1hmmfetch(1) HMMER Manual hmmfetch(1)
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6 hmmfetch - retrieve profile HMM(s) from a file
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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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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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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
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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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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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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)