Added cutNameMarkers functionality.

	modified:   README.md
	modified:   bin/cmdfatool.py
	modified:   fatool/fa.py
	modified:   fatool/sequence.py
	modified:   fatool/tests/test_sequence.py

README.md

@@ -174,3 +174,39 @@ optional arguments:
   -f FAFILE, --fafile FAFILE    file to show statistics usualy *.fa
   --report REPORT             log file if not supplied stdout
   --operator [OPERATOR [OPERATOR ...]]  user who have fired script it will be noted in log
+
+  findPrimer:
+
+usage: cmdfatool.py findPrimer [-h] -f FAFILE --start START --stop STOP --mode
+                               {FF,FR} [--minlen MINLEN] [--maxlen MAXLEN]
+                               [--mml MML] [--report REPORT]
+                               [--operator [OPERATOR [OPERATOR ...]]]
+
+optional arguments:
+  -h, --help            show this help message and exit
+  -f FAFILE, --fafile FAFILE  
+                        file to show statistics usualy *.fa
+  --start START         strat codon 5'
+  --stop STOP           stop codon 3'
+  --mode {FF,FR}        FF (start forward, stop forward) or FR (start 5' stop 3')
+  --minlen MINLEN       minimum length (detfault 50bp)
+  --maxlen MAXLEN       max length (detfault 1000bp)
+  --mml MML             mismatch level number of allowed missmatches in primers (detfault 0)
+  --report REPORT       report results into file if not supplied stdout
+  --operator [OPERATOR [OPERATOR ...]]
+                        user who have fired script it will be noted in report
+
+
+  cutNameMarker:
+
+
+usage: cmdfatool.py cutNameMarker [-h] -f FAFILE -m MARKER -l LENGTH
+                                  --keepMarker KEEPMARKER [-o OUTPUT]
+
+optional arguments:
+  -h, --help                  show this help message and exit
+  -f FAFILE, --fafile FAFILE  file to show statistics usualy *.fa
+  -m MARKER, --marker MARKER  marker that indicates start of cut
+  -l LENGTH, --length LENGTH  length of cut
+  --keepMarker KEEPMARKER     weather to keep marker or not default 1 (Yes)
+  -o OUTPUT, --output OUTPUT  output file default: output.fa

bin/cmdfatool.py

@@ -88,25 +88,43 @@ def main():
     sub_s.add_argument('--report', help='report results into file if not supplied stdout', type=argparse.FileType('w'))
     sub_s.add_argument('--operator', help='user who have fired script it will be noted in report', nargs='*', type=str)
     sub_s.set_defaults(func=statistics)
-    
-    sub_fm  = subparsers.add_parser('findMotif', help='finding given motif; display motif and its position in contig')
+    '''
+    sub_fm  = subparsers.add_parser('findMotif', help='display motifs position in contig')
     sub_fm.add_argument('-f', '--fafile', help='file to show statistics usualy *.fa', type=argparse.FileType('r'), required=True)
     sub_fm.add_argument('--mml', help='mismatch level number of allowed missmatches in primers (detfault 0)', type=str, default=0)
     sub_fm.add_argument('--report', help='report results into file if not supplied stdout', type=argparse.FileType('w'))
     sub_fm.add_argument('--operator', help='user who have fired script it will be noted in report', nargs='*', type=str)
     sub_fm.set_defaults(func=find_motif)
-    
+    '''
     sub_fp  = subparsers.add_parser('findPrimer', help='display list of founded primers')
     sub_fp.add_argument('-f', '--fafile', help='file to show statistics usualy *.fa', type=argparse.FileType('r'), required=True)
     sub_fp.add_argument('--start', help='strat codon 5\'', type=str, required=True)
     sub_fp.add_argument('--stop', help='stop codon 3\'', type=str, required=True)
-    sub_fp.add_argument('--mode', help='FF (start forward, stop forward) or FR (start 5\' stop 3\')', type=str, choices=['FF', 'FR'], required=True)
+    sub_fp.add_argument('--mode', help='FF (start forward, stop forward) or FR (start 5\' stop 3\')', type=str, choices=['FF', 'FR'], default = 'FR', required=True)
     sub_fp.add_argument('--minlen', help='minimum length (detfault 50bp)', type=int, default=50)
     sub_fp.add_argument('--maxlen', help='max length (detfault 1000bp)', type=int, default=1000)
     sub_fp.add_argument('--mml', help='mismatch level number of allowed missmatches in primers (detfault 0)', type=int, default=0)
     sub_fp.add_argument('--report', help='report results into file if not supplied stdout', type=argparse.FileType('w'))
     sub_fp.add_argument('--operator', help='user who have fired script it will be noted in report', nargs='*', type=str)
     sub_fp.set_defaults(func=find_primers)
+    
+    sub_cn = subparsers.add_parser('cutName', help='cuts name from position to given length')
+    sub_cn.add_argument('-f', '--fafile', help='file to show statistics usualy *.fa', type=argparse.FileType('r'), required=True)
+    sub_cn.add_argument('--start', help='start of cut', type=int, required=True)
+    sub_cn.add_argument('-l', '--length', help='length of cut', type=int, required=True)
+    sub_cn.set_defaults(func=cut_name)
+    
+    sub_lnam = subparsers.add_parser('cutNameMarker', help='cuts name leaving defined number of chars after begining of marker')
+    sub_lnam.add_argument('-f', '--fafile', help='file to show statistics usualy *.fa', type=argparse.FileType('r'), required=True)
+    sub_lnam.add_argument('-m', '--marker', help='marker that indicates start of cut', type=str, required=True)
+    sub_lnam.add_argument('-l', '--length', help='length of cut', type=int, required=True)
+    sub_lnam.add_argument('--keepMarker', help='weather to keep marker or not default 1 (Yes)', type=int, required=True)
+    sub_lnam.add_argument('-o', '--output', help='output file default: output.fa', type=argparse.FileType('w'), default='output.fa')
+    #sub_lnam.add_argument('-d', '--outputDir', help='output directory where multiple contigs will be saved', type=str)
+    sub_lnam.add_argument('--report', help='report results into file if not supplied stdout', type=argparse.FileType('w'))
+    sub_lnam.add_argument('--operator', help='user who have fired script it will be noted in report', nargs='*', type=str)
+    sub_lnam.set_defaults(func=cut_name_pattern)
+    
     '''
     sub_fap  = subparsers.add_parser('findPrimer', help='show statistics of fa file')
     sub_fap.add_argument('-f', '--fafile', help='file to show statistics usualy *.fa', type=argparse.FileType('r'), required=True)
@@ -122,9 +140,7 @@ def main():
     #parser.add_argument('--report', help='log file if not supplied stdout', type=argparse.FileType('w'))
 
