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#!/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')

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#!/usr/bin/awk -f

# Author: Laurent Manchon ([email protected])
# Split big blast output in xml format into severals files
# Type split_xml_blast without parameters to see usage.


BEGIN{

      {

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#!/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

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#!/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

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#!/bin/sh

# Flacon-style convert to mp3 and split tracks from flac+cue files
# Made by André Rendeiro ([email protected])

# 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

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#!/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

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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

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#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]:

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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"):

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#! /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'