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>)
12 hmmfetch -f [options] <hmmfile> <keyfile>
14 (retrieves all HMMs listed in <keyfile>)
15 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).
24 For maximum speed, the <hmmfile> should be indexed first, using hmm‐
27 fetch --index. The index is a binary file named <hmmfile>.ssi. How‐
28 ever, this is optional, and retrieval will still work from unindexed
29 files, albeit much more slowly.
30 The default mode is to retrieve a single profile by name or accession,
33 called the <key>. For example:
34 % hmmfetch Pfam-A.hmm Caudal_act
36 % hmmfetch Pfam-A.hmm PF00045
37 With the -f option, a <keyfile> containing a list of one or more keys
40 is read instead. The first whitespace-delimited field on each non-
41 blank non-comment line of the <keyfile> is used as a <key>, and any
42 remaining data on the line is ignored. This allows a variety of white‐
43 space delimited datafiles to be used as <keyfile>s.
44 When using -f and a <keyfile>, if hmmfile has been indexed, the keys
47 are retrieved in the order they occur in the keyfile, but if hmmfile
48 isn't indexed, keys are retrieved in the order they occur in the hmm‐
49 file. This is a side effect of an implementation that allows multiple
50 keys to be retrieved even if the <hmmfile> is a nonrewindable stream,
51 like a standard input pipe.
52 In normal use (without --index or -f options), <hmmfile> may be '-'
55 (dash), which means reading input from stdin rather than a file. With
56 the --index option, <hmmfile> may not be '-'; it does not make sense to
57 index a standard input stream. With the -f option, either <hmmfile> or
58 <keyfile> (but not both) may be '-'. It is often particularly useful
59 to read <keyfile> from standard input, because this allows use to use
60 arbitrary command line invocations to create a list of HMM names or
61 accessions, then fetch them all to a new file, just with one command.
62 By default, fetched HMMs are printed to standard output in HMMER3 for‐
65 mat.
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70 -h Help; print a brief reminder of command line usage and all
71 available options.
72 -f The second commandline argument is a <keyfile> instead of a sin‐
75 gle <key>. The first field on each line of the <keyfile> is
76 used as a retrieval <key> (an HMM name or accession). Blank
77 lines and comment lines (that start with a # character) are
78 ignored.
79 -o <f> Output HMM(s) to file <f> instead of to standard output.
82 -O Output HMM(s) to individual file(s) named <key> instead of stan‐
85 dard output. With the -f option, this can result in many files
86 being created.
87 --index
90 Instead of retrieving one or more profiles from <hmmfile>, index
91 the <hmmfile> for future retrievals. This creates a <hmm‐
92 file>.ssi binary index file.
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98 See hmmer(1) for a master man page with a list of all the individual
99 man pages for programs in the HMMER package.
100 For complete documentation, see the user guide that came with your
103 HMMER distribution (Userguide.pdf); or see the HMMER web page ().
104
109 Copyright (C) 2015 Howard Hughes Medical Institute.
110 Freely distributed under the GNU General Public License (GPLv3).
111 For additional information on copyright and licensing, see the file
113 called COPYRIGHT in your HMMER source distribution, or see the HMMER
114 web page ().
115
119 Eddy/Rivas Laboratory
120 Janelia Farm Research Campus
121 19700 Helix Drive
122 Ashburn VA 20147 USA
123 http://eddylab.org
124HMMER 3.1b2 February 2015 hmmfetch(1)