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资源说明：(abandoned) python utilities for manipulation of biological sequences
Package: Seq
============
**This project is deprecated - I'm leaving it here because some very old projects depend on it, but please don't use this for anything new!**
This package contains many utilities for biological sequence
manipulation that I have accumulated over the years. The first thing
to point out is that there is much duplication of functionality
provided by the biopython project. If you need to parse various
sequence file formats (fasta, genbank, etc), you should probably go
there instead. However, there are a few goodies in here that I haven't
found elsewhere. Some highlights:
Sequence de-duplication::
py> import Seq
py> seqs = ('TATATA','TATATA', 'TATAT', 'AAGCAG', 'AAGC', 'TTTTT')
py> print Seq.sequtil.coalesce(seqs)
{0: [1, 2], 3: [4], 5: []}
Multiple alignment formatting::
% alnview.py --help
Usage: alnview.py [options]
Create formatted sequence alignments with optional pdf output.
Options:
--version show program's version number and exit
-h, --help show this help message and exit
-f INFILE, --infile=INFILE
input FILE containing sequence alignment
-o OUTFILE, --outfile=OUTFILE
Write output to a pdf file.
-c, --add_consensus Include show a consensus sequence [False]
-d COMPARE_TO, --compare-to=COMPARE_TO
Number of the sequence to use as a reference.
Nucleotide positions identical to the reference will
be shown as a '.' The default behavior is to use the
consensus sequence as a reference. Use the -i option
to display the sequence numbers for reference. A value
of -1 suppresses this behavior.
-i, --number-sequences
Show sequence number to left of name. [False]
-x, --exclude-invariant
only show columns with at least min_subs non-consensus
bases (set min_subs using the -s option) [False]
-g, --exclude-gapcols
Remove columns containing only gap characters. [False]
-s NUMBER, --min_subs=NUMBER
minimum NUMBER of substitutions required to define a
position as variable. [1]
-n NUMBER, --name-max=NUMBER
maximum width of sequence name. [35]
-w NUMBER, --width=NUMBER
Width of sequence to display in each block in
characters [115]
-F NUMBER, --fontsize=NUMBER
Font size for pdf output [7]
-C CASE, --case=CASE Convert all characters to a uniform case
('upper','lower') [none]
-p NUMBER, --per-page=NUMBER
Sequences (lines) per page of pdf output. [75]
-r RANGE, --range=RANGE
Range of aligned positions to display (eg '-r
start,stop')
-O ORIENTATION, --orientation=ORIENTATION
Choose from portrait or landscape. [portrait]
-b NUMBER, --blocks-per-page=NUMBER
Number of aligned blocks of sequence per page [1]
-q, --quiet Suppress output of alignment to screen. [False]
-v, --verbose increase verbosity of screen output (eg, -v is
verbose, -vv is more so)
Dependencies
------------
* python 2.6+
* ReportLab (http://www.reportlab.com/software/opensource/) - for pdf-format multiple alignments.
* various freely-available bioinformatics tools (if you want to use
any of the run_* methods), eg clustalw, hmmer, fasta3*, infernal
Installation
------------
Uses the basic "setup.py" routine::
sudo python setup.py install
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