
                                  skipseq 
                                      
   
   
Function

   Reads and writes (returns) sequences, skipping the first few
   
Description

   skipseq skips the first few sequences in a multiple set of sequences,
   and writes out the rest of them.
   
   skipseq is a variant of the standard program for reading and writing
   sequences, seqret.
   
   seqret has an option to allow it to only read the first sequence from
   a multiple set of sequences (-firstonly). seqret cannot, however, skip
   the first few sequences from a multiple set of sequence, writing out
   the rest; this is what skipseq is for.
   
   In all other respects, skipseq is the same as seqret.
   
Usage

   Here is a sample session with skipseq
   
   This does not skip any sequences. It is exactly equivalent to seqret:
   

% skipseq 
Reads and writes (returns) sequences, skipping the first few
Input sequence(s): tembl:eclac*
Number of sequences to skip at start [0]: 
Output sequence [eclac.fasta]: 
   
   Go to the input files for this example
   Go to the output files for this example
   
   Example 2
   
   This skips the first input sequence, writing out the others:
   

% skipseq -skip 1 
Reads and writes (returns) sequences, skipping the first few
Input sequence(s): tembl:eclac*
Output sequence [eclac.fasta]: 
   
   Go to the output files for this example
   
Command line arguments

   Mandatory qualifiers:
  [-sequence]          seqall     Sequence database USA
   -skip               integer    Number of sequences to skip at start
  [-outseq]            seqoutall  Output sequence(s) USA

   Optional qualifiers: (none)
   Advanced qualifiers:
   -feature            boolean    Use feature information

   General qualifiers:
  -help                boolean    Report command line options. More
                                  information on associated and general
                                  qualifiers can be found with -help -verbose
   

   Mandatory qualifiers Allowed values Default
   [-sequence]
   (Parameter 1) Sequence database USA Readable sequence(s) Required
   -skip Number of sequences to skip at start Any integer value 0
   [-outseq]
   (Parameter 2) Output sequence(s) USA Writeable sequence(s)
   <sequence>.format
   Optional qualifiers Allowed values Default
   (none)
   Advanced qualifiers Allowed values Default
   -feature Use feature information Boolean value Yes/No No
   
Input file format

   skipseq reads one or more sequence USAs.
   
  Input files for usage example
  
   'tembl:eclac*' is a sequence entry in the example nucleic acid
   database 'tembl'
   
   See the documentation for seqret to see the full range of things that
   you can do when reading and writing sequences.
   
Output file format

   skipseq writes one or more sequences files, having optionally skipped
   the first few sequences.
   
