API

ribocore (common functions)

Common functions.

exception riboplot.ribocore.ArgumentError

Raised when invalid arguments are sent in the command line.

exception riboplot.ribocore.BamFileError

Errors related to BAM file

exception riboplot.ribocore.RNACountsError

For errors related to RNA Coverage generation using bedtools.

exception riboplot.ribocore.RiboCountError

General errors relating to ribocount.

exception riboplot.ribocore.RiboPlotError

General errors relating to riboplot.

riboplot.ribocore.bam_has_index(bam_file)

Check if bam file has an index. Returns True/False.

riboplot.ribocore.check_read_lengths(ribo_file, read_lengths)

Check if read lengths are valid (positive).

riboplot.ribocore.check_read_lengths_offsets(read_lengths, read_offsets)

Check if read length has corresponding read offset for all read lengths.

riboplot.ribocore.check_read_offsets(read_offsets)

Check if read offsets are valid (positive).

riboplot.ribocore.check_required_arguments(ribo_file, transcriptome_fasta, transcript_name=None)

Check required arguments of both riboplot and ribocount.

riboplot.ribocore.check_rna_file(rna_file)

Check if bedtools is available and if the given RNA-Seq bam file is valid.

riboplot.ribocore.create_bam_index(bam_file)

Create an index for the given BAM file.

riboplot.ribocore.filter_ribo_counts(counts, orf_start=None, orf_stop=None)

Filter read counts and return only upstream of orf_start or downstream of orf_stop.

Keyword arguments: counts – Ribo-Seq read counts obtained from get_ribo_counts. orf_start – Start position of the longest ORF. orf_stop – Stop position of the longest ORF.

riboplot.ribocore.get_fasta_record(fasta_file, transcript_name)

Return a single transcript from a valid fasta file as a record.

record[transcript_name] = sequence

Keyword arguments: fasta_file – FASTA format file of the transcriptome transcript_name – Name of the transcript as in the FASTA header

riboplot.ribocore.get_fasta_records(fasta, transcripts)

Return list of transcript records from the given fasta file. Each record will be of the form {‘sequence_id’: {‘sequence’: ‘AAA’, ‘length’: 3}}

trascripts should be provided as a list of sequence id’s.

riboplot.ribocore.get_first_transcript_name(fasta_file)

Return the first FASTA sequence from the given FASTA file.

Keyword arguments: fasta_file – FASTA format file of the transcriptome

riboplot.ribocore.get_longest_orf(orfs)

Find longest ORF from the given list of ORFs.

riboplot.ribocore.get_ribo_counts(ribo_fileobj, transcript_name, read_lengths, read_offsets)

For each mapped read of the given transcript in the BAM file (pysam AlignmentFile object), return the position (+1) and the corresponding frame (1, 2 or 3) to which it aligns.

Keyword arguments: ribo_fileobj – file object - BAM file opened using pysam AlignmentFile transcript_name – Name of transcript to get counts for read_length (optional) – If provided, get counts only for reads of this length.

riboplot.ribocore.get_three_frame_orfs(sequence, starts=None, stops=None)

Find ORF’s in frames 1, 2 and 3 for the given sequence.

Positions returned are 1-based (not 0)

Return format [{‘start’: start_position, ‘stop’: stop_position, ‘sequence’: sequence}, ]

Keyword arguments: sequence – sequence for the transcript starts – List of codons to be considered as start (Default: [‘ATG’]) stops – List of codons to be considered as stop (Default: [‘TAG’, ‘TGA’, ‘TAA’])

riboplot.ribocore.is_bam_valid(bam_file)

Check if bam file is valid. Raises a ValueError if pysam cannot read the file.

#TODO: pysam does not differentiate between BAM and SAM

riboplot.ribocore.is_fasta_valid(fasta_file)

Check if fasta file is valid. Raises a ValueError if pysam cannot read the file.

#TODO: pysam does not differentiate between BAM and SAM

riboplot.ribocore.lengths_offsets(value)

Split the given comma separated value to multiple integer values.

riboplot.ribocore.open_pysam_file(*args, **kwds)

Open a BAM or FASTA file with pysam (for use with “with” statement)

riboplot

class riboplot.riboplot.ErrorLogFormatter(fmt=None, datefmt=None)

Custom error log format for the HTML file

riboplot.riboplot.create_parser()

Argument parser.

riboplot.riboplot.get_color_palette(scheme)

Return colors for a given scheme. Default colors are returned for an item if undefined in scheme.

riboplot.riboplot.get_rna_counts(rna_file, transcript_name)

Get coverage for a given RNA BAM file, return read counts.

riboplot.riboplot.get_start_stops(transcript_sequence, start_codons=None, stop_codons=None)

Return start and stop positions for all frames in the given transcript.

riboplot.riboplot.main(args)

Main program

riboplot.riboplot.plot_profile(ribo_counts, transcript_name, transcript_length, start_stops, read_lengths=None, read_offsets=None, rna_counts=None, color_scheme='default', html_file='index.html', output_path='output')

Plot read counts (in all 3 frames) and RNA coverage if provided for a single transcript.

riboplot.riboplot.run()

Run program

riboplot.riboplot.set_axis_color(axis, color, alpha=None)

Sets the spine color of all sides of an axis (top, right, bottom, left).

ribocount

ribocount

class riboplot.ribocount.ErrorLogFormatter(fmt=None, datefmt=None)

Custom error log format for the HTML file

riboplot.ribocount.create_parser()

Argument parser.

riboplot.ribocount.main(args)

Main program

riboplot.ribocount.run()

Run program

config

class riboplot.config.ProductionConfig

Production configuration

class riboplot.config.TestingConfig

Testing configuration