
                                  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

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
