listor
Function
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
Command line arguments
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.
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.
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.
Author(s)
History
Target users
Comments