From 15b0ffda4dec316fe377cb28b47d1f5e4312cea1 Mon Sep 17 00:00:00 2001
From: Orion Buske <orion.buske@gmail.com>
Date: Fri, 7 Nov 2014 19:00:18 -0500
Subject: [PATCH] Added capture-c probe creation script

---
 src/capture_c/fa2oligo.py | 99 +++++++++++++++++++++++++++++++++++++++++++++++
 1 file changed, 99 insertions(+)
 create mode 100644 src/capture_c/fa2oligo.py

diff --git a/src/capture_c/fa2oligo.py b/src/capture_c/fa2oligo.py
new file mode 100644
index 0000000..ba32f00
--- /dev/null
+++ b/src/capture_c/fa2oligo.py
@@ -0,0 +1,99 @@
+#!/usr/bin/env python
+
+"""
+Given a single-sequence fasta, generate candidate oligonuclotide sequences
+around restriction sites in a fasta output.
+"""
+
+__author__ = 'Orion Buske (buske@cs.toronto.edu)'
+
+import os
+import sys
+import logging
+
+def read_fasta(filename):
+    parts = []
+    with open(filename) as ifp:
+        header = ifp.readline()
+        assert header.startswith('>')
+        seq_name = header.lstrip('>').strip()
+        logging.info('Designing probes for sequence: {}'.format(seq_name))
+        for line in ifp:
+            line = line.rstrip('\n')
+            assert not line.startswith('>')
+            parts.append(line)
+
+    return ''.join(parts)
+
+def generate_probes(fragment, probe_length, max_probe_distance):
+    probes = set()
+    if len(fragment) < probe_length:
+        return probes
+
+    # Number of steps to tile from each end
+    n_tiles = min(len(fragment), max_probe_distance) - probe_length
+    logging.debug('Tiling {} probes from each end'.format(n_tiles))
+
+    for offset in range(n_tiles):
+        oligo = fragment[offset:offset + probe_length]
+        probes.add(oligo)
+
+    # If smaller than max_probe_distance, probes already span full fragment
+    if len(fragment) > max_probe_distance:
+        # Otherwise, need to capture some probes from other end
+        for offset in range(n_tiles):
+            start = len(fragment) - offset - probe_length
+            end = len(fragment) - offset
+            oligo = fragment[start:end]
+            probes.add(oligo)
+
+    return probes
+
+def print_probes(probes):
+    for i, probe in enumerate(probes):
+        print('>probe_{}\n{}'.format(i, probe))
+
+def script(fasta_filename, restriction_site, probe_length, max_probe_distance):
+    seq = read_fasta(fasta_filename)
+    logging.info('Sequence is {}bp'.format(len(seq)))
+
+    fragments = seq.split(restriction_site)
+    logging.info('{} fragments expected after restriction with {}'.format(len(fragments), restriction_site))
+
+    probes = set()
+    for fragment in fragments:
+        logging.debug('Fragment of length: {}'.format(len(fragment)))
+        frag_probes = generate_probes(fragment, probe_length, max_probe_distance)
+        logging.debug('Designed {} probes'.format(len(frag_probes)))
+        probes.update(frag_probes)
+        
+    logging.info('Generated {} unique {}bp probe sequences'.format(len(probes), probe_length))
+    print_probes(probes)
+
+def parse_args(args):
+    from argparse import ArgumentParser
+    description = __doc__.strip()
+    
+    parser = ArgumentParser(description=description)
+    parser.add_argument('fasta_filename', metavar='FASTA',
+                        help='Single-sequence fasta to design probes for')
+    parser.add_argument('--restriction-site', default='GATC',
+                        help='Restriction site sequence (default for DpnII)')
+    parser.add_argument('--probe-length', default=120,
+                        help='The length of each probe oligo')
+    parser.add_argument('--max-probe-distance', default=140,
+                        help='Maximum distance from far end of probe to'
+                        ' nearest restriction site')
+    parser.add_argument('--log', default='INFO',
+                        help='Logging level (e.g. DEBUG, INFO, WARNING)')
+
+    return parser.parse_args(args)
+
+def main(args=sys.argv[1:]):
+    args = vars(parse_args(args))
+    logging.basicConfig(level=args.pop('log'))
+
+    script(**args)
+
+if __name__ == '__main__':
+    sys.exit(main())