1hmmfetch(1)                      HMMER Manual                      hmmfetch(1)
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NAME

6       hmmfetch - retrieve profile HMM(s) from a file
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SYNOPSIS

10       hmmfetch [options] <hmmfile> <key>
11        (retrieves HMM named <key>)
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13       hmmfetch -f [options] <hmmfile> <keyfile>
14        (retrieves all HMMs listed in <keyfile>)
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16       hmmfetch --index [options] <hmmfile>
17        (indexes <hmmfile> for fetching)
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DESCRIPTION

22       Quickly  retrieves  one or more profile HMMs from an <hmmfile> (a large
23       Pfam database, for example).
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26       The <hmmfile> must be indexed first, using hmmfetch --index.  The index
27       is a binary file named <hmmfile>.ssi.
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30       The  default mode is to retrieve a single profile by name or accession,
31       called the <key>.  For example:
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33         % hmmfetch Pfam-A.hmm Caudal_act
34         % hmmfetch Pfam-A.hmm PF00045
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37       With the -f option, a <keyfile> containing a list of one or  more  keys
38       is  read  instead.   The  first whitespace-delimited field on each non-
39       blank non-comment line of the <keyfile> is used as  a  <key>,  and  any
40       remaining  data on the line is ignored; this allows a variety of white‐
41       space delimited datafiles to be  used  as  <keyfile>s.   The  <keyfile>
42       argument  can  be  a '-' (dash) character, in which case the keyfile is
43       read from standard input; this allows unix ninjas to construct  sophis‐
44       ticated invocations using pipes.
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47       By default, the HMM is printed to standard output in HMMER3 format.
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OPTIONS

51       -h     Help;  print  a  brief  reminder  of  command line usage and all
52              available options.
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55       -f     The second commandline argument is a <keyfile> instead of a sin‐
56              gle  <key>.   The  first  field on each line of the <keyfile> is
57              used as a retrieval <key> (an HMM  name  or  accession).   Blank
58              lines  and  comment  lines  (that  start with a # character) are
59              ignored.
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62       -o <f> Output HMM(s) to file <f> instead of to standard output.
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65       -O     Output HMM(s) to individual file(s) named <key> instead of stan‐
66              dard  output.  With the -f option, this can result in many files
67              being created.
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70       --index
71              Instead of retrieving one or more profiles from <hmmfile>, index
72              the  <hmmfile>  for  future  retrievals.   This  creates a <hmm‐
73              file>.ssi binary index file.
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SEE ALSO

79       See hmmer(1) for a master man page with a list of  all  the  individual
80       man pages for programs in the HMMER package.
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83       For  complete  documentation,  see  the  user guide that came with your
84       HMMER  distribution  (Userguide.pdf);  or  see  the  HMMER   web   page
85       (@HMMER_URL@).
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91       @HMMER_COPYRIGHT@
92       @HMMER_LICENSE@
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94       For  additional  information  on  copyright and licensing, see the file
95       called COPYRIGHT in your HMMER source distribution, or  see  the  HMMER
96       web page (@HMMER_URL@).
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AUTHOR

101       Eddy/Rivas Laboratory
102       Janelia Farm Research Campus
103       19700 Helix Drive
104       Ashburn VA 20147 USA
105       http://eddylab.org
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109HMMER @HMMER_VERSION@            @HMMER_DATE@                      hmmfetch(1)
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