Sequence-Cytogenetic conversion API

Consists of a Perl executable CytoConvert.pl and the CytoConvert.pm module

The source can be downloaded from:

To run the executable CytoConvert.pl,  CytoConvert.pm must be in your current directory.
 

The executable may be called from a shell prompt with the following options:

Usage: perl CytoConvert.pl <options>

  Options:
  --mode <mode>
    available_ideograms, seq2cyto, cyto2seq (defaults to a best guess of seq2cyto/cyto2seq may be refined with input_type parameter)
 
  --infile <filename>
    The file containing list of sequence locations/features to convert (default: stdin)

  --input_type <type of input file>
    annotlist (bed, gff, etc.), genelist (list of gene names), cytolist (list of cytological band names), bestguess (default)

  --taxid <taxid>
    taxid of the requested ideogram

  --assm <gencoll accession>
    The gencoll accessions for the assembly mapped to the ideogram

  --resolution <resolution>
    Resolution of the requested ideogram (human default is 850, all others are blank)

  --outfile <filename>
    Filename to which output should be written (default: stdout)

  --help
    Display this text
 

The Perl module provides two functions having the following options:

NAME
    CytoConvert.pm

SYNOPSIS
        use CytoConvert;
        my $ideograms = GetAvailableIdeograms();
        my $content = DoBatchConvert({tax_id=>9606,assm_acc=>'GCF_000001305.13'}); # this will read input from stdin

DESCRIPTION
    API interface to convert between genomic sequence coordinates and cytological band names and vise-versa

  Functions
    "GetAvailableIdeograms"
        Input Parameters: none

        Returns: an array of hashes describing the available ideogram datasets

        Returned Hash Elements:

        - sci_name Scientific name of organism
        - taxid Numeric taxonomic id of organism for ideogram
        - assm_name Name of assembly
        - assm_acc Gencoll Accession for assembly
        - res Resolution of the cytogenetic bands (i.e. 400, 500,850...)
        - default_assm (1=default assembly unit, 0=not default assembly unit)

    "DoBatchConvertion"
        Input Parameters: Hash

        Input Hash Elements:
        - taxid (required) Numeric taxonomic id of organism for ideogram
        - assm_acc (required) Gencoll Accession for assembly
        - res Resolution of the cytogenetic bands (i.e. 400, 500,850...)
        - input_type 'bestguess'(default), 'annotlist', 'genelist', 'cytolist'
        - mode 'seq2cyto', 'cyto2seq'
        - content string containing contents to interpret as file
        - input_file filename to read input from (if content is undefined)
            defaults to stdin if content and input_file are both undefined

        Returns a string representation of the output file

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Last updated: 2013-07-10T09:54:50-04:00