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get_relative_data.pl

A program to collect data in bins around a relative position.

SYNOPSIS

get_relative_data.pl [–options] –in <filename> –out <filename>

get_relative_data.pl [–options] -i <filename> <data1> <data2…>

Options for data files:
-i --in <filename>                  input file: txt bed gff gtf refFlat ucsc
-o --out <filename>                 optional output file, default overwrite 

Options for new files
-d --db <name>                      annotation database: mysql sqlite
-f --feature <type>                 one or more feature types from db or gff

Options for data collection:
-D --ddb <name|file>                data or BigWigSet database
-a --data <dataset|filename>        data from which to collect: bw bam etc
-m --method [mean|median|stddev|    statistical method for collecting data
          min|max|range|sum|count|   default mean
          pcount|ncount]
-t --strand [all|sense|antisense]   strand of data relative to feature (all)
--force_strand                      use the specified strand in input file
--avoid                             avoid neighboring features
--avtype [type,type,...]            alternative types of feature to avoid
--long                              collect each window independently
-r --format <integer>               number of decimal places for numbers

Bin specification:
-w --win <integer>                  size of windows, default 50 bp
-n --num <integer>                  number of windows flanking reference, 20
--up <integer>                        or number of windows upstream
--down <integer>                      and number of windows downstream
-p --pos [5|m|3|p]                  reference position, default 5'

Post-processing:
-U --sum                            generate summary file
--smooth                            smoothen sparse data

General Options:
-g --groups                         write columns group index file for plotting
-z --gz                             compress output file
-c --cpu <integer>                  number of threads, default 4
--noparse                           do not parse input file into SeqFeatures
-v --version                        print version and exit
-h --help                           show extended documentation

OPTIONS

The command line flags and descriptions:

Options for data files

• –in <filename>

  Specify an input file containing either a list of database features or genomic coordinates for which to collect data. Any tab-delimited text file with recognizable headers is supported. Gene annotation file formats are also supported, including bed, gtf, gff3, refFlat, and UCSC native formats such as gene prediction tables are all supported. Gene annotation files will be parsed as sequence features. Files may be gzipped compressed.

• –out <filename>

  Specify the output file name. Required for new files; otherwise, input files will be overwritten unless specified.

Options for new files

• –db <name

  filename>

  Specify the name of a Bio::DB::SeqFeature::Store annotation database from which gene or feature annotation may be derived. A database is required for generating new data files with features. This option may skipped when using coordinate information from an input file (e.g. BED file), or when using an existing input file with the database indicated in the metadata.

• –feature [type, type:source]

  Specify the type of feature to map data around. The feature may be listed either as GFF type or GFF type:source. The list of features will be automatically generated from the database. This is only required when an input file is not specified.

Options for data collection

• –ddb <name

  filename>

  If the data to be collected is from a second database that is separate from the annotation database, provide the name of the data database here. Typically, a second Bio::DB::SeqFeature::Store or BigWigSet database is provided here.

• –data <dataset_name

  filename>

  Provide the name of the dataset to collect the values. If no dataset is specified on the command line, then the program will interactively present a list of datasets from the data database to select.

  The dataset may be a database file, including bigWig (.bw), bigBed (.bb), or Bam alignment (.bam) files. The files may be local or remote (specified with a http: or ftp: prefix).

  Alternatively, the dataset may be a feature type in a BioPerl Bio::DB::SeqFeature::Store or Bio::DB::BigWigSet database. Provide either the feature type or type:source.

  More than one datasource may be provided; use multiple data options or list the datasets at the end of the command.

• –method <text>

  Specify the method for combining all of the dataset values within the genomic region of the feature. Accepted values include:

  • mean (default)
  • median
  • sum
  • stddev Standard deviation of the population (within the region)
  • min
  • max
  • range Returns difference of max and min

  • count

    Counts the number of overlapping items.

  • pcount (precise count)

    Counts the number of items that precisely fall within the query region. Partially overlapping are not counted.

  • ncount (name count)

    Counts unique names. Useful when spliced alignments overlap more than one exon and you want to avoid double-counting.

• –strand [sense

  antisense

  all]

  Specify whether stranded data should be collected for each of the datasets. Either sense or antisense (relative to the feature) data may be collected. The default value is ‘all’, indicating all data will be collected.

• –force_strand

  For features that are not inherently stranded (strand value of 0) or that you want to impose a different strand, set this option when collecting stranded data. This will reassign the specified strand for each feature regardless of its original orientation. This requires the presence of a “strand” column in the input data file. This option only works with input file lists of database features, not defined genomic regions (e.g. BED files). Default is false.

