EMBOSS: notseq

| notseq

## Function

Write to file a subset of an input stream of sequences

## Description

notseq writes to file a subset of an input stream of sequences. The list of sequence names or accession numbers to exclude from output is provided as a string. Optionally, the excluded sequences are also written to file.

## Usage

Here is a sample session with notseq

In this case the excluded sequences (myg_phyca and lgb2_luplu) are not saved to any file:

    % notseq
    Write to file a subset of an input stream of sequences
    Input (gapped) sequence(s): globins.fasta
    Sequence names to exclude: myg_phyca,lgb2_luplu
    output sequence(s) [hbb_human.fasta]: mydata.seq

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

Example 2

Here is an example where the sequences to be excluded are saved to another file:

    % notseq -junkout hb.seq
    Write to file a subset of an input stream of sequences
    Input (gapped) sequence(s): globins.fasta
    Sequence names to exclude: hb*
    output sequence(s) [hbb_human.fasta]: mydata.seq

Go to the output files for this example

## Command line arguments

       Standard (Mandatory) qualifiers:
      [-sequence]          seqall     (Gapped) sequence(s) filename and optional
                                      format, or reference (input USA)
      [-exclude]           string     Enter a list of sequence names or accession
                                      numbers to exclude from the sequences read
                                      in. The excluded sequences will be written
                                      to the file specified in the 'junkout'
                                      parameter. The remainder will be written out
                                      to the file specified in the 'outseq'
                                      parameter.
                                      The list of sequence names can be separated
                                      by either spaces or commas.
                                      The sequence names can be wildcarded.
                                      The sequence names are case independent.
                                      An example of a list of sequences to be
                                      excluded is:
                                      myseq, hs*, one two three
                                      a file containing a list of sequence names
                                      can be specified by giving the file name
                                      preceeded by a '@', eg: '@names.dat' (Any
                                      string is accepted)
      [-outseq]            seqoutall  [.] Sequence set(s)
                                      filename and optional format (output USA)

       Additional (Optional) qualifiers:
       -junkoutseq         seqoutall  [/dev/null] This file collects the sequences
                                      which you have excluded from the main
                                      output file of sequences.

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

       "-sequence" 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

       "-outseq" associated qualifiers
       -osformat3          string     Output seq format
       -osextension3       string     File name extension
       -osname3            string     Base file name
       -osdirectory3       string     Output directory
       -osdbname3          string     Database name to add
       -ossingle3          boolean    Separate file for each entry
       -oufo3              string     UFO features
       -offormat3          string     Features format
       -ofname3            string     Features file name
       -ofdirectory3       string     Output directory

       "-junkoutseq" associated qualifiers
       -osformat           string     Output seq format
       -osextension        string     File name extension
       -osname             string     Base file name
       -osdirectory        string     Output directory
       -osdbname           string     Database name to add
       -ossingle           boolean    Separate file for each entry
       -oufo               string     UFO features
       -offormat           string     Features format
       -ofname             string     Features file name
       -ofdirectory        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
--- | --- | ---
[-sequence] (Parameter 1) | (Gapped) sequence(s) filename and optional format, or reference (input USA) | Readable sequence(s) | Required
[-exclude] (Parameter 2) | Enter a list of sequence names or accession numbers to exclude from the sequences read in. The excluded sequences will be written to the file specified in the 'junkout' parameter. The remainder will be written out to the file specified in the 'outseq' parameter. The list of sequence names can be separated by either spaces or commas. The sequence names can be wildcarded. The sequence names are case independent. An example of a list of sequences to be excluded is: myseq, hs*, one two three a file containing a list of sequence names can be specified by giving the file name preceeded by a '@', eg: '@names.dat' | Any string is accepted | An empty string is accepted
[-outseq] (Parameter 3) | Sequence set(s) filename and optional format (output USA) | Writeable sequence(s) | <*>.format
Additional (Optional) qualifiers | Allowed values | Default
-junkoutseq | This file collects the sequences which you have excluded from the main output file of sequences. | Writeable sequence(s) | /dev/null
Advanced (Unprompted) qualifiers | Allowed values | Default
(none)

## Input file format

notseq reads normal sequence USAs.

