1esl-afetch(1)                    Easel Manual                    esl-afetch(1)
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NAME

6       esl-afetch - retrieve alignments from a multi-MSA database
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SYNOPSIS

10       esl-afetch [options] msafile key
11         (single MSA retrieval)
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13       esl-afetch -f [options] msafile keyfile
14         (multiple MSA retrieval, from a file of keys)
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16       esl-afetch --index msafile
17         (index an MSA file for retrieval)
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DESCRIPTION

21       esl-afetch retrieves the alignment named key from an alignment database
22       in file msafile.  The msafile is a "multiple multiple  alignment"  file
23       in  Stockholm (e.g. native Pfam or Rfam) format.  The key is either the
24       name (ID) of the alignment, or its accession number (AC).
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27       Alternatively, esl-afetch -f provides the ability to fetch many  align‐
28       ments at once.  The -f option has it interpret the second argument as a
29       keyfile, a file consisting of one name or accession per line.
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32       The msafile should first be SSI indexed with esl-afetch --index for ef‐
33       ficient retrieval. An SSI index is not required, but without one align‐
34       ment retrieval may be painfully slow.
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OPTIONS

38       -h     Print brief help; includes version number and summary of all op‐
39              tions, including expert options.
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42       -f     Interpret  the  second  argument as a keyfile instead of as just
43              one key.  The keyfile contains one name or accession  per  line.
44              This option doesn't work with the --index option.
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48       -o <f> Output retrieved alignments to a file <f> instead of to stdout.
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51       -O     Output  retrieved alignment to a file named key.  This is a con‐
52              venience for saving some typing: instead of
53               % esl-afetch -o RRM_1 msafile RRM_1
54              you can just type
55               % esl-afetch -O msafile RRM_1
56              The -O option only works if you're retrieving  a  single  align‐
57              ment; it is incompatible with -f.
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60       --index
61              Instead  of  retrieving  a  key,  the special command esl-afetch
62              --index msafile produces an SSI index of the  names  and  acces‐
63              sions of the alignments in the msafile.  Indexing should be done
64              once on the msafile to prepare it for all future fetches.
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SEE ALSO

69       http://bioeasel.org/
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73       Copyright (C) 2020 Howard Hughes Medical Institute.
74       Freely distributed under the BSD open source license.
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AUTHOR

78       http://eddylab.org
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83Easel 0.48                         Nov 2020                      esl-afetch(1)
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