seqretsplit.txt

emboss的linux版本的源代码

                                seqretsplit 



Function

   Reads and writes (returns) sequences in individual files

Description

   seqretsplit is exactly the same as the program seqret except that when
   it writes out more than one sequence, it writes each sequence to an
   individual file.

   Its main use is therefore to split a file containing multiple
   sequences into many files, each containing one sequence.

   The names of the files it creates are derived from the ID name of the
   sequence, followed by an extension denoting the format of the
   sequence. You have no control over the names of the files it writes
   out.

   For example, if the files embl:hsfa11* are read in and the output is
   specified as wibble.seq, then the following files are expected to be
   created:

hsfa110.fasta
hsfa111.fasta
hsfa112.fasta
hsfa113.fasta
hsfa114.fasta

   (No file wibble.seq is created.)

   Why would you want to split a multiple sequence file into many
   individual files?

   EMBOSS programs can read in many sequences from one file where this is
   sensible. Sometimes EMBOSS programs can only read in one sequence at a
   time because that is the sensible way to do things, but your sequence
   is one sequence of many in a file. You can specify that sequence using
   the USA filename:sequenceID, but you may still feel more comfortable
   splitting your sequences up into many files first.

   Many non-EMBOSS programs will also have restrictions on whether they
   can read in multiple sequence files or not.

Usage

   Here is a sample session with seqretsplit


% seqretsplit tembl:hsfa* 
Reads and writes (returns) sequences in individual files
output sequence(s) [hsfau.fasta]: 

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

   The specification of the output file is not used in this case.

   At some point this ought to change and you will not be prompted for
   the output file at all.

Command line arguments

   Standard (Mandatory) qualifiers:
  [-sequence]          seqall     (Gapped) sequence(s) filename and optional
                                  format, or reference (input USA)
  [-outseq]            seqoutall  [.] Sequence set(s)
                                  filename and optional format (output USA)

   Additional (Optional) qualifiers: (none)
   Advanced (Unprompted) qualifiers:
   -feature            boolean    Use feature information
   -firstonly          boolean    Read one sequence and stop

   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
   -osformat2          string     Output seq format
   -osextension2       string     File name extension
   -osname2            string     Base file name
   -osdirectory2       string     Output directory
   -osdbname2          string     Database name to add
   -ossingle2          boolean    Separate file for each entry
   -oufo2              string     UFO features
   -offormat2          string     Features format
   -ofname2            string     Features file name
   -ofdirectory2       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 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

   seqretsplit reads a normal sequence USA.

  Input files for usage example

   'tembl:hsfa*' is a sequence entry in the example nucleic acid database
   'tembl'

Output file format

  Output files for usage example

  File: hsfau.fasta

>HSFAU X65923.1 H.sapiens fau mRNA
ttcctctttctcgactccatcttcgcggtagctgggaccgccgttcagtcgccaatatgc
agctctttgtccgcgcccaggagctacacaccttcgaggtgaccggccaggaaacggtcg
cccagatcaaggctcatgtagcctcactggagggcattgccccggaagatcaagtcgtgc
tcctggcaggcgcgcccctggaggatgaggccactctgggccagtgcggggtggaggccc
tgactaccctggaagtagcaggccgcatgcttggaggtaaagttcatggttccctggccc
gtgctggaaaagtgagaggtcagactcctaaggtggccaaacaggagaagaagaagaaga
agacaggtcgggctaagcggcggatgcagtacaaccggcgctttgtcaacgttgtgccca
cctttggcaagaagaagggccccaatgccaactcttaagtcttttgtaattctggctttc
tctaataaaaaagccacttagttcagtcaaaaaaaaaa

