Philipp Bayer philippbayer
philippbayer
/ big_table.csv
Created
August 16, 2016 07:48
Table 11.8 from https://www.researchgate.net/profile/Guido_Brandt/publication/271510016_Bestandig_ist_nur_der_Wandel_Die_Rekonstruktion_der_Besiedelungsgeschichte_Europas_wahrend_des_Neolithikums_mittels_palao-_und_populationsgenetischer_Verfahren/links/54c9f5ea0cf2807dcc285b9f.pdf
We can make this file beautiful and searchable if this error is corrected: It looks like row 3 should actually have 83 columns, instead of 8 in line 2.
This file contains hidden or bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| ,EGY,LIB,MOR,TUN,BER,KAZ,KYR,MON,TAJ,TUK,UZB,CHI,JAP,KOR,TAI,KHA,YAK,KOY,BUR,TUV,ALT,EVE,OSS,RUS,MAY,THA,VIE,ARM,AZE,GEO,IRA,IRQ,JOR,KUW,LEB,PAL,DRZ,UAE,SAU,SYR,TUR,YEM,AUS,FRA,GER,SWZ,BEL,CZE,HUN,POL,SVK,SLO,UKR,DEN,EST,FIN,ICE,LAT,LIT,NOR,SWE,ITA,POR,SPA,BAS,ALB,BOS,BUL,GRE,ROM,ENG,SCO,IRE,LBK,RSK,SCG,BAK,SMK,BBK,SKK,GBK,AK | |
| EGY,,0.01245,0.01319,0.00715,0.01008,0.03598,0.04494,0.06238,0.02335,0.02131,0.02084,0.05501,0.08637,0.07495,0.05289,0.03737,0.13086,0.14389,0.08129,0.10776,0.07019,0.1663,0.03793,0.03947,0.06878,0.05801,0.06368,0.0804,0.03544,0.02624,0.0175,0.0209,0.00809,0.01159,0.01931,0.0171,0.01289,0.00961,0.02313,0.04929,0.04464,0.01231,0.03044,0.0473,0.0644,0.03228,0.03649,0.03676,0.03025,0.03565,0.03031,0.03195,0.02504,0.03857,0.05281,0.03815,0.03736,0.03553,0.02851,0.04302,0.0349,0.03529,0.02309,0.04521,0.05932,0.02248,0.03886,0.03379,0.03181,0.05633,0.04491,0.03865,0.03903,0.03998,-0.01375,0.02018,-0.00498,0.0263,0.02453,0.01804,0.03597,0.01239 | |
| LIB,0.01261,,0.00932,0.00794,0.00925,0.03915,0.047 |
philippbayer
/ distance_matrix.csv
Last active
August 15, 2016 13:20
Table 4 from http://link.springer.com/article/10.1007/BF02715828
This file contains hidden or bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| Turkish | French | Central Asians | German | Bulgarian | British | Finnish | Greek | ||
|---|---|---|---|---|---|---|---|---|---|
| Turkish | 0.9509 | 0.9989 | 0.9503 | 0.9584 | 0.9994 | 0.9756 | 0.9506 | ||
| French | 0.0504 | 0.9502 | 0.9991 | 0.9923 | 0.9508 | 0.9277 | 0.9994 | ||
| Central Asians | 0.0011 | 0.051 | 0.9498 | 0.9577 | 0.9988 | 0.9753 | 0.9501 | ||
| German | 0.051 | 0.0009 | 0.0515 | 0.9918 | 0.9504 | 0.9273 | 0.9992 | ||
| Bulgarian | 0.0425 | 0.0077 | 0.0432 | 0.0082 | 0.9585 | 0.9352 | 0.9923 | ||
| British | 0.0006 | 0.0504 | 0.0012 | 0.0508 | 0.0424 | 0.9756 | 0.9507 | ||
| Finnish | 0.0247 | 0.0751 | 0.025 | 0.0755 | 0.067 | 0.0247 | 0.9276 | ||
| Greek | 0.0507 | 0.0006 | 0.0511 | 0.0008 | 0.0078 | 0.0506 | 0.0752 |
philippbayer
/ Broadband_data.csv
Created
July 28, 2016 12:30
This file contains hidden or bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| State | Land in km2 | pop/km2 | Fixed broadband per 100 people | |
|---|---|---|---|---|
| Australia | 7633565 | 3.14 | 27.9 | |
| Austria | 82445 | 101 | 28.1 | |
| Belgium | 30278 | 371 | 36.4 | |
| Canada | 9093507 | 3.65 | 35.8 | |
| Chile | 743812 | 22 | 14.6 | |
| Czech Republic | 77247 | 133 | 28.6 | |
| Denmark | 42434 | 131 | 41.9 | |
| Estonia | 42388 | 29 | 28.5 | |
| Finland | 303815 | 16.2 | 31.7 |
philippbayer
/ Survival.R
Created
July 14, 2016 13:34
This file contains hidden or bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| library(survival) | |
| # to make the survobj (source: https://rstudio-pubs-static.s3.amazonaws.com/5588_72eb65bfbe0a4cb7b655d2eee0751584.html ) | |
| a = read.table("table2.csv",stringsAsFactors=F,sep=",") | |
| a$survObj <- with(a, Surv(time, status == 1)) | |
| km <- survfit(survObj ~ 1, data = a, conf.type = "log-log") | |
| plot(km) |
philippbayer
/ PMs.csv
Last active
July 14, 2016 13:39
Source: https://en.wikipedia.org/wiki/List_of_Prime_Ministers_of_Australia (Status=2 died in office, or maybe abducted by Soviet submarines while swimming)
This file contains hidden or bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| V1 | Name | Start | End | Status | Length | survObj | |
