EMBOSS: splitsource

splitsource

Wiki

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Function

Split sequence(s) into original source sequences

Description

splitsource splits a synthetic sequence into original source sequences by processing the "source" features in the feature table.

Algorithm

The "source" feature annotated the origin of a sequence region. Synthetic sequences are characterized by having two or more "source" features each describing one of the original sequence fragments.

Usage

Here is a sample session with splitsource

Split a sequence into original subsequences

% splitsource ena:A01139 Split sequence(s) into original source sequences output sequence(s) [a01139.fasta]:

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

Command line arguments

Split sequence(s) into original source sequences
Version: EMBOSS:6.6.0.0

   Standard (Mandatory) qualifiers:
  [-sequence]          seqall     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    [N] Retain feature information

   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
   -scircular1         boolean    Sequence is circular
   -squick1            boolean    Read id and sequence only
   -sformat1           string     Input sequence format
   -iquery1            string     Input query fields or ID list
   -ioffset1           integer    Input start position offset
   -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 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 and exit. 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
   -version            boolean    Report version number and exit

Qualifier Type Description Allowed values Default

Standard (Mandatory) qualifiers

[-sequence]
(Parameter 1) seqall Sequence(s) filename and optional format, or reference (input USA) Readable sequence(s) Required

[-outseq]
(Parameter 2) seqoutall Sequence set(s) filename and optional format (output USA) Writeable sequence(s) <*>.format

Additional (Optional) qualifiers

(none)

Advanced (Unprompted) qualifiers

-feature boolean Retain feature information Boolean value Yes/No No

Associated qualifiers

"-sequence" associated seqall qualifiers

-sbegin1
-sbegin_sequence integer Start of each sequence to be used Any integer value 0

-send1
-send_sequence integer End of each sequence to be used Any integer value 0

-sreverse1
-sreverse_sequence boolean Reverse (if DNA) Boolean value Yes/No N

-sask1
-sask_sequence boolean Ask for begin/end/reverse Boolean value Yes/No N

-snucleotide1
-snucleotide_sequence boolean Sequence is nucleotide Boolean value Yes/No N

-sprotein1
-sprotein_sequence boolean Sequence is protein Boolean value Yes/No N

-slower1
-slower_sequence boolean Make lower case Boolean value Yes/No N

-supper1
-supper_sequence boolean Make upper case Boolean value Yes/No N

-scircular1
-scircular_sequence boolean Sequence is circular Boolean value Yes/No N

-squick1
-squick_sequence boolean Read id and sequence only Boolean value Yes/No N

-sformat1
-sformat_sequence string Input sequence format Any string

-iquery1
-iquery_sequence string Input query fields or ID list Any string

-ioffset1
-ioffset_sequence integer Input start position offset Any integer value 0

-sdbname1
-sdbname_sequence string Database name Any string

-sid1
-sid_sequence string Entryname Any string

-ufo1
-ufo_sequence string UFO features Any string

-fformat1
-fformat_sequence string Features format Any string

-fopenfile1
-fopenfile_sequence string Features file name Any string

"-outseq" associated seqoutall qualifiers

-osformat2
-osformat_outseq string Output seq format Any string

-osextension2
-osextension_outseq string File name extension Any string

-osname2
-osname_outseq string Base file name Any string

-osdirectory2
-osdirectory_outseq string Output directory Any string

-osdbname2
-osdbname_outseq string Database name to add Any string

-ossingle2
-ossingle_outseq boolean Separate file for each entry Boolean value Yes/No N

-oufo2
-oufo_outseq string UFO features Any string

-offormat2
-offormat_outseq string Features format Any string

-ofname2
-ofname_outseq string Features file name Any string

-ofdirectory2
-ofdirectory_outseq string Output directory Any string

General qualifiers

-auto boolean Turn off prompts Boolean value Yes/No N

-stdout boolean Write first file to standard output Boolean value Yes/No N

-filter boolean Read first file from standard input, write first file to standard output Boolean value Yes/No N

-options boolean Prompt for standard and additional values Boolean value Yes/No N

-debug boolean Write debug output to program.dbg Boolean value Yes/No N

-verbose boolean Report some/full command line options Boolean value Yes/No Y

-help boolean Report command line options and exit. More information on associated and general qualifiers can be found with -help -verbose Boolean value Yes/No N