### Input files for usage example

### File: globins.fasta

    >HBB_HUMAN Sw:Hbb_Human => HBB_HUMAN
    VHLTPEEKSAVTALWGKVNVDEVGGEALGRLLVVYPWTQRFFESFGDLSTPDAVMGNPKV
    KAHGKKVLGAFSDGLAHLDNLKGTFATLSELHCDKLHVDPENFRLLGNVLVCVLAHHFGK
    EFTPPVQAAYQKVVAGVANALAHKYH
    >HBB_HORSE Sw:Hbb_Horse => HBB_HORSE
    VQLSGEEKAAVLALWDKVNEEEVGGEALGRLLVVYPWTQRFFDSFGDLSNPGAVMGNPKV
    KAHGKKVLHSFGEGVHHLDNLKGTFAALSELHCDKLHVDPENFRLLGNVLVVVLARHFGK
    DFTPELQASYQKVVAGVANALAHKYH
    >HBA_HUMAN Sw:Hba_Human => HBA_HUMAN
    VLSPADKTNVKAAWGKVGAHAGEYGAEALERMFLSFPTTKTYFPHFDLSHGSAQVKGHGK
    KVADALTNAVAHVDDMPNALSALSDLHAHKLRVDPVNFKLLSHCLLVTLAAHLPAEFTPA
    VHASLDKFLASVSTVLTSKYR
    >HBA_HORSE Sw:Hba_Horse => HBA_HORSE
    VLSAADKTNVKAAWSKVGGHAGEYGAEALERMFLGFPTTKTYFPHFDLSHGSAQVKAHGK
    KVGDALTLAVGHLDDLPGALSNLSDLHAHKLRVDPVNFKLLSHCLLSTLAVHLPNDFTPA
    VHASLDKFLSSVSTVLTSKYR
    >MYG_PHYCA Sw:Myg_Phyca => MYG_PHYCA
    VLSEGEWQLVLHVWAKVEADVAGHGQDILIRLFKSHPETLEKFDRFKHLKTEAEMKASED
    LKKHGVTVLTALGAILKKKGHHEAELKPLAQSHATKHKIPIKYLEFISEAIIHVLHSRHP
    GDFGADAQGAMNKALELFRKDIAAKYKELGYQG
    >GLB5_PETMA Sw:Glb5_Petma => GLB5_PETMA
    PIVDTGSVAPLSAAEKTKIRSAWAPVYSTYETSGVDILVKFFTSTPAAQEFFPKFKGLTT
    ADQLKKSADVRWHAERIINAVNDAVASMDDTEKMSMKLRDLSGKHAKSFQVDPQYFKVLA
    AVIADTVAAGDAGFEKLMSMICILLRSAY
    >LGB2_LUPLU Sw:Lgb2_Luplu => LGB2_LUPLU
    GALTESQAALVKSSWEEFNANIPKHTHRFFILVLEIAPAAKDLFSFLKGTSEVPQNNPEL
    QAHAGKVFKLVYEAAIQLQVTGVVVTDATLKNLGSVHVSKGVADAHFPVVKEAILKTIKE
    VVGAKWSEELNSAWTIAYDELAIVIKKEMNDAA

The names (or accession numbers) of the sequences to be excluded can be entered as a file of such names by specifying an '@' followed by the name of the file containing the sequence names. For example: '@names.dat'.

The names or accession numbers of the sequences to be excluded are not standard EMBOSS USAs. Only the ID name or accession number can be specified, you cannot specify the sequences as 'database:ID', 'file:accession', 'format::file', etc.

## Output file format

notseq writes normal a sequence file.

### Output files for usage example

### File: mydata.seq

    >HBB_HUMAN Sw:Hbb_Human => HBB_HUMAN
    VHLTPEEKSAVTALWGKVNVDEVGGEALGRLLVVYPWTQRFFESFGDLSTPDAVMGNPKV
    KAHGKKVLGAFSDGLAHLDNLKGTFATLSELHCDKLHVDPENFRLLGNVLVCVLAHHFGK
    EFTPPVQAAYQKVVAGVANALAHKYH
    >HBB_HORSE Sw:Hbb_Horse => HBB_HORSE
    VQLSGEEKAAVLALWDKVNEEEVGGEALGRLLVVYPWTQRFFDSFGDLSNPGAVMGNPKV
    KAHGKKVLHSFGEGVHHLDNLKGTFAALSELHCDKLHVDPENFRLLGNVLVVVLARHFGK
    DFTPELQASYQKVVAGVANALAHKYH
    >HBA_HUMAN Sw:Hba_Human => HBA_HUMAN
    VLSPADKTNVKAAWGKVGAHAGEYGAEALERMFLSFPTTKTYFPHFDLSHGSAQVKGHGK
    KVADALTNAVAHVDDMPNALSALSDLHAHKLRVDPVNFKLLSHCLLVTLAAHLPAEFTPA
    VHASLDKFLASVSTVLTSKYR
    >HBA_HORSE Sw:Hba_Horse => HBA_HORSE
    VLSAADKTNVKAAWSKVGGHAGEYGAEALERMFLGFPTTKTYFPHFDLSHGSAQVKAHGK
    KVGDALTLAVGHLDDLPGALSNLSDLHAHKLRVDPVNFKLLSHCLLSTLAVHLPNDFTPA
    VHASLDKFLSSVSTVLTSKYR
    >GLB5_PETMA Sw:Glb5_Petma => GLB5_PETMA
    PIVDTGSVAPLSAAEKTKIRSAWAPVYSTYETSGVDILVKFFTSTPAAQEFFPKFKGLTT
    ADQLKKSADVRWHAERIINAVNDAVASMDDTEKMSMKLRDLSGKHAKSFQVDPQYFKVLA
    AVIADTVAAGDAGFEKLMSMICILLRSAY

