bbcflib::createlib Namespace Reference

Functions
def	getRestEnzymeOccAndSeq
def	parse_fragFile
def	coverageInRepeats
def	getEnzymeSeqId
def	lib_exists
def	createLibrary
def	get_libForGrp
Variables
string	hts_url = "http://htsstation.epfl.ch/4cseq/"
string	GlobalRepbasePath = "/archive/epfl/bbcf/data/genomes/repeats"

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Detailed Description

=========================
Module: bbcflib.createlib
=========================

Functions to create and manage a restrition fragments library in a 4c-seq analysis.

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Function Documentation

def bbcflib::createlib::coverageInRepeats	(		ex,
			infile,
			genomeName = 'mm9',
			repeatsPath = GlobalRepbasePath,
			outdir = None,
			via = 'lsf'
	)

Completes the segment info bed file with the coverage in repeats of each segment.
For now, works only for mm9, hg19 and dm3.

def bbcflib::createlib::createLibrary	(		ex,
			assembly_or_fasta,
			params,
			hts_url = hts_url,
			via = 'local'
	)

Main call to create the library

def bbcflib::createlib::getEnzymeSeqId	(		enzyme_id,
			byId = False,
			enzymes_list = [],
			url = hts_url
	)

Returns the restriction site corresponding to a given enzyme id (from existing enzymes)

def bbcflib::createlib::getRestEnzymeOccAndSeq	(		fasta_file,
			prim_site,
			sec_site,
			l_seg,
			l_type = 'typeI'
	)

Creates segments and fragments files of the new library from the genome sequence 
(via a call to getRestEnzymeOccAndSeq.pl).

def bbcflib::createlib::lib_exists	(		params,
			libs_list = None,
			url = hts_url
	)

Return id or filename corresponding to the library described in params.

def bbcflib::createlib::parse_fragFile	(		fragfile,
			chrom_dict = {}
	)

Parse fragment file to create segment info bed file and fragment bed file