-warning boolean Report warnings Boolean value Yes/No Y

-error boolean Report errors Boolean value Yes/No Y

-fatal boolean Report fatal errors Boolean value Yes/No Y

-die boolean Report dying program messages Boolean value Yes/No Y

-version boolean Report version number and exit Boolean value Yes/No N

Qualifier	Type	Description	Allowed values	Default
Standard (Mandatory) qualifiers
[-sequence] (Parameter 1)	seqall	Sequence(s) filename and optional format, or reference (input USA)	Readable sequence(s)	Required
[-outseq] (Parameter 2)	seqoutall	Sequence set(s) filename and optional format (output USA)	Writeable sequence(s)	<>*.format
Additional (Optional) qualifiers
(none)
Advanced (Unprompted) qualifiers
-feature	boolean	Retain feature information	Boolean value Yes/No	No
Associated qualifiers
"-sequence" associated seqall qualifiers
-sbegin1 -sbegin_sequence	integer	Start of each sequence to be used	Any integer value	0
-send1 -send_sequence	integer	End of each sequence to be used	Any integer value	0
-sreverse1 -sreverse_sequence	boolean	Reverse (if DNA)	Boolean value Yes/No	N
-sask1 -sask_sequence	boolean	Ask for begin/end/reverse	Boolean value Yes/No	N
-snucleotide1 -snucleotide_sequence	boolean	Sequence is nucleotide	Boolean value Yes/No	N
-sprotein1 -sprotein_sequence	boolean	Sequence is protein	Boolean value Yes/No	N
-slower1 -slower_sequence	boolean	Make lower case	Boolean value Yes/No	N
-supper1 -supper_sequence	boolean	Make upper case	Boolean value Yes/No	N
-scircular1 -scircular_sequence	boolean	Sequence is circular	Boolean value Yes/No	N
-squick1 -squick_sequence	boolean	Read id and sequence only	Boolean value Yes/No	N
-sformat1 -sformat_sequence	string	Input sequence format	Any string
-iquery1 -iquery_sequence	string	Input query fields or ID list	Any string
-ioffset1 -ioffset_sequence	integer	Input start position offset	Any integer value	0
-sdbname1 -sdbname_sequence	string	Database name	Any string
-sid1 -sid_sequence	string	Entryname	Any string
-ufo1 -ufo_sequence	string	UFO features	Any string
-fformat1 -fformat_sequence	string	Features format	Any string
-fopenfile1 -fopenfile_sequence	string	Features file name	Any string
"-outseq" associated seqoutall qualifiers
-osformat2 -osformat_outseq	string	Output seq format	Any string
-osextension2 -osextension_outseq	string	File name extension	Any string
-osname2 -osname_outseq	string	Base file name	Any string
-osdirectory2 -osdirectory_outseq	string	Output directory	Any string
-osdbname2 -osdbname_outseq	string	Database name to add	Any string
-ossingle2 -ossingle_outseq	boolean	Separate file for each entry	Boolean value Yes/No	N
-oufo2 -oufo_outseq	string	UFO features	Any string
-offormat2 -offormat_outseq	string	Features format	Any string
-ofname2 -ofname_outseq	string	Features file name	Any string
-ofdirectory2 -ofdirectory_outseq	string	Output directory	Any string
General qualifiers
-auto	boolean	Turn off prompts	Boolean value Yes/No	N
-stdout	boolean	Write first file to standard output	Boolean value Yes/No	N
-filter	boolean	Read first file from standard input, write first file to standard output	Boolean value Yes/No	N
-options	boolean	Prompt for standard and additional values	Boolean value Yes/No	N
-debug	boolean	Write debug output to program.dbg	Boolean value Yes/No	N
-verbose	boolean	Report some/full command line options	Boolean value Yes/No	Y
-help	boolean	Report command line options and exit. More information on associated and general qualifiers can be found with -help -verbose	Boolean value Yes/No	N
-warning	boolean	Report warnings	Boolean value Yes/No	Y
-error	boolean	Report errors	Boolean value Yes/No	Y
-fatal	boolean	Report fatal errors	Boolean value Yes/No	Y
-die	boolean	Report dying program messages	Boolean value Yes/No	Y
-version	boolean	Report version number and exit	Boolean value Yes/No	N

Input file format

The input is a standard EMBOSS sequence query (also known as a 'USA').

Major sequence database sources defined as standard in EMBOSS installations include srs:embl, srs:uniprot and ensembl

Data can also be read from sequence output in any supported format written by an EMBOSS or third-party application.

The input format can be specified by using the command-line qualifier -sformat xxx, where 'xxx' is replaced by the name of the required format. The available format names are: gff (gff3), gff2, embl (em), genbank (gb, refseq), ddbj, refseqp, pir (nbrf), swissprot (swiss, sw), dasgff and debug.

See: http://emboss.sf.net/docs/themes/SequenceFormats.html for further information on sequence formats.

