cutting by length added

	modified:   fatool/fa.py
	modified:   fatool/tests/test_fa.py

Author: blazejmarciniak

fatool/fa.py

@@ -1,7 +1,7 @@
 # -*- coding: utf-8 -*-
 
 
-import re
+import re #gex as re
 import math
 from fatool import Sequence
 import logging
@@ -51,11 +51,10 @@ def load_from_file(file):
 
     @staticmethod       
     def load_content(content):
-        #print content
-        nc = content.split('>')
+        ncs = re.findall(re.compile('(?=(^>[\S\s]+?)(^>|\Z))',re.M), content)
         contigs_list = []
-        for r in nc[1:]:
-            contigs_list.append(Sequence('>'+r.split('\n', 1)[0].rstrip(), re.sub('^>.*\n', '', '>'+r.rstrip())))
+        for r in ncs:
+            contigs_list.append(Sequence(r[0].split('\n', 1)[0].rstrip(), re.sub('^>.*\n', '', r[0].rstrip())))
         return contigs_list
 
     def write(self, fafile):
@@ -127,6 +126,14 @@ def remove(self, contigs_name_list):
             if not r.name in contigs_name_list:
                 new_contig_list.append(r)
         return Fa(new_contig_list, 'rem_'+self.name)
+        
+    def cut_min_len(self, min_len):
+        nc = []
+        for r in self.contigs:
+            if len(r) > min_len:
+                nc.append(r)
+        return Fa(nc,'cutof_'+str(min_len)+self.name)
+                
 
     def validate(self):
         '''

fatool/tests/test_fa.py

@@ -24,11 +24,11 @@ def test_setUpFa(self):
         f = Fa(cl, 'test-fa')
         self.assertEqual(cl, f.contigs)
         self.assertEqual('test-fa', f.name)
-        self.assertEqual({'name':0, 'name2':1, 'name3':2}, f.contigs_idx)
+        self.assertEqual({'>name':0, '>name2':1, '>name3':2}, f.contigs_idx)
         cl.append('something')
         with self.assertRaises(TypeError):
             Fa(cl, 'name4')
-    '''        
+            
     def test_str(self):
         cl = []
         cl.append(Sequence('>name', 'ACTGactg'))
@@ -69,29 +69,32 @@ def test_add_contigs(self):
     def test_show_names(self):
         cl = [Sequence('>name', 'ACTGactg'), Sequence('>name2', 'NNNNNNNNNACTGNNNN'), Sequence('>name3', 'CTNACtacgatNNNNNNN')]
         f = Fa(cl, 'test-fa')
-        self.assertEqual(['name','name2','name3'], f.show_names())
+        self.assertEqual(['>name','>name2','>name3'], f.show_names())
         f.add_contig(Sequence('>name2', 'ACTGaaaaaaa'), 1)
-        self.assertEqual(['name','name3','name2'], f.show_names())
+        self.assertEqual(['>name','>name3','>name2'], f.show_names())
         f.add_contig(Sequence('>name7', 'ACTGaaaaaaa'), 1)
-        self.assertEqual(['name','name3','name2','name7'], f.show_names())
+        self.assertEqual(['>name','>name3','>name2','>name7'], f.show_names())
 
     def test_extract(self):
         cl = [Sequence('>name', 'ACTGactg'), Sequence('>name2', 'NNNNNNNNNACTGNNNN'), Sequence('>name3', 'CTNACtacgatNNNNNNN')]
         f = Fa(cl, 'test-fa')
         self.assertEqual(cl, f.contigs)
         cl2 = [Sequence('>name2', 'NNNNNNNNNACTGNNNN'), Sequence('>name3', 'CTNACtacgatNNNNNNN')]
-        self.assertEqual(cl2, f.extract(['name2', 'name3']).contigs)
-        self.assertEqual('extr_test-fa', f.extract(['name2', 'name3']).name)
-        self.assertEqual(cl2, f.extract(['name2', 'name3', 'name321']).contigs)
+        self.assertEqual(cl2, f.extract(['>name2', '>name3']).contigs)
+        print 'printing contigs'
+        for c in f.extract(['name2', 'name3']).contigs:
+            print c
+        self.assertEqual('>extr_test-fa', f.extract(['>name2', '>name3']).name)
+        self.assertEqual(cl2, f.extract(['>name2', '>name3', '>name321']).contigs)
 
 
     def test_remove(self):
         cl = [Sequence('>name', 'ACTGactg'), Sequence('>name2', 'NNNNNNNNNACTGNNNN'), Sequence('>name3', 'CTNACtacgatNNNNNNN')]
         f = Fa(cl, 'test-fa')
-        self.assertEqual([Sequence('>name2', 'NNNNNNNNNACTGNNNN'), Sequence('>name3', 'CTNACtacgatNNNNNNN')], f.remove(['name']).contigs)
-        self.assertEqual([Sequence('>name', 'ACTGactg')], f.remove(['name2','name3']).contigs)
-        self.assertEqual([Sequence('>name', 'ACTGactg')], f.remove(['name2','name3','name234']).contigs)
-        self.assertEqual([Sequence('>name2', 'NNNNNNNNNACTGNNNN'), Sequence('>name3', 'CTNACtacgatNNNNNNN')], f.remove(['name']).contigs)
+        self.assertEqual([Sequence('>name2', 'NNNNNNNNNACTGNNNN'), Sequence('>name3', 'CTNACtacgatNNNNNNN')], f.remove(['>name']).contigs)
+        self.assertEqual([Sequence('>name', 'ACTGactg')], f.remove(['>name2','>name3']).contigs)
+        self.assertEqual([Sequence('>name', 'ACTGactg')], f.remove(['>name2','>name3','>name234']).contigs)
+        self.assertEqual([Sequence('>name2', 'NNNNNNNNNACTGNNNN'), Sequence('>name3', 'CTNACtacgatNNNNNNN')], f.remove(['>name']).contigs)
 
     def test_statistics(self):
         cl = [Sequence('>name', 'ACTGactg'), Sequence('>name2', 'NNNNNNNNNACTGNNNN'), Sequence('>name3', 'CTNACtacgatNNNNNNN'), Sequence('>name4', 'CTNAC')]
@@ -187,7 +190,7 @@ def tearDown(self):
         os.remove('f2.fa')
         os.remove('test.fa')
         pass
-    '''    
+        
     def test_conv_to_fq(self):
         cl = []
         test = 'ATGGAATCGGCTTTTAATACTGCAGGGGCGTTAAGTTGGCATGAACTCACAACCAATAATACCGAAGAGGCCATGCGCTTCTATGCTGAGATTTTTGGCTGGCACTTTAAAACCGTCAAAATGCCCCACGGTCACTATCACATTATTGAAAACGAGGGGATCAGCATTGGCGGAATTACCGACAGTTTAATCCCCACCCTTCCCTCACATTGGACTGGCTATATTACCGTTAACGATGTGGATCAAGTGGCTATCAGTGCTAAAAAACTCGGCGGTGACATTCTGTTTGGCCCTGAAGACATTCCAGAGGTGGGCCGTTTTTGTTGGATAAAAGACCCACAGGGCGCCATTATTGCGGCCATTAGCTATTTAAAACGTTGATGTAA'
@@ -198,4 +201,4 @@ def test_conv_to_fq(self):
         print fq
 
 if __name__ == "__main__":
-    unittest.main()
+    unittest.main()