file","")
	# converts the genotyping file to plink format, using the gid as sample name
	call = "./plink --23file "+ f + " F" + gid + "ID" + gid + "I 1"
	call += " --out 23andme_plink/genotypeid_" + gid
	print "convert gid " + gid
	subprocess.call(call,shell=True)

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<script type="text/javascript">
  // Trying to help @gedankenstuecke here. A bit hard because I don’t speak Rails (neither Ruby) and can’t try live what the output looks like.
  $(function () {
    $("#<%=p.object.phenotype_id.to_json%>").autocomplete({
      source: <%=raw(Phenotype.find_by_id(p.object.phenotype_id).known_phenotypes.to_json)%>
    });
  });
</script>

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Started GET "/users/6/edit" for $IP at 2011-09-29 10:41:56 -0700
  Processing by UsersController#edit as HTML
  Parameters: {"id"=>"6"}
  User Load (2.7ms)  SELECT "users".* FROM "users" WHERE "users"."persistence_token" = 'some_token' LIMIT 1
  User Load (4.1ms)  SELECT "users".* FROM "users" WHERE "users"."id" = 6 LIMIT 1
  CACHE (0.0ms)  SELECT "users".* FROM "users" WHERE "users"."id" = 6 LIMIT 1
  CACHE (0.0ms)  SELECT "users".* FROM "users" WHERE "users"."id" = 6 LIMIT 1
Rendered shared/_error_messages.html.erb (0.1ms)
  UserPhenotype Load (0.3ms)  SELECT "user_phenotypes".* FROM "user_phenotypes" WHERE ("user_phenotypes".user_id = 6)
  Phenotype Load (4.2ms)  SELECT "phenotypes".* FROM "phenotypes" WHERE "phenotypes"."id" = 3 LIMIT 1

gedankenstuecke

Started GET "/users/6/edit" for $IP at 2011-09-29 11:05:57 -0700
  Processing by UsersController#edit as HTML
  Parameters: {"id"=>"6"}
  User Load (3.2ms)  SELECT "users".* FROM "users" WHERE "users"."id" = 6 LIMIT 1
  CACHE (0.0ms)  SELECT "users".* FROM "users" WHERE "users"."id" = 6 LIMIT 1
  CACHE (0.0ms)  SELECT "users".* FROM "users" WHERE "users"."id" = 6 LIMIT 1
  CACHE (0.0ms)  SELECT "users".* FROM "users" WHERE "users"."id" = 6 LIMIT 1
Rendered shared/_error_messages.html.erb (0.1ms)
  UserPhenotype Load (2.3ms)  SELECT "user_phenotypes".* FROM "user_phenotypes" WHERE ("user_phenotypes".user_id = 6)
  Phenotype Load (2.9ms)  SELECT "phenotypes".* FROM "phenotypes" WHERE "phenotypes"."id" = 3 LIMIT 1

gedankenstuecke

# usage: just run "./compare_snps.py 23andme_file_1.txt 23andme_file_2.txt"

import sys

def read_23andme(filename):
	handle = open(filename,"r")
	snps = {}
	for line in handle:
		if line[0] != "#":
			line_array = line.split("\t")

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[{"id":1,"characteristic":"Eye color","known_variations":["Brown","Blue-grey","Green","Blue","Blue-green","Hazel","Mixed","Brown-green","Dark blue","Dark brown","Blue-green ","Light-mixed green","Hazel::Light brown","Braun","Blue grey","Gray-blue","Green-brown","Gray-blue with a center ring of yellowish light brown","Indeterminate brown-green with a subtle grey caste","Blue-grey; broken amber collarette"],"number_of_users":152},{"id":3,"characteristic":"Handedness","known_variations":["Right-handed","Left-handed","Ambidexterous","Left-handed for small motor movement, writing. right-handed for large motor movement, throwing","Right","Right handed","Right handed, only in golfsport left handed!"],"number_of_users":131},{"id":15,"characteristic":"Height","known_variations":["Tall ( >180cm )","188cm","Average  173cm","5'1\" or 155cm","Average ( 165cm < x < 180cm )","183 cm","Average","180cm","5'6\"","Tall ","5'10''","190cm","6'3\"","177.8 cm","193cm","188 cm","5'10\"","189cm","5'2\"","179cm","180 cm","5'5\"","5'4\

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{"snp":{"name":"rs1800795","chromosome":"7","position":"22733170","annotations":{"mendeley":[{"author":"Brandon L Pierce","title":"C-reactive protein, interleukin-6, and prostate cancer risk in men aged 65 years and older.","publication_year":2009,"number_of_readers":2,"open_access":false,"url":"http://www.mendeley.com/research/creactive-protein-interleukin6-and-prostate-cancer-risk-in-men-aged-65-years-and-older/","doi":null},{"author":"Petter Ljungman","title":"DNA variants, plasma levels and variability of interleukin-6 in myocardial infarction survivors: results from the AIRGENE study.","publication_year":2009,"number_of_readers":3,"open_access":false,"url":"http://www.mendeley.com/research/dna-variants-plasma-levels-and-variability-of-interleukin6-in-myocardial-infarction-survivors-results-from-the-airgene-study/","doi":null},{"author":"Joanne P Lagmay","title":"Prognostic significance of interleukin-6 single nucleotide polymorphism genotypes in neuroblastoma: rs1800795 (promoter) and rs8192284 (receptor

gedankenstuecke

{"id":1,"characteristic":"Eye color","description":"There is still work done on the genetics of the eye color and it is already known that different genes participate in the outcome and some associated SNPs have already been identified. \r\n\r\nFor more information about the genetics of eye color you can read the Wikipedia: http://en.wikipedia.org/wiki/Eye_color \r\n\r\nThe SNPedia did already start a project to self-report eye color. See: http://www.snpedia.com/index.php/Eye_color","known_variations":["Brown","Blue-grey","Green","Blue","Blue-green","Hazel","Mixed","Brown-green","Dark blue","Dark brown","Blue-green ","Light-mixed green","Hazel::Light brown","Braun","Blue grey","Gray-blue","Green-brown","Gray-blue with a center ring of yellowish light brown","Indeterminate brown-green with a subtle grey caste","Blue-grey; broken amber collarette"],"users":[{"user_id":6,"variation":"brown"},{"user_id":8,"variation":"Brown"},{"user_id":11,"variation":"brown"},{"user_id":13,"variation":"brown"},{"user_id":14,"var