Mac binaries

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

diff --git a/website/archive/binaries/mac/src/disembl/biopython-1.50/Bio/writers/SeqRecord/embl.py b/website/archive/binaries/mac/src/disembl/biopython-1.50/Bio/writers/SeqRecord/embl.py
new file mode 100644 (file)
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+++ b/website/archive/binaries/mac/src/disembl/biopython-1.50/Bio/writers/SeqRecord/embl.py
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+"""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