LBMC » NucleoMiner

configurator.CSV_SAMPLE_FILE = None

   Path to cvs file that contains sample information.

configurator.BOWTIE_BUILD_BIN = None

   Path for bowtie2 build bin.

configurator.BOWTIE2_BIN = None

   Path for bowtie2 bin.

configurator.SAMTOOLS_BIN = None

   Path for samtools bin.

configurator.BEDTOOLS_BIN = None

   Path for bedtools bin.

configurator.TF_BIN = None

   Path for TemplateFilter bin.

configurator.TF_TEMPLATES_FILE = None

   Path for TemplateFilter templates file.

configurator.ILLUMINA_OUTPUTFILE_PREFIX = None

   Prefix for Illumina fastq output files.

configurator.INDEX_DIR = None

   Path for index dir.

configurator.ALIGN_DIR = None

   Path for align dir.

configurator.LOG_DIR = None

   Path for log dir

configurator.CACHE_DIR = None

   Path for cache dir.

configurator.RESULTS_DIR = None

   Path for results dir

configurator.FASTA_REFERENCE_GENOME_FILES = None

   Dictionary where each fasta reference genomes is indexed by

   reference strain that it corresponds.

configurator.AREA_BLACK_LIST = None

   Dictionary where keys are strain and values are black listed of

   geneome region.

configurator.FASTA_INDEXES = None

   Dictionary of strain that indexes dictionaries where keys are

   chromosome reference from Fastq file and value are its

   correspondance for Templatefilter.

configurator.C2C_FILES = None

   Dictionary where each strain combination indexes genome aligment.

configurator.READ_LENGTH = None

   Length of Illumina reads.

configurator.MAPQ_THRES = None

   Aligment quality thresold.

configurator.TF_CORR = None

   TemplateFilter Template correlation threshold.

configurator.TF_MINW = None

   TemplateFilter minimum width of a nucleosome.

configurator.TF_MAXW = None

   TemplateFilter maximum  width of a nucleosome.

configurator.TF_OL = None

   TemplateFilter maximum allowed overlap for two nucleosomes.

wf.json_conf_file = 'src/nucleo_miner/nucleo_miner_config.json'

   Path to the json configuration file.

wf.samples = []

   List of samples where a sample is identify by an id (key: *id*) and

   a strain name (key *strain*).

wf.samples_mnase = []

   List of Mnase samples.

wf.strains = []

   List of reference strains.

libcoverage.create_bowtie_index(strain, strain_fasta_ref, index_dir, bowtie_build_bin)

   Creates bowtie index for a strain *strain*.

   Parameters:

      * **strain** -- the strain reference.

      * **strain_fasta_ref** -- fasta reference genome.

      * **index_dir** -- directories where to put bowtie index.

      * **bowtie_build_bin** -- bowtie2 build binary.

libcoverage.align_reads(sample, align_dir, log_dir, index_dir, illumina_outputfile_prefix, bowtie2_bin, samtools_bin, bedtools_bin)

   Aligns reads to reference genomes. It produces .sam files, that are

   converted to .bam, that are converted to .bed.

   Parameters:

      * **sample** -- a dict that describe a sample.

      * **align_dir** -- directory where aligned reads will be

        stored.

      * **log_dir** -- directory where logs will be stored.

      * **illumina_outputfile_prefix** -- prefix of Illumina

        sequencer fastq.gz output files.

      * **bowtie2_bin** -- bowtie2 binary.

      * **samtools_bin** -- samtools binary.

      * **bedtools_bin** -- bedtools binary.

      * **index_dir** -- bowtie index directory.

libcoverage.split_fr_4_TF(sample, align_dir, fasta_indexes, area_black_list, read_length, mapq_thres)

   Create TempleFilter input files form bed files. This function

   appends in two times. First, it collects reads from bed files and

   feeds a datastructure

   Parameters:

      * **sample** -- a dict that describe a sample.

      * **align_dir** -- directory where aligned reads will be

        stored.

      * **fasta_index** -- the chr reference from the illumina

        output file.

      * **area_black_list** -- the description of genome that will

        be omit.

      * **read_length** -- Length of Illumina reads.

      * **mapq_thres** -- mapping quality criterion threshold, see

        MAPQ in BED/BAM file format.

libcoverage.template_filter(sample, align_dir, log_dir, tf_bin, tf_templates_file, corr, minw, maxw, ol)

   Run TemplateFilter on a specifi sample. It produces .tab file.

   Parameters:

      * **sample** -- a dict that describe a sample.

      * **align_dir** -- directory where aligned reads will be

        stored.