  File: hsfau1.fasta

>HSFAU1 X65921.1 H.sapiens fau 1 gene
ctaccattttccctctcgattctatatgtacactcgggacaagttctcctgatcgaaaac
ggcaaaactaaggccccaagtaggaatgccttagttttcggggttaacaatgattaacac
tgagcctcacacccacgcgatgccctcagctcctcgctcagcgctctcaccaacagccgt
agcccgcagccccgctggacaccggttctccatccccgcagcgtagcccggaacatggta
gctgccatctttacctgctacgccagccttctgtgcgcgcaactgtctggtcccgccccg
tcctgcgcgagctgctgcccaggcaggttcgccggtgcgagcgtaaaggggcggagctag
gactgccttgggcggtacaaatagcagggaaccgcgcggtcgctcagcagtgacgtgaca
cgcagcccacggtctgtactgacgcgccctcgcttcttcctctttctcgactccatcttc
gcggtagctgggaccgccgttcaggtaagaatggggccttggctggatccgaagggcttg
tagcaggttggctgcggggtcagaaggcgcggggggaaccgaagaacggggcctgctccg
tggccctgctccagtccctatccgaactccttgggaggcactggccttccgcacgtgagc
cgccgcgaccaccatcccgtcgcgatcgtttctggaccgctttccactcccaaatctcct
ttatcccagagcatttcttggcttctcttacaagccgtcttttctttactcagtcgccaa
tatgcagctctttgtccgcgcccaggagctacacaccttcgaggtgaccggccaggaaac
ggtcgcccagatcaaggtaaggctgcttggtgcgccctgggttccattttcttgtgctct
tcactctcgcggcccgagggaacgcttacgagccttatctttccctgtaggctcatgtag
cctcactggagggcattgccccggaagatcaagtcgtgctcctggcaggcgcgcccctgg
aggatgaggccactctgggccagtgcggggtggaggccctgactaccctggaagtagcag
gccgcatgcttggaggtgagtgagagaggaatgttctttgaagtaccggtaagcgtctag
tgagtgtggggtgcatagtcctgacagctgagtgtcacacctatggtaatagagtacttc
tcactgtcttcagttcagagtgattcttcctgtttacatccctcatgttgaacacagacg
tccatgggagactgagccagagtgtagttgtatttcagtcacatcacgagatcctagtct
ggttatcagcttccacactaaaaattaggtcagaccaggccccaaagtgctctataaatt
agaagctggaagatcctgaaatgaaacttaagatttcaaggtcaaatatctgcaactttg
ttctcattacctattgggcgcagcttctctttaaaggcttgaattgagaaaagaggggtt
ctgctgggtggcaccttcttgctcttacctgctggtgccttcctttcccactacaggtaa
agtccatggttccctggcccgtgctggaaaagtgagaggtcagactcctaaggtgagtga
gagtattagtggtcatggtgttaggactttttttcctttcacagctaaaccaagtccctg
ggctcttactcggtttgccttctccctccctggagatgagcctgagggaagggatgctag
gtgtggaagacaggaaccagggcctgattaaccttcccttctccaggtggccaaacagga
gaagaagaagaagaagacaggtcgggctaagcggcggatgcagtacaaccggcgctttgt
caacgttgtgcccacctttggcaagaagaagggccccaatgccaactcttaagtcttttg
taattctggctttctctaataaaaaagccacttagttcagtcatcgcattgtttcatctt
tacttgcaaggcctcagggagaggtgtgcttctcgg

   One file for each input sequence is written out.

   The names of the files it creates are derived from the ID name of the
   sequence, followed by an extension denoting the format of the
   sequence. You have no control over the names of the files it writes
   out.

   For example, if the files embl:hsfa11* are read in and the output is
   specified as wibble.seq, then the following files are expected to be
   created:

hsfa110.fasta
hsfa111.fasta
hsfa112.fasta
hsfa113.fasta
hsfa114.fasta

   (No file wibble.seq is created.)

Data files

   None.

Notes

   None.

References

   None.

Warnings

   None.

Diagnostic Error Messages

   None.

Exit status

   It always exits with status 0.

Known bugs

   It shouldn't really prompt for the output filename.

   This isa side effect of the waysequence output works in EMBOSS.
   Writing multiple sequences to separate files (the -ossingle qualifier)
   does this, and seqretsplit has set it automatically on.

See also

   Program name                         Description
   biosed       Replace or delete sequence sections
   codcopy      Reads and writes a codon usage table
   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
   extractalign Extract regions from a sequence alignment
   extractfeat  Extract features from a sequence
   extractseq   Extract regions from a sequence
   listor       Write a list file of the logical OR of two sets of sequences
   makenucseq   Creates random nucleotide sequences
   makeprotseq  Creates random protein 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       Exclude a set of sequences and write 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
   skipseq      Reads and writes (returns) sequences, skipping 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)

   Peter Rice (pmr