Delete unneeded directory

[jabaws.git] / website / archive / binaries / mac / src / globplot / biopython-1.50 / Bio / writers / SeqRecord / embl.py

diff --git a/website/archive/binaries/mac/src/globplot/biopython-1.50/Bio/writers/SeqRecord/embl.py b/website/archive/binaries/mac/src/globplot/biopython-1.50/Bio/writers/SeqRecord/embl.py
deleted file mode 100644 (file)
index b30b368..0000000
--- a/website/archive/binaries/mac/src/globplot/biopython-1.50/Bio/writers/SeqRecord/embl.py
+++ /dev/null
@@ -1,85 +0,0 @@
-"""Part of an old unused and undocumented sequence writing framework (DEPRECATED)."""
-# Not clear on the distinction, if any, between 'embl' and 'embl/65'.  This
-# code might apply to either or both.
-
-# See 'http://www.ebi.ac.uk/embl/Documentation/User_manual/usrman.html' for a
-# definition of this file format.
-
-# This code only makes a best effort--the output may not be strictly valid.
-# So, for example, the EMBL ID is supposed to be alphanumeric, starting with a
-# letter, but we don't check for this, etc.
-
-
-# Example:
-# ID   AA03518    standard; DNA; FUN; 237 BP.
-# XX
-# AC   U03518;
-# XX
-# DE   Aspergillus awamori internal transcribed spacer 1 (ITS1) and 18S
-# DE   rRNA and 5.8S rRNA genes, partial sequence.
-# XX
-# SQ   Sequence 237 BP; 41 A; 77 C; 67 G; 52 T; 0 other;
-#      aacctgcgga aggatcatta ccgagtgcgg gtcctttggg cccaacctcc catccgtgtc        60
-#      tattgtaccc tgttgcttcg gcgggcccgc cgcttgtcgg ccgccggggg ggcgcctctg       120
-#      ccccccgggc ccgtgcccgc cggagacccc aacacgaaca ctgtctgaaa gcgtgcagtc       180
-#      tgagttgatt gaatgcaatc agttaaaact ttcaacaatg gatctcttgg ttccggc          237
-# //
-
-
-import textwrap
-
-from Bio import Alphabet
-from Bio import Writer
-
-class WriteEmbl(Writer.Writer):
-    def __init__(self, outfile):
-        Writer.Writer.__init__(self, outfile)
-        
-    def write(self, record):
-        seq = record.seq
-        assert seq.alphabet.size == 1, "cannot handle alphabet of size %d" % \
-               seq.alphabet.size
-        data = seq.data
-        upperdata = data.upper()
-
-# It'd be nice if the alphabet was usefully set, but for many interesting
-# cases (e.g., reading from FASTA files), it's not.
-
-        if isinstance(seq.alphabet, Alphabet.RNAAlphabet):
-            molecule = 'mRNA'
-            letters = ['A', 'C', 'G', 'U']
-        else:
-            molecule = 'DNA'
-            letters = ['A', 'C', 'G', 'T']
-
-        division = 'UNC'                # unknown
-
-        self.outfile.write("ID   %s  standard; %s; %s; %d BP.\n"
-                           % (record.id, molecule, division, len(data)))
-
-        desclist = textwrap.wrap(record.description, 74)
-        for l in desclist:
-            self.outfile.write("DE   %s\n" % l)
-
-        counts = [ upperdata.count(l) for l in letters ]
-        othercount = len(upperdata) - sum(counts)
-
-        countstring = ''.join([ " %d %s;" % p for p in zip(counts, letters) ])
-
-        self.outfile.write("SQ   Sequence %s BP;%s %d other;\n"
-                           % (len(data), countstring, othercount))
-
-        rowlength = 60
-        blocklength = 10
-        for i in xrange(0, len(data), rowlength):
-            self.outfile.write(" " * 5)
-            row = data[i:i+rowlength]
-            for b in xrange(0, rowlength, blocklength):
-                block = row[b:b+blocklength]
-                self.outfile.write("%-*s" % (blocklength+1, block))
-            self.outfile.write("%9d\n" % min(i+rowlength, len(data)))
-
-        self.outfile.write("//\n")
-
-
-make_writer = WriteEmbl