|---|---|---|---|---|---|---|---|
| 1 | Sir Edmund Barton | 1 January 1901 | 24 September 1903 | 1 | 996 | 996 | |
| 2 | John Gorton | 10 January 1968 | 10 March 1971 | 1 | 1155 | 1155 | |
| 3 | William McMahon | 10 March 1971 | 5 December 1972 | 1 | 636 | 636 | |
| 4 | Bob Hawke | 11 March 1983 | 20 December 1991 | 1 | 3206 | 3206 | |
| 5 | John Howard | 11 March 1996 | 3 December 2007 | 1 | 4284 | 4284 | |
| 6 | Malcolm Fraser | 11 November 1975 | 11 March 1983 | 1 | 2677 | 2677 | |
| 7 | Ben Chifley | 13 July 1945 | 19 December 1949 | 1 | 1620 | 1620 | |
| 8 | Andrew Fisher | 13 November 1908 | 2 June 1909 | 1 | 201 | 201 | |
| 9 | Andrew Fisher | 17 September 1914 | 27 October 1915 | 1 | 405 | 405 |
philippbayer
/ UPGMA_books
Created
June 9, 2016 13:27
A small example on how to use mash to make a wrong UPGMA tree
This file contains hidden or bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| # download | |
| wget http://www.gutenberg.org/cache/epub/2265/pg2265.txt -O Hamlet.txt | |
| wget http://www.gutenberg.org/cache/epub/1120/pg1120.txt -o Caesar.txt | |
| wget http://www.gutenberg.org/cache/epub/1120/pg1120.txt -O Caesar.txt | |
| wget http://www.gutenberg.org/cache/epub/1121/pg1121.txt -O as_you_like_it.txt | |
| wget http://www.gutenberg.org/cache/epub/1129/pg1129.txt -O macbeth.txt | |
| wget http://www.gutenberg.org/files/5500/5500-0.txt -O Advancement_of_Learning.txt | |
| wget http://www.gutenberg.org/cache/epub/2434/pg2434.txt -O New_Atlantis.txt | |
| wget http://www.gutenberg.org/files/52190/52190-0.txt -O Ecce_homo.txt |
philippbayer
/ _navbar.html.erb
Created
May 30, 2016 14:25
philippbayer
/ getFirstLast10Rows.py
Created
April 5, 2016 06:00
This tiny script takes bedtools (or similar) output and prints the first and last 10 rows for a contig
This file contains hidden or bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| import Queue | |
| import sys | |
| # prints first 10 and last 10 rows for each contig | |
| # does NOT guarantee that the first and 10 don't overlap (use uniq) | |
| fh = open(sys.argv[1]) | |
| header = fh.readline() | |
| q = Queue.Queue(10) # for the last elements | |
| current_contig = "" | |
| for line in fh: |
This file contains hidden or bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| HOMEBREW_VERSION: 0.9.5 | |
| ORIGIN: https://github.com/Linuxbrew/linuxbrew.git | |
| HEAD: 4a4df9a4a4708e9a0ff2794802f270f86775a091 | |
| Last commit: 25 hours ago | |
| HOMEBREW_PREFIX: /gpfs1/homes/pbayer/.linuxbrew | |
| HOMEBREW_REPOSITORY: /gpfs1/homes/pbayer/.linuxbrew | |
| HOMEBREW_CELLAR: /gpfs1/homes/pbayer/.linuxbrew/Cellar | |
| HOMEBREW_BOTTLE_DOMAIN: https://linuxbrew.bintray.com | |
| CPU: 24-core 64-bit haswell | |
| Kernel: Linux 2.6.32-431.11.2.el6.x86_64 x86_64 GNU/Linux |
This file contains hidden or bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| 2016-02-29 13:13:28 +1000 | |
| ./install.sh | |
| ++ pwd | |
| + ROOT=/tmp/masurca20160229-26095-1pbb98n/MaSuRCA-2.3.2b | |
| + '[' -z /gpfs1/homes/pbayer/.linuxbrew/Cellar/masurca/2.3.2b ']' | |
| + mkdir -p dist-bin | |
| + PATH=/home/pbayer/.rbenv/versions/2.3.0/bin:/gpfs1/homes/pbayer/.rbenv/libexec:/home/pbayer/.rbenv/plugins/ruby-build/bin:/gpfs1/homes/pbayer/.linuxbrew/bin:/gpfs1/homes/pbayer/.linuxbrew/sbin:/home/pbayer/.rbenv/shims:/90days/uqccha18/groupEnv/flashlite/scripts:/90days/uqccha18/groupEnv/flashlite/apps/bin:/90days/uqccha18/groupEnv/flashlite/bin:.:/home/pbayer/.linuxbrew/bin:/home/pbayer/.rbenv/bin:/home/pbayer/jre1.8.0_74/bin:/home/pbayer/localpython/bin:/home/pbayer/localperl/bin:/opt/openmpi/bin:/usr/lib64/qt-3.3/bin:/opt/torque-rcc/default/bin:/opt/torque-rcc/default/sbin:/usr/local/bin:/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/sbin:/opt/bio/ncbi/bin:/opt/bio/mpiblast/bin:/opt/bio/EMBOSS/bin:/opt/bio/clustalw/bin:/opt/bio/tcoffee/bin:/opt/bio/hmmer/bin:/opt/bio/phylip/exe:/opt/bio/mrbayes:/opt/bio/fasta:/opt/bio/glim |