Making one_based a Fasta parameter

[vejnar]

Hi,

I am mostly working as 0-based. Specifying "one_based=False" every sequence() call is not very convenient.

A default behavior should be setup when Fasta is instantiated. Please consider applying the following patch:

diff --git a/pyfasta/fasta.py b/pyfasta/fasta.py
index 05d1fa1..1f510ef 100644
--- a/pyfasta/fasta.py
+++ b/pyfasta/fasta.py
@@ -41,7 +41,7 @@ class DuplicateHeaderException(Exception):

 class Fasta(Mapping):
     def __init__(self, fasta_name, record_class=NpyFastaRecord,
-                flatten_inplace=False, key_fn=None):
+                flatten_inplace=False, key_fn=None, one_based=True):
         """
             >>> from pyfasta import Fasta, FastaRecord

@@ -68,6 +68,7 @@ class Fasta(Mapping):
         self.fasta_name = fasta_name
         self.record_class = record_class
         self.key_fn = key_fn
+        self.one_based = one_based
         self.index, self.prepared = self.record_class.prepare(self,
                                               self.gen_seqs_with_headers(key_fn),
                                               flatten_inplace)
@@ -130,7 +131,7 @@ class Fasta(Mapping):
         return self.chr[i]

     def sequence(self, f, asstring=True, auto_rc=True
-            , exon_keys=None, one_based=True):
+            , exon_keys=None, one_based=None):
         """
         take a feature and use the start/stop or exon_keys to return
         the sequence from the assocatied fasta file:
@@ -197,6 +198,8 @@ class Fasta(Mapping):
         assert 'chr' in f and f['chr'] in self, (f, f['chr'], self.keys())
         fasta    = self[f['chr']]
         sequence = None
+        if one_based is None:
+            one_based = self.one_based
         if not exon_keys is None:
             sequence = self._seq_from_keys(f, fasta, exon_keys, one_based=one_based)

@@ -210,7 +213,7 @@ class Fasta(Mapping):
         if asstring: return sequence
         return np.array(sequence, dtype='c')

-    def _seq_from_keys(self, f, fasta, exon_keys, base='locations', one_based=True):
+    def _seq_from_keys(self, f, fasta, exon_keys, base='locations', one_based=None):
         """Internal:
         f: a feature dict
         fasta: a Fasta object
@@ -222,6 +225,8 @@ class Fasta(Mapping):
             {'CDS': [(25210018, 25210251)]}, 'start': 25210018, 'chr':
             '11', 'strand': -1} set(['TRNA', 'CDS'])
         """
+        if one_based is None:
+            one_based = self.one_based
         fbase = f.get(base, f)
         for ek in exon_keys:
             if not ek in fbase: continue