### Output files for usage example 2

### File: mydata.seq

    >MYG_PHYCA Sw:Myg_Phyca => MYG_PHYCA
    VLSEGEWQLVLHVWAKVEADVAGHGQDILIRLFKSHPETLEKFDRFKHLKTEAEMKASED
    LKKHGVTVLTALGAILKKKGHHEAELKPLAQSHATKHKIPIKYLEFISEAIIHVLHSRHP
    GDFGADAQGAMNKALELFRKDIAAKYKELGYQG
    >GLB5_PETMA Sw:Glb5_Petma => GLB5_PETMA
    PIVDTGSVAPLSAAEKTKIRSAWAPVYSTYETSGVDILVKFFTSTPAAQEFFPKFKGLTT
    ADQLKKSADVRWHAERIINAVNDAVASMDDTEKMSMKLRDLSGKHAKSFQVDPQYFKVLA
    AVIADTVAAGDAGFEKLMSMICILLRSAY
    >LGB2_LUPLU Sw:Lgb2_Luplu => LGB2_LUPLU
    GALTESQAALVKSSWEEFNANIPKHTHRFFILVLEIAPAAKDLFSFLKGTSEVPQNNPEL
    QAHAGKVFKLVYEAAIQLQVTGVVVTDATLKNLGSVHVSKGVADAHFPVVKEAILKTIKE
    VVGAKWSEELNSAWTIAYDELAIVIKKEMNDAA

### File: hb.seq

    >HBB_HUMAN Sw:Hbb_Human => HBB_HUMAN
    VHLTPEEKSAVTALWGKVNVDEVGGEALGRLLVVYPWTQRFFESFGDLSTPDAVMGNPKV
    KAHGKKVLGAFSDGLAHLDNLKGTFATLSELHCDKLHVDPENFRLLGNVLVCVLAHHFGK
    EFTPPVQAAYQKVVAGVANALAHKYH
    >HBB_HORSE Sw:Hbb_Horse => HBB_HORSE
    VQLSGEEKAAVLALWDKVNEEEVGGEALGRLLVVYPWTQRFFDSFGDLSNPGAVMGNPKV
    KAHGKKVLHSFGEGVHHLDNLKGTFAALSELHCDKLHVDPENFRLLGNVLVVVLARHFGK
    DFTPELQASYQKVVAGVANALAHKYH
    >HBA_HUMAN Sw:Hba_Human => HBA_HUMAN
    VLSPADKTNVKAAWGKVGAHAGEYGAEALERMFLSFPTTKTYFPHFDLSHGSAQVKGHGK
    KVADALTNAVAHVDDMPNALSALSDLHAHKLRVDPVNFKLLSHCLLVTLAAHLPAEFTPA
    VHASLDKFLASVSTVLTSKYR
    >HBA_HORSE Sw:Hba_Horse => HBA_HORSE
    VLSAADKTNVKAAWSKVGGHAGEYGAEALERMFLGFPTTKTYFPHFDLSHGSAQVKAHGK
    KVGDALTLAVGHLDDLPGALSNLSDLHAHKLRVDPVNFKLLSHCLLSTLAVHLPNDFTPA
    VHASLDKFLSSVSTVLTSKYR

## Data files

None.

## Notes

notseq was written for the case where a file containing several sequences was being used as a small database, but some of the sequences were no longer required. notseq splits the input sequences into those that you wish to keep and those you wish to exclude.

Wildcarded names and accession numbers may be specified in the input string by using `*`.

The names (or accession numbers) of the sequences to be excluded can be entered as a file of such names by specifying an `@` followed by the name of the file containing the sequence names. For example: `@names.dat`.

## References

None.

## Warnings

The input string does not support the full USA syntax; only the name or accession number should be specified, not the database or file that these entries may occur in.

## Diagnostic Error Messages

If no matches are found to any of the specified sequence names, the message "This is a warning: No matches found." is displayed.

## Exit status

It exits with a status of 0 unless no matches are found to any of the input sequences name, in which case it exits with a status of -1.

## 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
listor | Write a list file of the logical OR of two sets of sequences
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
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 (9 Jan 2001) - Gary Williams

Added ability to specify names to exclude as a list file (June 2002) - Gary Williams

## Target users

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

## Comments

None