Radhouane Aniba radaniba

## read_and_convert_phylo_trees.py
import ete2

def tree_to_phyloxml (ete_tree):
"""
Convert an Ete2 tree to PhyloXML.

:Parameters:
ete_tree
An Ete2 format tree

## largedata.py
"""Object-oriented approach to handle very large (i.e., genomic) multi-sequence fasta files.

LFastaSeq is the central class of this module providing nucleotide-based access to individual sequence entries as if those entries were separate objects in memory.
Example for use in a command line pipe: varlist_generator | gedit <seq_file> > out_file
This writes a new sequence to <out_file> with nucleotide changes incorporated as specified by the list of variations <varlist>."""

import sys
import IOhelper


## readexcel.rb
### IMPORTS

require 'roo'
require 'pp'

### IMPLEMENTATION ###

# A Excel spreadsheet reader that can clean up column names and convert data.
#
# Assumptions: The data is read off the first sheet of the workbook. The sheet

## bulk-bigwig.pl
# author : Radhouane Aniba

#!/usr/bin/perl -w

@files = <FOLDER_FOR_BigWigs/*.bigWig>;

# For this example we have 4 bigwig files

open(BEDFILE, "FILENAME");
while(<BEDFILE>)

## ambigous.rb
checkseqs [options] INFILE [INFILE, INFILE ...]

where options are:

  --repair-with-conc: patch ambiguous characters with the consensus sequence and save
  --overwrite: newly created files can write over pre-existing ones

Consensus is calculated on a 50% threshold.

#!/usr/bin/env ruby

## fulltextsearch.sql
# CREATE a TABLE TO USE FOR testing fulltext INDEX AND full-text search
DROP TABLE IF EXISTS test;
CREATE TABLE test (
id int UNSIGNED PRIMARY KEY AUTO_INCREMENT,
title char(100) NOT NULL,
article text NOT NULL,
fulltext (article) # CREATE the fulltext INDEX ON FIELD article
)engine=myisam; # Fulltext INDEX only works WITH MyISAM TABLES, which IS usually DEFAULT

# A way TO CREATE a fulltext INDEX ON an already existing TABLE

## format.pl
#!/usr/bin/perl

# This script takes something like this as input:
# ID  WorkId  Date
# 1   2       12-10-2009
# 2   16      01-01-2008</pre>

# And prints out this:
#+-----+----------+---------------+
#|ID   |WorkId    |Date           |

## exon-intron.pl
use Bio::EnsEMBL::Registry;
use Bio::SeqIO;
use Bio::Seq;

my $sp = "mouse";
my $ensembl = "Bio::EnsEMBL::Registry";
$ensembl->load_registry_from_db(
  -host    => 'ensembldb.ensembl.org',
  -user    => 'anonymous',
  -verbose => '1'

## conservation2.pl
#!/usr/bin/perl -w


my $numb = 1;
open(RefGenes, "< ../RefGenes.bed");
while(<RefGenes>)
 {

 print("$numb\r");

## conservedbases.R
cmd_args <- commandArgs(TRUE)

chr <- cmd_args[1]
cbeg <- cmd_args[2]
cend <- cmd_args[3]

tmp <- read.table("tmp",header=F)
nbases <- length(which(tmp$V1 != 0))
vec <- tmp$V1
i <- 1
	import ete2

	def tree_to_phyloxml (ete_tree):
	"""
	Convert an Ete2 tree to PhyloXML.

	:Parameters:
	ete_tree
	An Ete2 format tree
	"""Object-oriented approach to handle very large (i.e., genomic) multi-sequence fasta files.

	LFastaSeq is the central class of this module providing nucleotide-based access to individual sequence entries as if those entries were separate objects in memory.
	Example for use in a command line pipe: varlist_generator \| gedit <seq_file> > out_file
	This writes a new sequence to <out_file> with nucleotide changes incorporated as specified by the list of variations <varlist>."""

	import sys
	import IOhelper
	### IMPORTS

	require 'roo'
	require 'pp'

	### IMPLEMENTATION ###

	# A Excel spreadsheet reader that can clean up column names and convert data.
	#
	# Assumptions: The data is read off the first sheet of the workbook. The sheet
	# author : Radhouane Aniba

	#!/usr/bin/perl -w

	@files = <FOLDER_FOR_BigWigs/*.bigWig>;

	# For this example we have 4 bigwig files

	open(BEDFILE, "FILENAME");
	while(<BEDFILE>)
	checkseqs [options] INFILE [INFILE, INFILE ...]

	where options are:

	--repair-with-conc: patch ambiguous characters with the consensus sequence and save
	--overwrite: newly created files can write over pre-existing ones

	Consensus is calculated on a 50% threshold.

	#!/usr/bin/env ruby
	# CREATE a TABLE TO USE FOR testing fulltext INDEX AND full-text search
	DROP TABLE IF EXISTS test;
	CREATE TABLE test (
	id int UNSIGNED PRIMARY KEY AUTO_INCREMENT,
	title char(100) NOT NULL,
	article text NOT NULL,
	fulltext (article) # CREATE the fulltext INDEX ON FIELD article
	)engine=myisam; # Fulltext INDEX only works WITH MyISAM TABLES, which IS usually DEFAULT

	# A way TO CREATE a fulltext INDEX ON an already existing TABLE
	#!/usr/bin/perl

	# This script takes something like this as input:
	# ID WorkId Date
	# 1 2 12-10-2009
	# 2 16 01-01-2008</pre>

	# And prints out this:
	#+-----+----------+---------------+
	#\|ID \|WorkId \|Date \|
	use Bio::EnsEMBL::Registry;
	use Bio::SeqIO;
	use Bio::Seq;

	my $sp = "mouse";
	my $ensembl = "Bio::EnsEMBL::Registry";
	$ensembl->load_registry_from_db(
	-host => 'ensembldb.ensembl.org',
	-user => 'anonymous',
	-verbose => '1'
	#!/usr/bin/perl -w



	my $numb = 1;
	open(RefGenes, "< ../RefGenes.bed");
	while(<RefGenes>)
	{

	print("$numb\r");
	cmd_args <- commandArgs(TRUE)

	chr <- cmd_args[1]
	cbeg <- cmd_args[2]
	cend <- cmd_args[3]

	tmp <- read.table("tmp",header=F)
	nbases <- length(which(tmp$V1 != 0))
	vec <- tmp$V1
	i <- 1