     args = parser.parse_args()
-    #if args.version:
-    #    print version
-    #    exit(0)
+    
         
     args.func(args)
     
@@ -366,17 +382,21 @@ def reverse(args):
     fa = Fa.load_from_file(args.fafile)
     fa.reverse()
     fa.write(args.output)
+    rep += '\n\n------------------------------------------------------'
+    rep += '\nFinished:\t'+str(datetime.datetime.now())
     if args.report:
         with args.report as log_file:
             log_file.write(rep)
     else:
         print rep
+        
 
 def find_motif(args):
     print 'not available yet'
     pass
 
 def find_primers(args):
+    rep = str(make_log_header('reverse', args.operator))
     fa = Fa.load_from_file(args.fafile)
     logger = logging.getLogger(__name__)
     logger.setLevel(logging.DEBUG)
@@ -386,8 +406,24 @@ def find_primers(args):
         rep += '\n================\n\t\t'+r.name+'\n'
         for q in r.find_aprox_primers(args.start, args.stop, str(args.mode), int(args.mml), args.minlen, args.maxlen):
             rep += q+'\n'
+    rep += '\n\n------------------------------------------------------'
+    rep += '\nFinished:\t'+str(datetime.datetime.now())
+    if args.report:
+        with args.report as log_file:
+            log_file.write(rep)
+    else:
+        print rep
+        
+def cut_name_pattern(args):
+    rep = str(make_log_header('cutNameMarker', args.operator))
+    fa = Fa.load_from_file(args.fafile)
+    for r in fa.contigs:
+        r.leave_name_after_marker(args.marker, args.length, args.keepMarker)
+    fa.write(args.output)
     
-    print rep
+def cut_name(args):
+    pass
+
         
 if __name__ == '__main__':
     exit(main())

fatool/fa.py

@@ -11,7 +11,6 @@ def __init__(self, contigs_list, name):
         logger = logging.getLogger(__name__)
         
         logger.debug('creating Fa object')
-        logger.info('but info works')
         self.name = name
         self.contigs = []
         self.contigs_idx = {}

