Module: bbcflib.c4seq

This module provides functions to run a 4c-seq analysis from reads mapped on a reference genome.

bbcflib.c4seq.c4seq_workflow(ex, job, primers_dict, assembly, c4_url=None, script_path='', logfile=<open file '<stdout>', mode 'w' at 0x2b3dfcadb150>, via='lsf')[source]

Main * open the 4C-seq minilims and create execution * 0. get/create the library * 1. if necessary, calculate the density file from the bam file (mapseq.parallel_density_sql) * 2. calculate the count per fragment for each denstiy file with gfminer:score_by_feature to calculate)

bbcflib.c4seq.density_to_countsPerFrag(ex, file_dict, groups, assembly, regToExclude, script_path, via='lsf')[source]

Main function to compute normalised counts per fragments from a density file.


Create a dictionary with infos for each primer (from file primers.fa)


remove NA present in the 4th column of a file

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