Module: bbcflib.microbiome

bbcflib.microbiome.bam_to_annot_counts(bamfiles, annotations_file, pref_name='', output=None)[source]

Scan each bam file of a list and calculate the corrected counts for each annotation key present in the “annotations_file”.

bbcflib.microbiome.microbiome_workflow(ex, job, assembly, logfile=<open file '<stdout>', mode 'w' at 0x2b3dfcadb150>, via='lsf')[source]

Main:

    1. retrieve bam files from mapseq job
  • 0.a. merge bam files (=> 1 bam file per group)
    1. for each group:
  • 1.a get counts per group (=> 1 file per group)
  • 1.b get counts per Level (Kingdom, Phylum, Class, Order, Family, Genus and Species) (=> 1 file per level / per group)
    1. combine counts
  • 2.a combine counts for all groups (=> 1 combined file)
  • 2.b combine counts per level for all groups (=> 1 combined file per Level)
    1. generate barplots (=> 1 plot per group + per level + per combined files)

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