| #!/usr/bin/env julia | |
| using Luxor | |
| function pidigits(n) | |
| result = Int[] | |
| k, a::BigInt, b::BigInt, a1::BigInt, b1::BigInt = 2, 4, 1, 12, 4 | |
| while n > 0 | |
| p, q, k = k * k, 2k + 1, k + 1 | |
| a, b, a1, b1 = a1, b1, p * a + q * a1, p * b + q * b1 |
| library(doParallel) | |
| rpts <- list(list(out="one.html", params=list(some_var="One")), | |
| list(out="two.html", params=list(some_var="Two")), | |
| list(out="three.html", params=list(some_var="Three")), | |
| list(out="four.html", params=list(some_var="Four"))) | |
| do_rpt <- function(r) { | |
| require(rmarkdown) |
| #!/usr/bin/env perl | |
| # | |
| # Downloaded from http://www.uppmax.uu.se/system/files/fastqFormatDetect.pl_.txt on Jan 19, 2016. | |
| # | |
| # Author: Martin Dahlo / modified Jacques Dainat | |
| # | |
| # Usage: perl scriptname.pl <infile> [-a -t <max seconds to search>] | |
| # ex. | |
| # perl scriptname.pl reads.fq | |
| # perl scriptname.pl reads.fq -a |
| Download Google Drive files with WGET | |
| Example Google Drive download link: | |
| https://docs.google.com/open?id=[ID] | |
| To download the file with WGET you need to use this link: | |
| https://googledrive.com/host/[ID] | |
| Example WGET command: |
| "title" "gpl" "bioc_package" "manufacturer" "organism" "data_row_count" | |
| "Illumina Sentrix Array Matrix (SAM) - GoldenGate Methylation Cancer Panel I" "GPL15380" "GGHumanMethCancerPanelv1" "Illumina" "Homo sapiens" 1536 | |
| "Illumina HumanMethylation27 BeadChip (HumanMethylation27_270596_v.1.2)" "GPL8490" "IlluminaHumanMethylation27k" "Illumina, Inc." "Homo sapiens" 27578 | |
| "Illumina HumanMethylation450 BeadChip (HumanMethylation450_15017482)" "GPL13534" "IlluminaHumanMethylation450k" "Illumina, Inc." "Homo sapiens" 485577 | |
| "GE Healthcare/Amersham Biosciences CodeLink™ ADME Rat 16-Assay Bioarray" "GPL2898" "adme16cod" "GE Healthcare" "Rattus norvegicus" 1280 | |
| "[AG] Affymetrix Arabidopsis Genome Array" "GPL71" "ag" "Affymetrix" "Arabidopsis thaliana" 8297 | |
| "[ATH1-121501] Affymetrix Arabidopsis ATH1 Genome Array" "GPL198" "ath1121501" "Affymetrix" "Arabidopsis thaliana" 22810 | |
| "[Bovine] Affymetrix Bovine Genome Array" "GPL2112" "bovine" "Affymetrix" "Bos taurus" 24128 | |
| "[Canine] Affymetrix Canine Genome 1.0 Array" "GPL39 |
| #!/usr/local/bin/python3.3 | |
| from bs4 import BeautifulSoup as bs4 | |
| import requests | |
| import feedparser | |
| import urllib.parse | |
| def findfeed(site): | |
| raw = requests.get(site).text | |
| result = [] | |
| possible_feeds = [] |
| #add 'node_modules' to .gitignore file | |
| git rm -r --cached node_modules | |
| git commit -m 'Remove the now ignored directory node_modules' | |
| git push origin <branch-name> |
SAM and BAM filtering one-liners
@author: David Fredman, david.fredmanAAAAAA@gmail.com (sans poly-A tail)
@dependencies: http://sourceforge.net/projects/bamtools/ and http://samtools.sourceforge.net/
Please extend with additional/faster/better solutions via a pull request!
BWA mapping (using piping for minimal disk I/O)
