EMBOSS: listor

| listor

## Function

Write a list file of the logical OR of two sets of sequences

## Description

listor reads in two sets of sequences (typically specified as list files) and writes out a list file that result from the logical union of the two sets. A list file is a file with a list of Uniform Sequence Addresses (USAs), for example, a list of file names. When comparing sequences from the input sets, no use is made of the ID name or accession number; only the sequence itself is compared. The comparison of the sequences is case-independent. The logical union is an OR operation by default. Other available operations are: `AND`, `XOR` and `NOT`.

## Algorithm

All the input sequences are kept in memory while the logical unions of the two input sets of sequences is calculated. listor is therefore restricted by the available memory.

## Usage

Here is a sample session with listor

Write the logical OR of two lists:

    % listor ../data/file2
    Write a list file of the logical OR of two sets of sequences
    List of USAs output file [file1.list]:

Go to the input files for this example
Go to the output files for this example

Example 2

Write the logical AND of two lists:

    % listor ../data/file2 -operator and
    Write a list file of the logical OR of two sets of sequences
    List of USAs output file [file1.list]:

Go to the output files for this example

Example 3

Write the logical XOR of two lists:

    % listor ../data/file2 -operator xor
    Write a list file of the logical OR of two sets of sequences
    List of USAs output file [file1.list]:

Go to the output files for this example

Example 4

Write the logical NOT of two lists:

    % listor ../data/file2 -operator not
    Write a list file of the logical OR of two sets of sequences
    List of USAs output file [file1.list]:

Go to the output files for this example

## Command line arguments

       Standard (Mandatory) qualifiers:
      [-firstsequences]    seqset     Sequence set filename and optional format,
                                      or reference (input USA)
      [-secondsequences]   seqset     Sequence set filename and optional format,
                                      or reference (input USA)
      [-outfile]           outfile    [*.listor] The list of sequence names will
                                      be written to this list file

       Additional (Optional) qualifiers:
       -operator           menu       [OR] The following logical operators combine
                                      the sequences in the following ways:
                                      OR - gives all that occur in one set or the
                                      other
                                      AND - gives only those which occur in both
                                      sets
                                      XOR - gives those which only occur in one
                                      set or the other, but not in both
                                      NOT - gives those which occur in the first
                                      set except for those that also occur in the
                                      second (Values: O (OR - merger of both
                                      sets); A (AND - only those in both sets); X
                                      (XOR - only those not in both sets); N (NOT
                                      - those of the first set that are not in the
                                      second))

       Advanced (Unprompted) qualifiers: (none)
       Associated qualifiers:

       "-firstsequences" associated qualifiers
       -sbegin1            integer    Start of each sequence to be used
       -send1              integer    End of each sequence to be used
       -sreverse1          boolean    Reverse (if DNA)
       -sask1              boolean    Ask for begin/end/reverse
       -snucleotide1       boolean    Sequence is nucleotide
       -sprotein1          boolean    Sequence is protein
       -slower1            boolean    Make lower case
       -supper1            boolean    Make upper case
       -sformat1           string     Input sequence format
       -sdbname1           string     Database name
       -sid1               string     Entryname
       -ufo1               string     UFO features
       -fformat1           string     Features format
       -fopenfile1         string     Features file name

       "-secondsequences" associated qualifiers
       -sbegin2            integer    Start of each sequence to be used
       -send2              integer    End of each sequence to be used
       -sreverse2          boolean    Reverse (if DNA)
       -sask2              boolean    Ask for begin/end/reverse
       -snucleotide2       boolean    Sequence is nucleotide
       -sprotein2          boolean    Sequence is protein
       -slower2            boolean    Make lower case
       -supper2            boolean    Make upper case
       -sformat2           string     Input sequence format
       -sdbname2           string     Database name
       -sid2               string     Entryname
       -ufo2               string     UFO features
       -fformat2           string     Features format
       -fopenfile2         string     Features file name

       "-outfile" associated qualifiers
       -odirectory3        string     Output directory

       General qualifiers:
       -auto               boolean    Turn off prompts
       -stdout             boolean    Write first file to standard output
       -filter             boolean    Read first file from standard input, write
                                      first file to standard output
       -options            boolean    Prompt for standard and additional values
       -debug              boolean    Write debug output to program.dbg
       -verbose            boolean    Report some/full command line options
       -help               boolean    Report command line options. More
                                      information on associated and general
                                      qualifiers can be found with -help -verbose
       -warning            boolean    Report warnings
       -error              boolean    Report errors
       -fatal              boolean    Report fatal errors
       -die                boolean    Report dying program messages

Standard (Mandatory) qualifiers | Allowed values | Default
--- | --- | ---
[-firstsequences] (Parameter 1) | Sequence set filename and optional format, or reference (input USA) | Readable set of sequences | Required
[-secondsequences] (Parameter 2) | Sequence set filename and optional format, or reference (input USA) | Readable set of sequences | Required
[-outfile] (Parameter 3) | The list of sequence names will be written to this list file | Output file | <*>.listor
Additional (Optional) qualifiers | Allowed values | Default
-operator | The following logical operators combine the sequences in the following ways: OR - gives all that occur in one set or the other AND - gives only those which occur in both sets XOR - gives those which only occur in one set or the other, but not in both NOT - gives those which occur in the first set except for those that also occur in the second |
O | (OR - merger of both sets)
A | (AND - only those in both sets)
X | (XOR - only those not in both sets)
N | (NOT - those of the first set that are not in the second)
| OR
Advanced (Unprompted) qualifiers | Allowed values | Default
(none)

## Input file format

The input sets of sequences can be of any valid USAs. The program was written to perform logical operations on list files, but in practice, wildcarded database entries and file names are also perfectly legal specifications of the input sequences.

