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.\" DO NOT MODIFY THIS FILE! It was generated by help2man 1.46.4.
.TH SEQMAGICK "1" "June 2017" "seqmagick 0.6.1" "User Commands"
.SH NAME
seqmagick \- Manipulate sequence files
.SH SYNOPSIS
usage: seqmagick [\-h] [\-V] [\-v] [\-q]
.IP
help, convert, info, mogrify, primer\-trim, quality\-filter, extract\-ids, backtrans\-align
\&...
.SH DESCIPTION
Seqmagick is a little utility to expose the file format conversion
in BioPython in a convenient way.
.SH OPTIONS
.SS "positional arguments:"
.IP
help, convert, info, mogrify, primer\-trim, quality\-filter, extract\-ids, backtrans\-align
.TP
help
Detailed help for actions using help <action>
.TP
convert
Convert between sequence formats
.TP
info
Info action
.TP
mogrify
Modify sequence file(s) in place.
.TP
primer\-trim
Find a primer sequence in a gapped alignment, trim to
amplicon
.TP
quality\-filter
Filter reads based on quality scores
.TP
extract\-ids
Extract the sequence IDs from a file
.TP
backtrans\-align
Given a protein alignment and unaligned nucleotides,
align the nucleotides using the protein alignment.
Protein and nucleotide sequence files must contain the
same number of sequences, in the same order, with the
same IDs.
.SS "optional arguments:"
.TP
\fB\-h\fR, \fB\-\-help\fR
show this help message and exit
.TP
\fB\-V\fR, \fB\-\-version\fR
Print the version number and exit
.TP
\fB\-v\fR, \fB\-\-verbose\fR
Be more verbose. Specify \fB\-vv\fR or \fB\-vvv\fR for even more
.TP
\fB\-q\fR, \fB\-\-quiet\fR
Suppress output
.SH AUTHOR
This manpage was written by Andreas Tille for the Debian distribution and can be used for any other usage of the program.
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