maskfeat.txt

emboss的linux版本的源代码

                                 maskfeat 



Function

   Mask off features of a sequence

Description

   maskfeat reads in a sequence with its associated features. The
   features can be found in the annotation of the sequence if it is in a
   format such as EMBL or SWISSPROT which includes features in the
   annotation, or they may be supplied explicitly in a GFF file by using
   the command-lin option '-gff filename'.

   The feature table is then searched for features whose type matches the
   specified feature type to be masked. By default, the type is 'repeat*'
   (i.e. any type whose name starts with 'repeat'). You can specify the
   name of any other type of feature, or features that you wish to mask.
   If you wish to specify more than one type of feature, separate their
   names with spaces or commas. The names of the types of feature to be
   found may be wild-carded with asterisks '*' to find gruops of feature
   types sharing a common part of their names.

   If you are unsure of the names of feature types in use, please consult
   http://www3.ebi.ac.uk/Services/WebFeat/ for a list of the EMBL feature
   types and see Appendix A of the Swissprot user manual in
   http://www.expasy.ch/txt/userman.txt for a list of the Swissprot
   feature types.

   If any features matching the specified names of feature types are
   found, then those regions of the sequence will be masked out by
   replacing that part of the sequence by masking characters. The default
   masking characters are 'X' for a protein sequence and 'N' for a
   nucleic acid sequence, although you can specify your own masking
   character, if required.

   Some non-EMBOSS programs (for example FASTA) are capable of treating
   lower-case regions as if they are masked. maskfeat can mask a region
   to lower-case instead of replacing the sequence with 'N's or 'X's if
   you use the qualifier '-tolower' or use a space character as the
   masking character.

Usage

   Here is a sample session with maskfeat

   Mask out a feature whose type is "repeat_region" from position 2331 to
   2356:


% maskfeat tembl:ab000360 
Mask off features of a sequence.
output sequence [ab000360.fasta]: 

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

   Example 2

   Change to lower-case a feature whose type is "repeat_region" from
   position 2331 to 2356. Note that '-supper' is used to make the whole
   sequence upper-case before the lower-case masking:


% maskfeat tembl:ab000360 -tolower -supper 
Mask off features of a sequence.
output sequence [ab000360.fasta]: 

   Go to the output files for this example

Command line arguments

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

   Additional (Optional) qualifiers (* if not always prompted):
   -type               string     [repeat*] By default any feature in the
                                  feature table with a type starting 'repeat'
                                  is masked. You can set this to be any
                                  feature type you wish to mask.
                                  See http://www3.ebi.ac.uk/Services/WebFeat/
                                  for a list of the EMBL feature types and see
                                  Appendix A of the Swissprot user manual in
                                  http://www.expasy.ch/txt/userman.txt for a
                                  list of the Swissprot feature types.
                                  The type may be wildcarded by using '*'.
                                  If you wish to mask more than one type,
                                  separate their names with spaces or commas,
                                  eg:
                                  *UTR repeat* (Any string is accepted)
   -tolower            toggle     [N] The region can be 'masked' by converting
                                  the sequence characters to lower-case, some
                                  non-EMBOSS programs e.g. fasta can
                                  interpret this as a masked region. The
                                  sequence is unchanged apart from the case
                                  change. You might like to ensure that the
                                  whole sequence is in upper-case before
                                  masking the specified regions to lower-case
                                  by using the '-supper' flag.
*  -maskchar           string     ['X' for protein, 'N' for nucleic] Character
                                  to use when masking.
                                  Default is 'X' for protein sequences, 'N'
                                  for nucleic sequences.
                                  If the mask character is set to be the SPACE
                                  character or a null character, then the
                                  sequence is 'masked' by changing it to
                                  lower-case, just as with the '-lowercase'
                                  flag. (Any string up to 1 characters)

   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
   -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

   maskfeat reads in a sequence USA. You can optionally specify a GFF
   feature file to use with the command-line option '-gff filename'.

  Input files for usage example

   'tembl:ab000360' is a sequence entry in the example nucleic acid
   database 'tembl'

  Database entry: tembl:ab000360

ID   AB000360   standard; DNA; HUM; 2582 BP.
XX
AC   AB000360;
XX
SV   AB000360.1
XX
DT   27-OCT-1997 (Rel. 53, Created)
DT   27-OCT-1997 (Rel. 53, Last updated, Version 1)
XX
DE   Homo sapiens PIGC gene, complete cds.
XX
KW   glycosylphosphatidylinositol-synthesis gene; PIGC.
XX
OS   Homo sapiens (human)
OC   Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia
;
OC   Eutheria; Primates; Catarrhini; Hominidae; Homo.
XX
RN   [1]
RP   1-2582
RA   Hong Y.;
RT   ;
RL   Submitted (08-JAN-1997) to the EMBL/GenBank/DDBJ databases.
RL   Yeongjin Hong, Research Institute for Microbial Diseases, Immunoregulation
;
RL   3-1 Yamada-oka, Suita, Osaka 565, Japan
RL   (E-mail:[e-mail], Tel:[phone], Fax:[phone])
XX
RN   [2]
RA   Hong Y., Ohishi K., Inoue N., Endo Y., Fujita T., Takeda J., Kinoshita T.;
RT   "Structures and chromosomal localizations of the
RT   glycosylphosphatidylinositol synthesis gene PIGC and its pseudogene
RT   PIGCP1";
RL   Genomics 44:347-349(1997).
XX
DR   SWISS-PROT; Q92535; PIGC_HUMAN.
XX
FH   Key             Location/Qualifiers
FH
FT   source          1..2582
FT                   /chromosome="1"
FT                   /db_xref="taxon:9606"
FT                   /sequenced_mol="DNA"
FT                   /organism="Homo sapiens"
FT                   /map="1q23-q25"
FT   exon            808..2266
FT   CDS             1101..1994
FT                   /codon_start=1
FT                   /db_xref="SWISS-PROT:Q92535"
FT                   /transl_table=1
FT                   /gene="PIGC"
FT                   /standard_name="glycosylphosphatidylinositol-synthesis


  [Part of this file has been deleted for brevity]

FT   variation       2259
FT                   /replace="t"
FT   repeat_region   2331..2356
FT                   /rpt_unit=gt
XX
SQ   Sequence 2582 BP; 694 A; 494 C; 581 G; 813 T; 0 other;
     ggatccctgc tgcagagggg gtaacggtgt ctggcttgcc aagcaatatt tgttgtggtc        6
0
     tatcatggaa gaaataaagt cgggcaatat gaattttttt tttctcaaat ttgccggatg       12
0
     gctgtggtgt ttctgactct tagttttctc attgtgaaaa aggaatgatt atcttcttcg       18
0
     atcctctcaa gagtttcctt gttttgagta gattgatagc tctttaaagg atgctaagct       24
0
     cagctaatgg aagaagagtc tagtttcttt gaggctttga ttttggttaa actatagagc       30
0
     tcataccttt ctgtatggtg cagcttacta ttgtctttgg attggtaact taaaaaatac       36
0
     aaataacatg cctttgagaa ccaataaaaa ctatggatat tatccctata aatttacaca       42