Input files for usage example

Database entry: ena:A01139

ID   A01139; SV 1; linear; unassigned DNA; PAT; PRO; 279 BP.
XX
AC   A01139;
XX
DT   16-MAR-1994 (Rel. 38, Created)
DT   14-FEB-2001 (Rel. 66, Last updated, Version 5)
XX
DE   Fusion DNA (L.lactis MSP signal sequence and H.medicinalis desulfatohirudin
DE   coding sequence)
XX
KW   .
XX
OS   Lactococcus lactis
OC   Bacteria; Firmicutes; Bacilli; Lactobacillales; Streptococcaceae;
OC   Lactococcus.
XX
OS   Hirudo medicinalis (medicinal leech)
OC   Eukaryota; Metazoa; Lophotrochozoa; Annelida; Clitellata; Hirudinida;
OC   Hirudinea; Arhynchobdellida; Hirudiniformes; Hirudinidae; Hirudo.
XX
RN   [1]
RP   1-279
RA   Suri B., Schmitz A.;
RT   "Bacterial vectors.";
RL   Patent number EP0449770-A2/2, 02-OCT-1991.
RL   CIBA-GEIGY AG.
XX
FH   Key             Location/Qualifiers
FH
FT   source          1..81
FT                   /organism="Lactococcus lactis"
FT                   /focus
FT                   /strain="LM0230"
FT                   /mol_type="unassigned DNA"
FT                   /db_xref="taxon:1358"
FT   source          82..279
FT                   /organism="Hirudo medicinalis"
FT                   /mol_type="unassigned DNA"
FT                   /db_xref="taxon:6421"
FT   CDS             1..279
FT                   /transl_table=11
FT                   /note="fusion of MSP signal peptide and hirudin"
FT                   /protein_id="CAA00134.1"
FT                   /translation="MKKKIISAILMSTVILSAAAPLSGVYAVVYTDCTESGQNLCLCEG
FT                   SNVCGQGNKCILGSDGEKNQCVTGEGTPKPQSHNDGDFEEIPEEYLQ"
FT   sig_peptide     1..81
FT                   /product="MSP signal peptide"
FT   mat_peptide     82..279
FT                   /product="desulfatohirudin"
XX
SQ   Sequence 279 BP; 76 A; 66 C; 68 G; 69 T; 0 other;
     atgaaaaaaa agattatctc agctatttta atgtctacag tgatactttc tgctgcagcc        60
     ccgttgtcag gtgtttacgc tgttgtttac accgactgca ccgaatctgg tcagaacctg       120
     tgcctgtgcg aaggttctaa cgtttgcggt cagggtaaca aatgcatcct gggttctgac       180
     ggtgaaaaaa accagtgcgt taccggcgaa ggtaccccga aaccgcagtc tcacaacgac       240
     ggtgacttcg aagaaatccc ggaagaatac ctgcagtag                              279
//

Output file format

The output is a standard EMBOSS sequence file.

The results can be output in one of several styles by using the command-line qualifier -osformat xxx, where 'xxx' is replaced by the name of the required format. The available format names are: embl, genbank, gff, pir, swiss, dasgff, debug, listfile, dbmotif, diffseq, excel, feattable, motif, nametable, regions, seqtable, simple, srs, table, tagseq.

See: http://emboss.sf.net/docs/themes/SequenceFormats.html for further information on sequence formats.

Output files for usage example

File: a01139.fasta

>A01139_1_1-81 organism="Lactococcus lactis" strain="LM0230" Fusion DNA (L.lactis MSP signal sequence and H.medicinalis desulfatohirudin coding sequence)
atgaaaaaaaagattatctcagctattttaatgtctacagtgatactttctgctgcagcc
ccgttgtcaggtgtttacgct
>A01139_2_82-279 organism="Hirudo medicinalis" Fusion DNA (L.lactis MSP signal sequence and H.medicinalis desulfatohirudin coding sequence)
gttgtttacaccgactgcaccgaatctggtcagaacctgtgcctgtgcgaaggttctaac
gtttgcggtcagggtaacaaatgcatcctgggttctgacggtgaaaaaaaccagtgcgtt
accggcgaaggtaccccgaaaccgcagtctcacaacgacggtgacttcgaagaaatcccg
gaagaatacctgcagtag

Data files

None.

Notes

None.

References

None.

Warnings

None.

Diagnostic Error Messages

None.

Exit status

It always exits with status 0.

Known bugs

None.

Program name	Description
aligncopy	Read and write alignments
aligncopypair	Read and write pairs from alignments
biosed	Replace or delete sequence sections
codcopy	Copy and reformat a codon usage table
cutseq	Remove a section from a sequence
degapseq	Remove non-alphabetic (e.g. gap) characters from sequences
descseq	Alter the name or description of a sequence
entret	Retrieve 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	Read and write a feature table
featmerge	Merge two overlapping feature tables
featreport	Read and write a feature table
feattext	Return a feature table original text
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	Mask all ambiguity characters in nucleotide sequences with N
maskambigprot	Mask 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 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
nthseqset	Read and write (return) one set of sequences from many
pasteseq	Insert one sequence into another
revseq	Reverse and complement a nucleotide sequence
seqcount	Read and count sequences
seqret	Read and write (return) sequences
seqretsetall	Read and write (return) many sets of sequences
seqretsplit	Read sequences and write them to individual files
sizeseq	Sort sequences by size
skipredundant	Remove redundant sequences from an input set
skipseq	Read and write (return) 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	Remove vectors from the ends of nucleotide sequence(s)
yank	Add a sequence reference (a full USA) to a list file

Author(s)

Peter Rice
European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK

History

Target users

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

Comments

None

Wiki

Function

Description

Algorithm

Usage

Command line arguments

Input file format

Input files for usage example

Database entry: ena:A01139

Output file format

Output files for usage example

File: a01139.fasta

Data files

Notes

References

Warnings

Diagnostic Error Messages

Exit status

Known bugs

See also

Author(s)

History

Target users

Comments