      * **log_dir** -- directory where logs will be stored.

      * **tf_bin** -- path to the TemplateFilter binary.

      * **tf_templates_file** -- path to the TemplateFilter

        templates file.

      * **corr** -- correlation threshold transmits to

        TemplateFilter.

      * **minw** -- minimum width of a nuc, transmits to

        TemplateFilter.

      * **maxw** -- maximum width of a nuc, transmits to

        TemplateFilter.

      * **ol** -- maximum overlaps for 2 nuc, transmits to

        TemplateFilter.

   aggregate_intra_strain_nucs(samples, lod_thres = -20, coord_max = 2e+07)

       wp_nucs_strain_ref2 = NULL, corr_thres = 0.5, lod_thres = -100,

       only_f = FALSE, only_r = FALSE)

   get_all_reads(marker, combi, form = "wp")

   get_sneps(marker, combi, form, all_samples)

| Version:        | 2.3.3                                               |

       plot_wp_nucs = TRUE, plot_wp_nuc_model = TRUE, plot_common_nucs = TRUE,

       plot_anovas = FALSE, plot_anova_boxes = FALSE, plot_wp_nucs_4_nonmnase = FALSE,

       aggregated_intra_strain_nucs = NULL, aligned_inter_strain_nucs = NULL,

       height = 10, config = NULL)

configurator.CSV_SAMPLE_FILE = None

   Path to cvs file that contains sample information.

configurator.ILLUMINA_OUTPUTFILE_PREFIX = None

   Prefix for Illumina fastq output files.

configurator.FASTA_REFERENCE_GENOME_FILES = None

   Dictionary where each fasta reference genomes is indexed by

   reference strain that it corresponds.

configurator.FASTA_INDEXES = None

   Dictionary of strain that indexes dictionaries where keys are

   chromosome reference from Fastq file and value are its

   correspondance for Templatefilter.

configurator.AREA_BLACK_LIST = None

   Dictionary where keys are strain and values are black listed of

   geneome region.

configurator.C2C_FILES = None

   Dictionary where each strain combination indexes genome aligment.

wf.json_conf_file = 'src/nucleo_miner/nucleo_miner_config.json'

   Path to the json configuration file.

wf.samples = []

   List of samples where a sample is identify by an id (key: *id*) and

   a strain name (key *strain*).

wf.samples_mnase = []

   List of Mnase samples.

wf.strains = []

   List of reference strains.

     for strain in strains:

       per_strain_stats[strain] = create_bowtie_index(strain, 

         config["FASTA_REFERENCE_GENOME_FILES"][strain], config["INDEX_DIR"], 

         config["BOWTIE_BUILD_BIN"])

     for sample in samples:

       per_sample_align_stats["sample_%s" % sample["id"]] = align_reads(sample, 

         config["ALIGN_DIR"], config["LOG_DIR"], config["INDEX_DIR"], 

         config["ILLUMINA_OUTPUTFILE_PREFIX"], config["BOWTIE2_BIN"], 

         config["SAMTOOLS_BIN"], config["BEDTOOLS_BIN"])

     for sample in samples:

       per_sample_convert_stats["sample_%s" % sample["id"]] = split_fr_4_TF(sample, 

         config["ALIGN_DIR"], config["FASTA_INDEXES"], config["AREA_BLACK_LIST"], 

         config["READ_LENGTH"],config["MAPQ_THRES"])

     for sample in samples_mnase:

       per_mnase_sample_stats["sample_%s" % sample["id"]] = template_filter(sample, 

         config["ALIGN_DIR"], config["LOG_DIR"], config["TF_BIN"], 

         config["TF_TEMPLATES_FILE"], config["TF_CORR"], config["TF_MINW"], 

         config["TF_MAXW"], config["TF_OL"])  

version = '2.3.27'

release = '2.3.27'

| Version:      | 2.3.27                                            |

Version: 2.3.27

export(FDR, lod_score_vecs, dfadd, filter_tf_inputs, filter_tf_outputs, sign_from_strand, flat_reads, get_comp_strand, aggregate_intra_strain_nucs, align_inter_strain_nucs, translate_roi, fetch_mnase_replicates, substract_region, union_regions, remove_aligned_wp, translate_regions, extract_wp, crop_fuzzy, get_fuzzy, get_all_reads, get_design, plot_dist_samples, analyse_design, get_sneps, perform_anovas, watch_samples, compute_inter_all_strain_curs, switch_pairlist, build_replicates, ARAB2ROM, ROM2ARAB)

  return(data.frame(tmp_strain_maps))

  non_inter_fuzzy = rec_substract_region(region1, region2)