Modules

vamp.utils

class vamp.utils.ContigComposition

Association of two genomic intervals, used to represent the composition of one interval by another

vamp.utils.find_deletions(contig_composition_list, verbose=False)

Find contigs with deletions and return tuple containing list of idicies of contigs to be replaced along with replacement. e.g.:

([2, 3],
 {'seq': 'chr', 'start': 3, 'end': 5, 'contig': 'contig1',
  'contig_start': 5, 'contig_end': 10, 'strand': '+', 'contig_size': 20})

replaces contig_composition_list[2:3] with the new contig composition specified

vamp.utils.get_sequence_length_from_maf(maf_file, reference_species, sequence_id)

Return length of the reference_species.sequence_id

vamp.utils.get_sequence_net_alignment(maf_filename, reference_species, sequence_id, species, verbose=False)

Return alignment created by stitching MAF blocks along entire sequence (including gaps) Also returns a list of intervals relative to the alignment that indicate the MAF block, block start, and block end of the source of that piece of the alignment

vamp.utils.read_contig_composition_summary(filename)

Read contig composition summary and return attributes

vamp.utils.replace_alignment_with_block(alignment, block, reference_species, sequence_id, verbose=False)

Return updated alignment, interval

vamp.utils.subtract_intervals(interval1, interval2)

Subtract two intervals, return list of resulting intervals

vamp.utils.summarize_contig_composition(interval_list, src_tag, start_tag, end_tag, strand_tag, source_size_tag)

Summarize the contig composition in a list of tuples (seq, start, end, contig, contig_start, contig_end, strand, contig_size)

vamp.utils.update_contig_composition_summary(contig_composition_summary, replacements)

Update list of ContigComposition objects with replacements Replacements are a list of tuples containing a list of indicies of contigs to be replaced along with replacements The replacements must be non-overlapping and sorted

vamp.utils.update_sequence_with_replacements(seq, replacements, replacement_seq_dict)

Update Seq object with replacements Replacements must be non-overlapping and sorted

seq_utils.convert_coordinates

Convert coordinates from GFF or BED file using multi-fasta alignments

seq_utils.fasta_from_gff

Extract fasta sequences from regions defined in GFF/BED file and output fasta to stdout

seq_utils.summarize_alignments

SYNOPSIS

TODO summarize_alignments multi_align_fasta reference_sequence [-h,–help] [-v,–verbose] [–version]

DESCRIPTION

TODO This describes how to use this script. This docstring will be printed by the script if there is an error or if the user requests help (-h or –help).

EXAMPLES

TODO: Show some examples of how to use this script.

EXIT STATUS

TODO: List exit codes

AUTHOR

TODO: lparsons <lparsons@princeton.edu>

LICENSE

BSD 2-Clause License http://www.opensource.org/licenses/BSD-2-Clause

VERSION

$Id$

seq_utils.summarize_alignments.parse_event(event, reference_sequence, alternate_sequence)

Parse a simple event with reference_position, reference_base, and new_base and determine the type and add padding if necessary (for VCF compatibility)

seq_utils.summarize_alignments.summary_of_alignment(alignment, reference_sequence_id)

Summarizes changes in given alignment (pairwise only) Input: alignment = Bio.AlignIO object

reference_index = index of the reference sequence in alignment (default is 1)

Output: dictionary with key for each non-reference sequence in alignment

Each key has a dictionary with keys (match_count, mismatch_count, mismatches, contiguous_change_count)

mismatches is list of mismatches by base: ‘RefBase(RefPos)NewBase’ contiguout_change_count is the number of contiguous change “events”

seq_utils.utils

Utility classes and methods for working with sequence data

class seq_utils.utils.GenomicRegion(region_string)

A genomic region specified by chr:start-end, using 1-based cooredinates

seq_utils.utils.convert_interval_gapped_to_nongapped(seq, start, end)

Take position with gaps and return position without gaps Uses 0-based positions

seq_utils.utils.convert_interval_nongapped_to_gapped(seq, start, end, include_end_gaps=False)

Take position without gaps and return position with gaps Uses 0-based positions