convert and mogrify

Convert and mogrify achieve similar goals. convert performs some operation on a file (from changing format to something more complicated) and writes to a new file. mogrify modifies a file in place, and would not normally be used to convert formats.

The two have similar signatures:

seqmagick convert [options] infile outfile

vs:

seqmagick mogrify [options] infile

Options are shared between convert and mogrify.

Examples

Basic Conversion

convert can be used to convert between any file types BioPython supports (which is many). For a full list of supported types, see the BioPython SeqIO wiki page.

By default, file type is inferred from file extension, so:

seqmagick convert a.fasta a.sto

converts an existing file a.fasta from FASTA to Stockholm format. Neat! But there’s more.

Sequence Modification

A wealth of options await you when you’re ready to do something slightly more complicated with your sequences.

Let’s say I just want a few of my sequences:

$ seqmagick convert --head 5 examples/test.fasta examples/test.head.fasta
$ seqmagick info examples/test*.fasta
name                      alignment  min_len  max_len  avg_len  num_seqs
examples/test.fasta       FALSE      972      9719     1573.67  15
examples/test.head.fasta  FALSE      978      990      984.00   5

Or I want to remove any gaps, reverse complement, select the last 5 sequences, and remove any duplicates from an alignment in place:

seqmagick mogrify --tail 5 --reverse-complement --ungap --deduplicate-sequences examples/test.fasta examples/test.fasta

You can even define your own functions in python and use them via --apply-function.

Note

To maximize flexibility, most transformations passed as options to mogrify and convert are processed in order, so:

seqmagick convert --min-length 50 --cut 1:5 a.fasta b.fasta

will work fine, but:

seqmagick convert --cut 1:5 --min-length 50 a.fasta b.fasta

will never return records, since the cutting transformation happens before the minimum length predicate is applied.

Command-line Arguments

Traceback (most recent call last):
  File "../seqmagick.py", line 7, in <module>
    sys.exit(cli.main(sys.argv[1:]))
  File "/var/build/user_builds/seqmagick/checkouts/0.6.0/seqmagick/scripts/cli.py", line 12, in main
    action, arguments = parse_arguments(argv)
  File "/var/build/user_builds/seqmagick/checkouts/0.6.0/seqmagick/scripts/cli.py", line 58, in parse_arguments
    for name, mod in subcommands.itermodules():
  File "/var/build/user_builds/seqmagick/checkouts/0.6.0/seqmagick/subcommands/__init__.py", line 7, in itermodules
    __import__('%s.%s' % (root, command), fromlist=[command]))
  File "/var/build/user_builds/seqmagick/checkouts/0.6.0/seqmagick/subcommands/convert.py", line 8, in <module>
    from Bio import Alphabet, SeqIO
ImportError: No module named Bio