1hmmfetch(1) HMMER Manual hmmfetch(1)
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6 hmmfetch - retrieve profiles from a file
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10 hmmfetch [options] hmmfile key
11 (retrieve HMM named key)
12 hmmfetch -f [options] hmmfile keyfile
14 (retrieve all HMMs listed in keyfile)
15 hmmfetch --index [options] hmmfile
17 (index hmmfile for fetching)
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21 Quickly retrieves one or more profile HMMs from an hmmfile (a large
22 Pfam database, for example).
23 For maximum speed, the hmmfile should be indexed first, using hmmfetch
26 --index. The index is a binary file named hmmfile.ssi. However, this
27 is optional, and retrieval will still work from unindexed files, albeit
28 much more slowly.
29 The default mode is to retrieve a single profile by name or accession,
32 called the key. For example:
33 % hmmfetch Pfam-A.hmm Caudal_act
35 % hmmfetch Pfam-A.hmm PF00045
36 With the -f option, a keyfile containing a list of one or more keys is
39 read instead. The first whitespace-delimited field on each non-blank
40 non-comment line of the keyfile is used as a key, and any remaining
41 data on the line is ignored. This allows a variety of whitespace delim‐
42 ited datafiles to be used as a keyfile.
43 When using -f and a keyfile, if hmmfile has been indexed, the keys are
46 retrieved in the order they occur in the keyfile, but if hmmfile isn't
47 indexed, keys are retrieved in the order they occur in the hmmfile.
48 This is a side effect of an implementation that allows multiple keys to
49 be retrieved even if the hmmfile is a nonrewindable stream, like a
50 standard input pipe.
51 In normal use (without --index or -f options), hmmfile may be '-'
54 (dash), which means reading input from stdin rather than a file. With
55 the --index option, hmmfile may not be '-'; it does not make sense to
56 index a standard input stream. With the -f option, either hmmfile or
57 keyfile (but not both) may be '-'. It is often particularly useful to
58 read keyfile from standard input, because this allows use to use arbi‐
59 trary command line invocations to create a list of HMM names or acces‐
60 sions, then fetch them all to a new file, just with one command.
61 By default, fetched HMMs are printed to standard output in HMMER3 for‐
64 mat.
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69 -h Help; print a brief reminder of command line usage and all
70 available options.
71 -f The second commandline argument is a keyfile instead of a single
74 key. The first field on each line of the keyfile is used as a
75 retrieval key (an HMM name or accession). Blank lines and com‐
76 ment lines (that start with a # character) are ignored.
77 -o <f> Output HMM(s) to file <f> instead of to standard output.
80 -O Output HMM(s) to individual file(s) named key instead of stan‐
83 dard output.
84 --index
87 Instead of retrieving one or more profiles from hmmfile, index
88 the hmmfile for future retrievals. This creates a hmmfile.ssi
89 binary index file.
90
95 See hmmer(1) for a master man page with a list of all the individual
96 man pages for programs in the HMMER package.
97 For complete documentation, see the user guide that came with your HM‐
100 MER distribution (Userguide.pdf); or see the HMMER web page (http://hm‐
101 mer.org/).
102
107 Copyright (C) 2020 Howard Hughes Medical Institute.
108 Freely distributed under the BSD open source license.
109 For additional information on copyright and licensing, see the file
111 called COPYRIGHT in your HMMER source distribution, or see the HMMER
112 web page (http://hmmer.org/).
113
117 http://eddylab.org
118HMMER 3.3.2 Nov 2020 hmmfetch(1)