  Output files for usage example
  
  File: eclac.fasta
  
>ECLAC J01636.1 E.coli lactose operon with lacI, lacZ, lacY and lacA genes.
gacaccatcgaatggcgcaaaacctttcgcggtatggcatgatagcgcccggaagagagt
caattcagggtggtgaatgtgaaaccagtaacgttatacgatgtcgcagagtatgccggt
gtctcttatcagaccgtttcccgcgtggtgaaccaggccagccacgtttctgcgaaaacg
cgggaaaaagtggaagcggcgatggcggagctgaattacattcccaaccgcgtggcacaa
caactggcgggcaaacagtcgttgctgattggcgttgccacctccagtctggccctgcac
gcgccgtcgcaaattgtcgcggcgattaaatctcgcgccgatcaactgggtgccagcgtg
gtggtgtcgatggtagaacgaagcggcgtcgaagcctgtaaagcggcggtgcacaatctt
ctcgcgcaacgcgtcagtgggctgatcattaactatccgctggatgaccaggatgccatt
gctgtggaagctgcctgcactaatgttccggcgttatttcttgatgtctctgaccagaca
cccatcaacagtattattttctcccatgaagacggtacgcgactgggcgtggagcatctg
gtcgcattgggtcaccagcaaatcgcgctgttagcgggcccattaagttctgtctcggcg
cgtctgcgtctggctggctggcataaatatctcactcgcaatcaaattcagccgatagcg
gaacgggaaggcgactggagtgccatgtccggttttcaacaaaccatgcaaatgctgaat
gagggcatcgttcccactgcgatgctggttgccaacgatcagatggcgctgggcgcaatg
cgcgccattaccgagtccgggctgcgcgttggtgcggatatctcggtagtgggatacgac
gataccgaagacagctcatgttatatcccgccgtcaaccaccatcaaacaggattttcgc
ctgctggggcaaaccagcgtggaccgcttgctgcaactctctcagggccaggcggtgaag
ggcaatcagctgttgcccgtctcactggtgaaaagaaaaaccaccctggcgcccaatacg
caaaccgcctctccccgcgcgttggccgattcattaatgcagctggcacgacaggtttcc
cgactggaaagcgggcagtgagcgcaacgcaattaatgtgagttagctcactcattaggc
accccaggctttacactttatgcttccggctcgtatgttgtgtggaattgtgagcggata
acaatttcacacaggaaacagctatgaccatgattacggattcactggccgtcgttttac
aacgtcgtgactgggaaaaccctggcgttacccaacttaatcgccttgcagcacatcccc
ctttcgccagctggcgtaatagcgaagaggcccgcaccgatcgcccttcccaacagttgc
gcagcctgaatggcgaatggcgctttgcctggtttccggcaccagaagcggtgccggaaa
gctggctggagtgcgatcttcctgaggccgatactgtcgtcgtcccctcaaactggcaga
tgcacggttacgatgcgcccatctacaccaacgtaacctatcccattacggtcaatccgc
cgtttgttcccacggagaatccgacgggttgttactcgctcacatttaatgttgatgaaa
gctggctacaggaaggccagacgcgaattatttttgatggcgttaactcggcgtttcatc
tgtggtgcaacgggcgctgggtcggttacggccaggacagtcgtttgccgtctgaatttg
acctgagcgcatttttacgcgccggagaaaaccgcctcgcggtgatggtgctgcgttgga
gtgacggcagttatctggaagatcaggatatgtggcggatgagcggcattttccgtgacg
tctcgttgctgcataaaccgactacacaaatcagcgatttccatgttgccactcgcttta
atgatgatttcagccgcgctgtactggaggctgaagttcagatgtgcggcgagttgcgtg
actacctacgggtaacagtttctttatggcagggtgaaacgcaggtcgccagcggcaccg
cgcctttcggcggtgaaattatcgatgagcgtggtggttatgccgatcgcgtcacactac
gtctgaacgtcgaaaacccgaaactgtggagcgccgaaatcccgaatctctatcgtgcgg
tggttgaactgcacaccgccgacggcacgctgattgaagcagaagcctgcgatgtcggtt
tccgcgaggtgcggattgaaaatggtctgctgctgctgaacggcaagccgttgctgattc
gaggcgttaaccgtcacgagcatcatcctctgcatggtcaggtcatggatgagcagacga
tggtgcaggatatcctgctgatgaagcagaacaactttaacgccgtgcgctgttcgcatt
atccgaaccatccgctgtggtacacgctgtgcgaccgctacggcctgtatgtggtggatg
aagccaatattgaaacccacggcatggtgccaatgaatcgtctgaccgatgatccgcgct
ggctaccggcgatgagcgaacgcgtaacgcgaatggtgcagcgcgatcgtaatcacccga
gtgtgatcatctggtcgctggggaatgaatcaggccacggcgctaatcacgacgcgctgt
atcgctggatcaaatctgtcgatccttcccgcccggtgcagtatgaaggcggcggagccg
acaccacggccaccgatattatttgcccgatgtacgcgcgcgtggatgaagaccagccct
tcccggctgtgccgaaatggtccatcaaaaaatggctttcgctacctggagagacgcgcc
cgctgatcctttgcgaatacgcccacgcgatgggtaacagtcttggcggtttcgctaaat


