SEQMAGICK

NAME

seqmagick - Manipulate sequence files

SYNOPSIS

usage: seqmagick [-h] [-V] [-v] [-q]

help, convert, info, mogrify, primer-trim, quality-filter, extract-ids, backtrans-align ...

DESCIPTION

Seqmagick is a little utility to expose the file format conversion in BioPython in a convenient way.

OPTIONS

positional arguments:

help, convert, info, mogrify, primer-trim, quality-filter, extract-ids, backtrans-align

help

Detailed help for actions using help <action>

convert

Convert between sequence formats

info

Info action

mogrify

Modify sequence file(s) in place.

primer-trim

Find a primer sequence in a gapped alignment, trim to amplicon

quality-filter

Filter reads based on quality scores

extract-ids

Extract the sequence IDs from a file

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.

optional arguments:

-h, --help

show this help message and exit

-V, --version

Print the version number and exit

-v, --verbose

Be more verbose. Specify -vv or -vvv for even more

-q, --quiet

Suppress output

AUTHOR

This manpage was written by Andreas Tille for the Debian distribution and can be used for any other usage of the program.