• –avoid

  Indicate whether neighboring features should be avoided when calculating values in a window. After collecting the data, each window is checked for overlapping features; if the window overlaps another feature, no value is reported for that window. This option requires using an annotation database (–db option). This is useful to avoid scoring windows that overlap a neighboring gene, for example. The default is false (return all values regardless of overlap).

• –avtype [type,type,…]

  Provide a feature type (primary_tag or primary_tag:source) or a comma-delimited list of types to be used when avoiding neighboring features. The default is to avoid features of the same type as that of the query, i.e. collecting data around a feature of type ‘gene’ will avoid other ‘gene’ features. This option allows you to avoid other features too, such as ‘tRNA’ or ‘repeat’.

• –long

  Indicate that data should be collected independently for each long window. This may be enabled automatically if the sum of the entire window length passes a predefined threshold. The default for ‘short’ windows is to collect all of the point data from the dataset first, and then divide the results into the different windows. Datasets consisting of “long” features, for example long alignments, may be counted more than once in long mode when they span multiple windows.

• –format <integer>

  Specify the number of decimal positions to format the collected scores. Default is not to format, often leading to more than the intended significant digits.

Bin specification

• –win <integer>

  Specify the window size. The default is 50 bp.

• –num <integer>

  Specify the number of windows on either side of the feature position (total number will be 2 x [num]). The default is 20, or 1 kb on either side of the reference position if the default window size is used.

• –up <integer>

• –down <integer>

  Alternatively specify the exact number of windows upstream and downstream of the reference position. If only one option is set, then the other option is assumed to be zero.

• –pos [5

  m

  3]

  Indicate the relative position of the feature around which the data is mapped. Three values are accepted: “5” indicates the 5’ prime end is used, “3” indicates the 3’ end is used, and “m” indicates the middle of the feature is used. The default is to use the 5’ end, or the start position of unstranded features.

Post-processing

• –(no)sum

  Indicate that the data should be averaged across all features at each position, suitable for graphing. A separate text file will be written with the suffix ‘_summed’ with the averaged data. Default is true (sum).

• –smooth

  Indicate that windows without values should (not) be interpolated from neighboring values. The default is false (nosmooth).

General options

• –groups

  Optionally write a secondary file with the list of column group names and their corresponding dataset group. This can be used to assist in designating the metadata when plotting files, for example in R with pheatmap. The file is named the output basename appended with .groups.txt.

• –gz

  Specify whether (or not) the output file should be compressed with gzip.

• –cpu <integer>

  Specify the number of CPU cores to execute in parallel. This requires the installation of Parallel::ForkManager. With support enabled, the default is 2. Disable multi-threaded execution by setting to 1.

• –noparse

  Prevent input annotation files from being automatically parsed into sequence features. Coordinates will be used as is and new data columns will be appended to the input file.

• –version

  Print the version number.

• –help

  Display this help

DESCRIPTION

This program will collect data around a relative coordinate of a genomic feature or region. The data is collected in a series of windows flanking the feature start (5’ position for stranded features), end (3’ position), or the midpoint position. The number and size of windows are specified via command line arguments, or the program will default to 20 windows on both sides of the relative position (40 total) of 50 bp size, corresponding to 2 kb total (+/- 1 kb). Windows without a value may be interpolated (smoothed) from neigboring values, if available.

Stranded data may be collected. If the feature does not have an inherent strand, one may be specified to enforce stranded collection or a particular orientation.

When features overlap, or the collection windows of one feature overlaps with another feature, then data may be ignored and not collected (–avoid).

EXAMPLES

These are some examples of some common scenarios for collecting data.

• Collect scores in intervals around start

  You want to collect the mean score from a bigWig file in twenty 50 bp intervals flanking the start position of each feature in Bed file.

    get_relative_data.pl --data scores.bw --in input.bed
  

• Collect scores in intervals around middle

  You want to collect median scores in 20 bp intervals extending 500 bp from the midpoint of each feature.

    get_relative_data.pl --win 20 --num 25 --pos m --data scores.bw --in \
    input.txt
  

• Collect scores in intervals from annotation database

  You want to collect scores in intervals around the transcription start site of genes in an annotation database, but also avoid intervals that may overlap neighboring genes. You want to collect alignment counts from a Bam file in a stranded fashion.

    get_relative_data.pl --db annotation --feature gene --avoid --strand \
    sense --method count --data alignments.bam --out gene_tss
  

AUTHOR

Timothy J. Parnell, PhD
Howard Hughes Medical Institute
Dept of Oncological Sciences
Huntsman Cancer Institute
University of Utah
Salt Lake City, UT, 84112

This package is free software; you can redistribute it and/or modify it under the terms of the Artistic License 2.0.