  [Part of this file has been deleted for brevity]

gttacccaacttaatcgccttgcagcacatccccctttcgccagctggcgtaatagcgaa
gaggcccgcaccgatcgcccttcccaacagttgcgcagcctgaatggcgaatggcgcttt
gcctggtttccggcaccagaagcggtgccggaaagctggctggagtgcgatcttcctgag
gccgatactgtcgtcgtcccctcaaactggcagatgcacggttacgatgcgcccatctac
accaacgtaacctatcccattacggtcaatccgccgtttgttcccacggagaatccgacg
ggttgttactcgctcacatttaatgttgatgaaagctggctacaggaaggccagacgcga
attatttttgatggcgttaactcggcgtttcatctgtggtgcaacgggcgctgggtcggt
tacggccaggacagtcgtttgccgtctgaatttgacctgagcgcatttttacgcgccgga
gaaaaccgcctcgcggtgatggtgctgcgttggagtgacggcagttatctggaagatcag
gatatgtggcggatgagcggcattttccgtgacgtctcgttgctgcataaaccgactaca
caaatcagcgatttccatgttgccactcgctttaatgatgatttcagccgcgctgtactg
gaggctgaagttcagatgtgcggcgagttgcgtgactacctacgggtaacagtttcttta
tggcagggtgaaacgcaggtcgccagcggcaccgcgcctttcggcggtgaaattatcgat
gagcgtggtggttatgccgatcgcgtcacactacgtctgaacgtcgaaaacccgaaactg
tggagcgccgaaatcccgaatctctatcgtgcggtggttgaactgcacaccgccgacggc
acgctgattgaagcagaagcctgcgatgtcggtttccgcgaggtgcggattgaaaatggt
ctgctgctgctgaacggcaagccgttgctgattcgaggcgttaaccgtcacgagcatcat
cctctgcatggtcaggtcatggatgagcagacgatggtgcaggatatcctgctgatgaag
cagaacaactttaacgccgtgcgctgttcgcattatccgaaccatccgctgtggtacacg
ctgtgcgaccgctacggcctgtatgtggtggatgaagccaatattgaaacccacggcatg
gtgccaatgaatcgtctgaccgatgatccgcgctggctaccggcgatgagcgaacgcgta
acgcgaatggtgcagcgcgatcgtaatcacccgagtgtgatcatctggtcgctggggaat
gaatcaggccacggcgctaatcacgacgcgctgtatcgctggatcaaatctgtcgatcct
tcccgcccggtgcagtatgaaggcggcggagccgacaccacggccaccgatattatttgc
ccgatgtacgcgcgcgtggatgaagaccagcccttcccggctgtgccgaaatggtccatc
aaaaaatggctttcgctacctggagagacgcgcccgctgatcctttgcgaatacgcccac
gcgatgggtaacagtcttggcggtttcgctaaatactggcaggcgtttcgtcagtatccc
cgtttacagggcggcttcgtctgggactgggtggatcagtcgctgattaaatatgatgaa
aacggcaacccgtggtcggcttacggcggtgattttggcgatacgccgaacgatcgccag
ttctgtatgaacggtctggtctttgccgaccgcacgccgcatccagcgctgacggaagca
aaacaccagcagcagtttttccagttccgtttatccgggcaaaccatcgaagtgaccagc
gaatacctgttccgtcatagcgataacgagctcctgcactggatggtggcgctggatggt
aagccgctggcaagcggtgaagtgcctctggatgtcgctccacaaggtaaacagttgatt
gaactgcctgaactaccgcagccggagagcgccgggcaactctggctcacagtacgcgta
gtgcaaccgaacgcgaccgcatggtcagaagccgggcacatcagcgcctggcagcagtgg
cgtctggcggaaaacctcagtgtgacgctccccgccgcgtcccacgccatcccgcatctg
accaccagcgaaatggatttttgcatcgagctgggtaataagcgttggcaatttaaccgc
cagtcaggctttctttcacagatgtggattggcgataaaaaacaactgctgacgccgctg
cgcgatcagttcacccgtgcaccgctggataacgacattggcgtaagtgaagcgacccgc
attgaccctaacgcctgggtcgaacgctggaaggcggcgggccattaccaggccgaagca
gcgttgttgcagtgcacggcagatacacttgctgatgcggtgctgattacgaccgctcac
gcgtggcagcatcaggggaaaaccttatttatcagccggaaaacctaccggattgatggt
agtggtcaaatggcgattaccgttgatgttgaagtggcgagcgatacaccgcatccggcg
cggattggcctgaactgccagctggcgcaggtagcagagcgggtaaactggctcggatta
gggccgcaagaaaactatcccgaccgccttactgccgcctgttttgaccgctgggatctg
ccattgtcagacatgtataccccgtacgtcttcccgagcgaaaacggtctgcgctgcggg
acgcgcgaattgaattatggcccacaccagtggcgcggcgacttccagttcaacatcagc
cgctacagtcaacagcaactgatggaaaccagccatcgccatctgctgcacgcggaagaa
ggcacatggctgaatatcgacggtttccatatggggattggtggcgacgactcctggagc
ccgtcagtatcggcggaattccagctgagcgccggtcgctaccattaccagttggtctgg
tgtcaaaaataataataa
   