fatool/sequence.py

@@ -10,7 +10,7 @@
 class Sequence(object):
     def __init__(self, name, seq):
         if Sequence.validate_name_string(name):
-            self.name = name.lstrip('>')
+            self.name = name
         else:
             raise NameError('Sequence name have to start with ">"') 
         self.seq = seq
@@ -193,9 +193,35 @@ def cut(self, length, step):
         contig_end = len(self.seq)  # last position of contig
         contig_list = []  # contig list returning by function
         while i+length <= contig_end:
-            contig_list.append(Sequence('>'+self.name+'_frag_'+str(i + 1)+':'+str(i + length), str(self.seq[i:i+length])))
+            contig_list.append(Sequence(self.name+'_frag_'+str(i + 1)+':'+str(i + length), str(self.seq[i:i+length])))
             i = i+step
         return contig_list
+        
+    def cut_name(self, length, start = 0):
+        self.name = self.name[start:length]
+        print self.name
+        
+    def leave_name_after_marker(self, mark, length = 0, keep_marker = 1):
+        m = re.search(re.escape(mark), self.name)
+        logger = logging.getLogger(__name__)
+        logger.setLevel(logging.DEBUG)
+        logger.debug(m)
+        logger.debug(keep_marker)
+        if m:
+            # keep original marker or skip it
+            
+            if keep_marker == 1:
+                s = m.start()
+            else:
+                s = m.end()
+            # defined length or return string to end
+            if length > 0:
+                self.name = '>'+self.name[s:s+length].lstrip('>')
+            else:
+                self.name = '>'+self.name[s:].lstrip('>')
+            return 1
+        return 0
+        
 
     def reverse(self):
         '''
@@ -207,7 +233,7 @@ def reverse(self):
         rev = rev.translate(maketrans('ACTGactg', 'TGACtgac'))
         # creating 80 chars lines
         #rev = re.sub("(.{80})", '\\1\n', rev, 0)
-        return Sequence('>rev_'+self.name, rev)
+        return Sequence('>rev_'+self.name.lstrip('>'), rev)
 
 
     def normalize(self):
@@ -367,7 +393,7 @@ def __str__(self):
         '''
         creates nicely outputed string
         '''
-        return '>'+self.name+'\n'+re.sub("(.{80})", '\\1\n', self.seq, 0)+'\n'
+        return self.name+'\n'+re.sub("(.{80})", '\\1\n', self.seq, 0)+'\n'
 
 
     def __len__(self):

fatool/tests/test_sequence.py

@@ -12,7 +12,7 @@ def setUp(self):
     def test_setUpSequence(self):
         c = Sequence('>name', 'ACTGactg')
         self.assertTrue( isinstance(c, Sequence) )
-        self.assertEqual(c.name, 'name')
+        self.assertEqual(c.name, '>name')
         self.assertEqual(c.seq, 'ACTGactg')
 
     def test_contig_str(self):
@@ -376,11 +376,32 @@ def test_find_aprox_primers(self):
             'TTTAGCACTGATAGCCACTTGATCCACATCGTTAACGGTAATATAGCCAGTCCAATGTGAGG',
         ]
         
-        for r in c.find_aprox_primers('TTTT', 'GGGG', 'FF', 1,60,65):
-            print r
-        
+        #for r in c.find_aprox_primers('TTTT', 'GGGG', 'FF', 1,60,65):
+        #    print r
+       
         self.assertEqual(t_TTTT_GGGG_FF_60_65,  c.find_aprox_primers('TTTT', 'CCCC', 'FR', 1,60,65))
         
+    def test_leave_name_after_marker(self):
+        c = Sequence('>test_something_special_gene=qwerty_ready', 'ACTGTACGGA')
+        self.assertEqual(1, c.leave_name_after_marker('gene=', 20))
+        self.assertEqual('>gene=qwerty_ready', c.name)
+        #self.assertEqual()
+        c2 = Sequence('>test_something_special_gene=qwerty_ready', 'ACTGTACGGA')
+        self.assertEqual(1, c2.leave_name_after_marker('gene=', 11))
+        self.assertEqual('>gene=qwerty', c2.name)
+        c = Sequence('>test_something_special_gene=qwerty_ready', 'ACTGTACGGA')
+        self.assertEqual(1, c.leave_name_after_marker('gene='))
+        self.assertEqual('>gene=qwerty_ready', c.name)
+        c2 = Sequence('>test_something_special_gene=qwerty_ready', 'ACTGTACGGA')
+        self.assertEqual(1, c2.leave_name_after_marker('gene=', 6, 0))
+        self.assertEqual('>qwerty', c2.name)
+        
+    def test_cut_name(self):
+        c = Sequence('>test_something_special_gene=qwerty_ready', 'ACTGTACGGA')
+        c.cut_name(5)
+        self.assertEqual('>test', c.name)
+        c.cut_name(10)
+        self.assertEqual('>test', c.name)
         
     
 if __name__ == "__main__":