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

6       esl-seqstat - summarize contents of a sequence file
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SYNOPSIS

10       esl-seqstat [options] seqfile
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DESCRIPTION

14       esl-seqstat summarizes the contents of the seqfile.  It prints the for‐
15       mat, alphabet type, number of sequences, total number of residues,  and
16       the mean, smallest, and largest sequence length.
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19       If seqfile is - (a single dash), sequence input is read from stdin.
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OPTIONS

26       -h     Print  brief  help;   includes version number and summary of all
27              options, including expert options.
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30       -a     Additionally show a summary statistic  line  showing  the  name,
31              length,  and  description  of  each individual sequence. Each of
32              these lines is prefixed by an = character,  in  order  to  allow
33              these lines to be easily grepped out of the output.
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36       -c     Additionally print the residue composition of the sequence file.
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EXPERT OPTIONS

42       --informat <s>
43              Assert that input seqfile is in format <s>, bypassing format au‐
44              todetection.  Common choices for <s> include: fasta, embl,  gen‐
45              bank.   Alignment  formats  also  work;  common choices include:
46              stockholm, a2m, afa, psiblast, clustal, phylip.  For more infor‐
47              mation,  and  for  codes  for some less common formats, see main
48              documentation.  The string <s>  is  case-insensitive  (fasta  or
49              FASTA both work).
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53       --amino
54              Assert that the seqfile contains protein sequences.
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57       --dna  Assert that the seqfile contains DNA sequences.
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60       --rna  Assert that the seqfile contains RNA sequences.
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SEE ALSO

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

75       http://eddylab.org
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80Easel 0.48                         Nov 2020                     esl-seqstat(1)
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