  Output files for usage example 2
  
  File: eclac.fasta
  
>ECLACA X51872.1 Escherichia coli lacA gene for thiogalactoside transacetylase
gtgaatgaagtcgcttaagcaatcaatgtcggatgcggcgcgacgcttatccgaccaaca
tatcataacggagtgatcgcattgaacatgccaatgaccgaaagaataagagcaggcaag
ctatttaccgatatgtgcgaaggcttaccggaaaaaagacttcgtgggaaaacgttaatg
tatgagtttaatcactcgcatccatcagaagttgaaaaaagagaaagcctgattaaagaa
atgtttgccacggtaggggaaaacgcctgggtagaaccgcctgtctatttctcttacggt
tccaacatccatataggccgcaatttttatgcaaatttcaatttaaccattgtcgatgac
tacacggtaacaatcggtgataacgtactgattgcacccaacgttactctttccgttacg
ggacaccctgtacaccatgaattgagaaaaaacggcgagatgtactcttttccgataacg
attggcaataacgtctggatcggaagtcatgtggttattaatccaggcgtcaccatcggg
gataattctgttattggcgcgggtagtatcgtcacaaaagacattccaccaaacgtcgtg
gcggctggcgttccttgtcgggttattcgcgaaataaacgaccgggataagcactattat
ttcaaagattataaagttgaatcgtcagtttaaattataaaaattgcctgatacgctgcg
cttatcaggcctacaagttcagcgatctacattagccgcatccggcatgaacaaagcgca
ggaacaagcgtcgcatcatgcctctttgacccacagctgcggaaaacgtactggtgcaaa
acgcagggttatgatcatcagcccaacgacgcacagcgcatgaaatgcccagtccatcag
gtaattgccgctgatactacgcagcacgccagaaaaccacggggcaagcccggcgatgat
aaaaccgattccctgcataaacgccaccagcttgccagcaatagccggttgcacagagtg
atcgagcgccagcagcaaacagagcggaaacgcgccgcccagacctaacccacacaccat
cgcccacaataccggcaattgcatcggcagccagataaagccgcagaaccccaccagttg
taacaccagcgccagcattaacagtttgcgccgatcctgatggcgagccatagcaggcat
cagcaaagctcctgcggcttgcccaagcgtcatcaatgccagtaaggaaccgctgtactg
cgcgctggcaccaatctcaatatagaaagcgggtaaccaggcaatcaggctggcgtaacc
gccgttaatcagaccgaagtaaacacccagcgtccacgcgcggggagtgaataccacgcg
aaccggagtggttgttgtcttgtgggaagaggcgacctcgcgggcgctttgccaccacca
ggcaaagagcgcaacaacggcaggcagcgccaccaggcgagtgtttgataccaggtttcg
ctatgttgaactaaccagggcgttatggcggcaccaagcccaccgccgcccatcagagcc
gcggaccacagccccatcaccagtggcgtgcgctgctgaaaccgccgtttaatcaccgaa
gcatcaccgcctgaatgatgccgatccccaccccaccaagcagtgcgctgctaagcagca
gcgcactttgcgggtaaagctcacgcatcaatgcaccgacggcaatcagcaacagactga
tggcgacactgcgacgttcgctgacatgctgatgaagccagcttccggccagcgccagcc
cgcccatggtaaccaccggcagagcggtcgac
>ECLACI V00294.1 E. coli laci gene (codes for the lac repressor).
ccggaagagagtcaattcagggtggtgaatgtgaaaccagtaacgttatacgatgtcgca
gagtatgccggtgtctcttatcagaccgtttcccgcgtggtgaaccaggccagccacgtt
tctgcgaaaacgcgggaaaaagtggaagcggcgatggcggagctgaattacattcccaac
cgcgtggcacaacaactggcgggcaaacagtcgttgctgattggcgttgccacctccagt
ctggccctgcacgcgccgtcgcaaattgtcgcggcgattaaatctcgcgccgatcaactg
ggtgccagcgtggtggtgtcgatggtagaacgaagcggcgtcgaagcctgtaaagcggcg
gtgcacaatcttctcgcgcaacgcgtcagtgggctgatcattaactatccgctggatgac
caggatgccattgctgtggaagctgcctgcactaatgttccggcgttatttcttgatgtc
tctgaccagacacccatcaacagtattattttctcccatgaagacggtacgcgactgggc
gtggagcatctggtcgcattgggtcaccagcaaatcgcgctgttagcgggcccattaagt
tctgtctcggcgcgtctgcgtctggctggctggcataaatatctcactcgcaatcaaatt
cagccgatagcggaacgggaaggcgactggagtgccatgtccggttttcaacaaaccatg
caaatgctgaatgagggcatcgttcccactgcgatgctggttgccaacgatcagatggcg
ctgggcgcaatgcgcgccattaccgagtccgggctgcgcgttggtgcggatatctcggta
gtgggatacgacgataccgaagacagctcatgttatatcccgccgtcaaccaccatcaaa
caggattttcgcctgctggggcaaaccagcgtggaccgcttgctgcaactctctcagggc
caggcggtgaagggcaatcagctgttgcccgtctcactggtgaaaagaaaaaccaccctg


