| listor

## Function

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

## Description

listor reads in two sets of sequences and writes out a list file (file of file names) that result from the logical union of these two sets of sequences. It is a simple way of manipulating and editing lists or sets of sequences to produce a list file.

When comparing sequences to see if they are the same between two sets of sequences, no use is made of the ID name or accession number of the sequences. Only the sequences themselves are 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.

The (default) logical OR of the two sets of sequences is simply the result of merging the two sets of sequences, (without listing any shared sequences twice).

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 ignored (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.

## Usage

An example of the four types of logical operation performed with the two sets of sequences comprising these sequences follows. The two sets of sequences are in the files named file1 and file2. There are 2 sequences which are duplicated between these two files ('two' and 'three') and the sequences 'one' and 'four' are unique to the files 'file1' and 'file2' respectively.

Here is a sample session with listor

Write the logical OR of two lists:

    % listor ../../data/file1 ../../data/file2
    Writes a list file of the logical OR of two sets of sequences
    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/file1 ../../data/file2 -operator and
    Writes a list file of the logical OR of two sets of sequences
    Output file [file1.list]:

Go to the output files for this example

Example 3

Write the logical XOR of two lists:

    % listor ../../data/file1 ../../data/file2 -operator xor
    Writes a list file of the logical OR of two sets of sequences
    Output file [file1.list]:

Go to the output files for this example

Example 4

Write the logical NOT of two lists:

    % listor ../../data/file1 ../../data/file2 -operator not
    Writes a list file of the logical OR of two sets of sequences
    Output file [file1.list]:

Go to the output files for this example

## Command line arguments

       Mandatory qualifiers:
      [-firstset]          seqset     Sequence set USA
      [-secondset]         seqset     Sequence set USA
      [-outlist]           outfile    The list of sequence names will be written
                                      to this list file

       Optional qualifiers:
       -operator           menu       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

       Advanced qualifiers: (none)
       Associated qualifiers:
      "-firstset" related qualifiers
       -sbegin1             integer    First base used
       -send1               integer    Last base used, def=seq length
       -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
       -sopenfile1          string     Input filename
       -sdbname1            string     Database name
       -sid1                string     Entryname
       -ufo1                string     UFO features
       -fformat1            string     Features format
       -fopenfile1          string     Features file name
      "-secondset" related qualifiers
       -sbegin2             integer    First base used
       -send2               integer    Last base used, def=seq length
       -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
       -sopenfile2          string     Input filename
       -sdbname2            string     Database name
       -sid2                string     Entryname
       -ufo2                string     UFO features
       -fformat2            string     Features format
       -fopenfile2          string     Features file name
      "-outlist" related qualifiers
       -odirectory3         string     Output directory

       General qualifiers:
       -auto                boolean    Turn off prompts
       -stdout              boolean    Write standard output
       -filter              boolean    Read standard input, write standard output
       -options             boolean    Prompt for required and optional values
       -debug               boolean    Write debug output to program.dbg
       -acdlog              boolean    Write ACD processing log to program.acdlog
       -acdpretty           boolean    Rewrite ACD file as program.acdpretty
       -acdtable            boolean    Write HTML table of options
       -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 deaths

Mandatory qualifiers | Allowed values | Default
--- | --- | ---
[-firstset] (Parameter 1) | Sequence set USA | Readable sequences | Required
[-secondset] (Parameter 2) | Sequence set USA | Readable sequences | Required
[-outlist] (Parameter 3) | The list of sequence names will be written to this list file | Output file | <sequence>.listor
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 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: ../../data/file1

    >one
    tagctagcg
    >two
    tagctagcggctacgt
    >three
    tagctattttatgctacgtcagtgac

### File: ../../data/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 program stores all of the input sequences in memory while it is working out the logical unions of the two sets of sequences. This means that it 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.

## References

None.

## Warnings

If you try to do a logical union with all of the sequences in EMBL and another sequence set, this program will attempt to read all of the EMBL sequences into memory at once. This will probably not succeed.

## Diagnostic Error Messages

None.

## Exit status

It always exits with status 0.

## Known bugs

None.

## See also

Program name | Description
--- | ---
biosed | Replace or delete sequence sections
cutseq | Removes a specified section from a sequence
degapseq | Removes gap characters from sequences
descseq | Alter the name or description of a sequence
entret | Reads and writes (returns) flatfile entries
extractfeat | Extract features from a sequence
extractseq | Extract regions from a sequence
maskfeat | Mask off features of a sequence
maskseq | Mask off regions of a sequence
newseq | Type in a short new sequence
noreturn | Removes carriage return from ASCII files
notseq | Excludes a set of sequences and writes out the remaining ones
nthseq | Writes one sequence from a multiple set of sequences
pasteseq | Insert one sequence into another
revseq | Reverse and complement a sequence
seqret | Reads and writes (returns) sequences
seqretsplit | Reads and writes (returns) sequences in individual files
skipseq | Reads and writes (returns) sequences, skipping the first few
splitter | Split a sequence into (overlapping) smaller sequences
trimest | Trim poly-A tails off EST sequences
trimseq | Trim ambiguous bits off the ends of sequences
union | Reads sequence fragments and builds one sequence
vectorstrip | Strips out DNA between a pair of vector sequences
yank | Reads a sequence range, appends the full USA to a list file

## Author(s)

Gary Williams (gwilliam © hgmp.mrc.ac.uk)
HGMP-RC, 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