Changeset 59

Timestamp:

Dec 22, 2009, 9:29:24 AM (15 years ago)

Author:

Rick van der Zwet

Message:

Do the reading_frames as well

Location:

liacs/dbdm/dbdm_4

Files:

• parse_fasta.py (copied) (copied from liacs/dbdm/dbdm_4/parse-fasta.py ) (3 diffs)
• reading_frames.py (moved) (moved from liacs/dbdm/dbdm_4/parse-fasta.py ) (1 diff)

liacs/dbdm/dbdm_4/parse_fasta.py

@@ -9 +9 @@
 import Bio.Data.CodonTable
 from MultiReplace  import MultiReplace
+from reading_frames import reading_frames
 
 fasta_translate = { 
@@ -90 +91 @@
 print file1
 stats(seq1)
-print file1
-stats(seq1)
+reading_frames(seq1)
+print file2
+stats(seq2)
+reading_frames(seq2)
+
 
 # Strictly speaking there is a gap of about 4 kbs (4000 bs) between seq1 and
@@ -99 +103 @@
 result = result + "n" * 4000;
 stats(result)
+reading_frames(result)
 
 # Write to file for later further processing

liacs/dbdm/dbdm_4/reading_frames.py

@@ -1 +1 @@
 #!/usr/bin/env python
 #
-# Parse 2 FASTA files and print statistics
+# Parse FASTA file and print statistics on reading frames
 # BSDLicence
 # Rick van der Zwet - 0433373 - <info@rickvaderzwet.nl>
-from Bio import SeqIO,Seq
-from Bio import Alphabet
-from Bio.Alphabet.IUPAC import ambiguous_dna,unambiguous_dna
-import Bio.Data.CodonTable
-from MultiReplace  import MultiReplace
+import sys
 
-fasta_translate = { 
-    'r' : 'ga', # purine
-    'y' : 'tc', # pyrimide
-    'k' : 'gt', # keto
-    'm' : 'ac', # amino 
-    's' : 'gc', # strong
-    'w' : 'at', # weak
-    'b' : 'gtc',
-    'd' : 'gat',
-    'h' : 'act',
-    'v' : 'gca',
-    }
-    
-fasta = MultiReplace(fasta_translate)
+def _frame_stat(seq, start=0):
+    pdict = {}
+    for n in range(start,len(seq),2):
+        codon = seq[n:n+3]
+        if len(codon) < 3:
+            continue
+        if not pdict.has_key(codon):
+            pdict[codon] = 1
+        else:
+            pdict[codon] += 1
 
-def parse_file(file):
-    handle = open(file, "rU")
-    for seq_record in SeqIO.parse(handle, "fasta",ambiguous_dna):
-        # How to translate damm thing into plain nucleic acid codes
-        # http://en.wikipedia.org/wiki/FASTA_format
-        retval = seq_record.seq.__str__()
-    
-    handle.close()
-    return(retval)
+    return(pdict)
 
-def stats(seq):
-    pdict = {}
-    for n in range(1, len(seq)):
-        protein = seq[n]
-        if not pdict.has_key(protein):
-            pdict[protein] = 1
-        else:
-            pdict[protein] += 1
-    
-    print pdict
+def reading_frames(seq):
+    '''Parse from left to right and right to left, at position 1,2,3 in
+    in the so called nucleotide triplets 
+    See: http://en.wikipedia.org/wiki/Genetic_code'''
+
+    # Populate all empty
+    final = {}
+    for a in 'acgtn':
+        for b in 'acgtn':
+            for c in 'acgtn': 
+                final[a + b + c] = [0,0,0,0,0,0]
+
+    for start in [0,1,2]:
+        print "Normal; start %i" % (start)
+        retval = _frame_stat(seq,start)
+        for codon,v in retval.iteritems():
+            final[codon][start] += v
+        print "Reverse; start %i" % (start)
+        retval = _frame_stat(seq[::-1],start)
+        for codon,v in retval.iteritems():
+            final[codon][start+3] += v
+
+    print "CODON :  N:0   , N:1  , N:2  ,  R:0 , R:1  , R:2  "
+
+    for codon in sorted(final.keys()):
+        print codon,"  : ", ",".join(["%6i" % x for x in final[codon]])
 
 
-def concat(head,tail,max_length=1000):
-    "Concat two strings together removing common parts"
-    l_head = len(head)
-    l_tail = len(tail)
 
-    # Start/Stop at the right time
-    start = 1
-    if (l_head < l_tail):
-        stop = l_head + 1
-    else:
-        stop = l_tail + 1
-
-    # Make sure not to run for-ever
-    if (stop > max_length):
-        stop = max_length
-
-    # Find largest common part
-    # XXX: Not very effient (on very large overlap sets
-    for i in reversed(range(start,stop)):
-        #print "tail[0:%i] '%s' == '%s'" % (i, head[-i:], tail[0:i])
-        if head[-i:] == tail[0:i]:
-            return((i,(tail[0:i]),head + tail[i:]))
-
-    # None found return full part
-    return(-1,'',head + tail)
-
-
-# Get data
-file1 = parse_file("data/AE005174v2-1.fas")
-file2 = parse_file("data/AE005174v2-2.fas")
-
-file1 = fasta.replace(file1)
-file2 = fasta.replace(file2)
-
-# Find overlap
-(retval, common, result) = concat(file2,file1)
-print retval, common
-
-# Strictly speaking there is a gap of about 4 kbs (4000 bs) between file1 and
-# file2, so lets' put that into the the statistics as well. Due to circular
-# nature, does not matter wether we add it in the beginning or in the end
-result = result + "n" * 4000;
-stats(result)
-
-# Write to file for later further processing
-out = open("full_contig.raw","w")
-out.write(result)
-out.close()
+if __name__ == "__main__":
+    # Load data
+    try:
+        handle = open(sys.argv[1],"rU")
+    except IndexError:
+        print "Usage %s <data_file>" % (sys.argv[0])
+        sys.exit(64)
+    except IOError:
+        print "Unable to open '%s'" % (sys.argv[1])
+        sys.exit(64)
+    
+    seq = handle.read()
+    handle.close()
+    reading_frames(seq)