### Input files for usage example

### File: file1

    >one
    tagctagcg
    >two
    tagctagcggctacgt
    >three
    tagctattttatgctacgtcagtgac

### File: file2

    >two
    tagctagcggctacgt
    >three
    tagctattttatgctacgtcagtgac
    >four
    gcgcggcgcgcgtgcgtcgttgctggggccc

## Output file format

The ouput is simply a list of the USAs (format and sequence specification) resulting from the required logical union of the two sets of input sequence.

The order that the USAs are written out is not necessarily the same as the order of either of the input sets of sequences.

The results of the four types of logical union follows. Note that the duplicated sequences in these two files have been given the same name. This is not necessary for the operation of listor as it compares the sequences themselves, not the ID names of the sequences.

### Output files for usage example

### File: file1.list

    fasta::../../data/file1:one
    fasta::../../data/file1:two
    fasta::../../data/file1:three
    fasta::../../data/file2:four

### Output files for usage example 2

### File: file1.list

    fasta::../../data/file1:two
    fasta::../../data/file1:three

### Output files for usage example 3

### File: file1.list

    fasta::../../data/file1:one
    fasta::../../data/file2:four

### Output files for usage example 4

### File: file1.list

    fasta::../../data/file1:one

## Data files

None.

## Notes

The inputs can be any valid USA but typically reference a list file. Some other reference such as a wildcarded database entries or file name are equally valid.

The (default) logical OR of the two sets of sequences is simply the result of merging the two sets of sequences. A sequences appearing in both input sets is referenced once only in the output file. A logical `AND` simply lists those sequences that occur in both sets of sequences.

A logical `XOR` lists those sequences that ONLY occur in the first set or only occur in the second set - sequences occuring in both sets are omitted (the opposite of an `AND`).

A logical `NOT` lists all those sequences in the first set except for those that also occur in the second set.

## References

None.

## Warnings

listor is restricted by the available memory. Doing logical unions involving all of the sequences in large databases, such as EMBL, is probably impractical unless you are lucky enough to have extraordinary amounts of memory on your machine.

## Diagnostic Error Messages

None.

## Exit status

It always exits with status 0.

## Known bugs

None.

## See also

Program name | Description
--- | ---
aligncopy | Reads and writes alignments
aligncopypair | Reads and writes pairs from alignments
biosed | Replace or delete sequence sections
codcopy | Copy and reformat a codon usage table
cutseq | Removes a section from a sequence
degapseq | Removes non-alphabetic (e.g. gap) characters from sequences
descseq | Alter the name or description of a sequence
entret | Retrieves sequence entries from flatfile databases and files
extractalign | Extract regions from a sequence alignment
extractfeat | Extract features from sequence(s)
extractseq | Extract regions from a sequence
featcopy | Reads and writes a feature table
featreport | Reads and writes a feature table
makenucseq | Create random nucleotide sequences
makeprotseq | Create random protein sequences
maskambignuc | Masks all ambiguity characters in nucleotide sequences with N
maskambigprot | Masks all ambiguity characters in protein sequences with X
maskfeat | Write a sequence with masked features
maskseq | Write a sequence with masked regions
newseq | Create a sequence file from a typed-in sequence
nohtml | Remove mark-up (e.g. HTML tags) from an ASCII text file
noreturn | Remove carriage return from ASCII files
nospace | Remove all whitespace from an ASCII text file
notab | Replace tabs with spaces in an ASCII text file
notseq | Write to file a subset of an input stream of sequences
nthseq | Write to file a single sequence from an input stream of sequences
pasteseq | Insert one sequence into another
revseq | Reverse and complement a nucleotide sequence
seqret | Reads and writes (returns) sequences
seqretsplit | Reads sequences and writes them to individual files
sizeseq | Sort sequences by size
skipredundant | Remove redundant sequences from an input set
skipseq | Reads and writes (returns) sequences, skipping first few
splitter | Split sequence(s) into smaller sequences
trimest | Remove poly-A tails from nucleotide sequences
trimseq | Remove unwanted characters from start and end of sequence(s)
trimspace | Remove extra whitespace from an ASCII text file
union | Concatenate multiple sequences into a single sequence
vectorstrip | Removes vectors from the ends of nucleotide sequence(s)
yank | Add a sequence reference (a full USA) to a list file

## Author(s)

Gary Williams (gwilliam © rfcgr.mrc.ac.uk)
MRC Rosalind Franklin Centre for Genomics Research Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SB, UK

## History

Written (1 Aug 2001) - Gary Williams

## Target users

This program is intended to be used by everyone and everything, from naive users to embedded scripts.

## Comments

None