View cutdiff_output_parser.py
This file contains 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
#!/usr/bin/python | |
from sys import argv | |
import csv,StringIO | |
import math | |
expr = open(argv[1], 'r') | |
output = open(argv[1] + '.bed','w') | |
output_log = open(argv[1] + '_log2.bed','w') |
View split_xml_blast_output.awk
This file contains 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
#!/usr/bin/awk -f | |
# Author: Laurent Manchon (lmanchon@univ-montp2.fr) | |
# Split big blast output in xml format into severals files | |
# Type split_xml_blast without parameters to see usage. | |
BEGIN{ | |
{ |
View jaspar2fasta.pl
This file contains 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
#!/usr/bin/perl -w | |
# Convert JASPAR matrices to fasta-like format | |
# Written by Martin C Frith | |
# I intend that anyone who finds this code useful be free to use, | |
# modify, or redistribute it without any restrictions | |
=head1 NAME | |
jaspar2fasta - conversion of JASPAR database release for use with clover |
View ChIP_mapping_pipeline.sh
This file contains 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
#!/bin/bash | |
# Pipeline for PE samples | |
# paths and variables to change | |
RAW=/sysdev/s3/share/data/oikopleura/chip-seq/raw | |
MAPPED=/sysdev/s3/share/data/oikopleura/chip-seq/mapped | |
GENOMEREF=~/data/oikopleura/assembly/Oikopleura_reference_unmasked_v3.0.fa | |
CHRSIZES=~/data/oikopleura/assembly/Oikopleura_reference_chrSizes.tsv |
View flac+cue2mp3.sh
This file contains 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
#!/bin/sh | |
# Flacon-style convert to mp3 and split tracks from flac+cue files | |
# Made by André Rendeiro (afrendeiro@gmail.com) | |
# Rename | |
{ | |
find . -name '* *' | while read file; do target=`echo "$file" | sed 's/ /_/g'`; mv "$file" "$target"; done | |
find . -name '* *' | while read file; do target=`echo "$file" | sed 's/ /_/g'`; mv "$file" "$target"; done | |
find . -name '* *' | while read file; do target=`echo "$file" | sed 's/ /_/g'`; mv "$file" "$target"; done |
View speedtouchkey.py
This file contains 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
#!/usr/bin/env python | |
#original: http://www.korokithakis.net/posts/thomsonspeedtouch-routers-and-wpa-keys/ | |
#modified from: http://pastie.org/3108591 | |
import sys | |
import hashlib | |
from binascii import hexlify, unhexlify | |
from itertools import product | |
from multiprocessing import Process |
View annotateTSSs.sh
This file contains 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
awk -v OFS='\t' '$6 == "+" {print $1, $2, $2+1, $4, $5, $6}' annotationFile.bed > tmp | |
awk -v OFS='\t' '$6 == "-" {print $1, $3, $3+1, $4, $5, $6}' annotationFile.bed >> tmp | |
bedtools sort -i tmp > annotationFile.TSSs.bed |
View gradeStuff.py
This file contains 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
#Create a method that reads in a score (1-100) and prints out the corresponding character (grade). | |
#Assume the following grade assignment: 'A' = 100-81 points, 'B' = 80-61 points, 'C' = 60-41 points, 'D' = 40-21 points and 'E' = 20-1 points. | |
# Don't use the "if" control structure | |
score = 1 | |
scale = [range(81,100), range(61,80), range(41,60), range(21,40), range(1,20)] | |
grades = ["A", "B", "C", "D", "E"] | |
for grade in range(0, len(scale)): | |
while score in scale[grade]: |
View getChrSizesFromFasta.py
This file contains 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 csv | |
from Bio import SeqIO | |
fastagenome = "data/oikopleura/assembly/Oikopleura_reference_unmasked_v3.0.fa" | |
output = "data/oikopleura/assembly/Oikopleura_reference_chrSizes.tsv" | |
myfile = open(output, "wb") | |
spamwriter = csv.writer(myfile, delimiter='\t', quoting=csv.QUOTE_MINIMAL) | |
for seq_record in SeqIO.parse(fastagenome, "fasta"): |
View pairwiseAlign.py
This file contains 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
#! /usr/bin/python | |
# Forward-recursion with pruning | |
# An algorithm for doing exact alignment of two sequences | |
# Forward recursion is used, with pruning of cells | |
# two sequences to align | |
S1 = 'APPLR' | |
S2 = 'APPLS' |
OlderNewer