  [Part of this file has been deleted for brevity]

gttacccaacttaatcgccttgcagcacatccccctttcgccagctggcgtaatagcgaa
gaggcccgcaccgatcgcccttcccaacagttgcgcagcctgaatggcgaatggcgcttt
gcctggtttccggcaccagaagcggtgccggaaagctggctggagtgcgatcttcctgag
gccgatactgtcgtcgtcccctcaaactggcagatgcacggttacgatgcgcccatctac
accaacgtaacctatcccattacggtcaatccgccgtttgttcccacggagaatccgacg
ggttgttactcgctcacatttaatgttgatgaaagctggctacaggaaggccagacgcga
attatttttgatggcgttaactcggcgtttcatctgtggtgcaacgggcgctgggtcggt
tacggccaggacagtcgtttgccgtctgaatttgacctgagcgcatttttacgcgccgga
gaaaaccgcctcgcggtgatggtgctgcgttggagtgacggcagttatctggaagatcag
gatatgtggcggatgagcggcattttccgtgacgtctcgttgctgcataaaccgactaca
caaatcagcgatttccatgttgccactcgctttaatgatgatttcagccgcgctgtactg
gaggctgaagttcagatgtgcggcgagttgcgtgactacctacgggtaacagtttcttta
tggcagggtgaaacgcaggtcgccagcggcaccgcgcctttcggcggtgaaattatcgat
gagcgtggtggttatgccgatcgcgtcacactacgtctgaacgtcgaaaacccgaaactg
tggagcgccgaaatcccgaatctctatcgtgcggtggttgaactgcacaccgccgacggc
acgctgattgaagcagaagcctgcgatgtcggtttccgcgaggtgcggattgaaaatggt
ctgctgctgctgaacggcaagccgttgctgattcgaggcgttaaccgtcacgagcatcat
cctctgcatggtcaggtcatggatgagcagacgatggtgcaggatatcctgctgatgaag
cagaacaactttaacgccgtgcgctgttcgcattatccgaaccatccgctgtggtacacg
ctgtgcgaccgctacggcctgtatgtggtggatgaagccaatattgaaacccacggcatg
gtgccaatgaatcgtctgaccgatgatccgcgctggctaccggcgatgagcgaacgcgta
acgcgaatggtgcagcgcgatcgtaatcacccgagtgtgatcatctggtcgctggggaat
gaatcaggccacggcgctaatcacgacgcgctgtatcgctggatcaaatctgtcgatcct
tcccgcccggtgcagtatgaaggcggcggagccgacaccacggccaccgatattatttgc
ccgatgtacgcgcgcgtggatgaagaccagcccttcccggctgtgccgaaatggtccatc
aaaaaatggctttcgctacctggagagacgcgcccgctgatcctttgcgaatacgcccac
gcgatgggtaacagtcttggcggtttcgctaaatactggcaggcgtttcgtcagtatccc
cgtttacagggcggcttcgtctgggactgggtggatcagtcgctgattaaatatgatgaa
aacggcaacccgtggtcggcttacggcggtgattttggcgatacgccgaacgatcgccag
ttctgtatgaacggtctggtctttgccgaccgcacgccgcatccagcgctgacggaagca
aaacaccagcagcagtttttccagttccgtttatccgggcaaaccatcgaagtgaccagc
gaatacctgttccgtcatagcgataacgagctcctgcactggatggtggcgctggatggt
aagccgctggcaagcggtgaagtgcctctggatgtcgctccacaaggtaaacagttgatt
gaactgcctgaactaccgcagccggagagcgccgggcaactctggctcacagtacgcgta
gtgcaaccgaacgcgaccgcatggtcagaagccgggcacatcagcgcctggcagcagtgg
cgtctggcggaaaacctcagtgtgacgctccccgccgcgtcccacgccatcccgcatctg
accaccagcgaaatggatttttgcatcgagctgggtaataagcgttggcaatttaaccgc
cagtcaggctttctttcacagatgtggattggcgataaaaaacaactgctgacgccgctg
cgcgatcagttcacccgtgcaccgctggataacgacattggcgtaagtgaagcgacccgc
attgaccctaacgcctgggtcgaacgctggaaggcggcgggccattaccaggccgaagca
gcgttgttgcagtgcacggcagatacacttgctgatgcggtgctgattacgaccgctcac
gcgtggcagcatcaggggaaaaccttatttatcagccggaaaacctaccggattgatggt
agtggtcaaatggcgattaccgttgatgttgaagtggcgagcgatacaccgcatccggcg
cggattggcctgaactgccagctggcgcaggtagcagagcgggtaaactggctcggatta
gggccgcaagaaaactatcccgaccgccttactgccgcctgttttgaccgctgggatctg
ccattgtcagacatgtataccccgtacgtcttcccgagcgaaaacggtctgcgctgcggg
acgcgcgaattgaattatggcccacaccagtggcgcggcgacttccagttcaacatcagc
cgctacagtcaacagcaactgatggaaaccagccatcgccatctgctgcacgcggaagaa
ggcacatggctgaatatcgacggtttccatatggggattggtggcgacgactcctggagc
ccgtcagtatcggcggaattccagctgagcgccggtcgctaccattaccagttggtctgg
tgtcaaaaataataataa
   
   See the documentation for seqret to see the full range of things that
   you can do when reading and writing sequences.
   
Data files

   None.
   
Notes

   None.
   
References

   None.
   
Warnings

   You may skip all of the input files.
   If the -skip value is greater than or equal to the number of input
   sequences, there is no warning: this is legal.
   
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
   listor       Writes a list file of the logical OR of two sets of sequences
   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
   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
   
   skipseq is a variant of the standard program for reading and writing
   sequences, seqret.
   
Author(s)

   This application was written by Peter Rice
   (peter.rice@uk.lionbioscience.com)
   
History

   Written (25 June 2002) - Peter Rice
   
Target users

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