diff rmapq_wrapper.py @ 0:f6e5bb5aa2f5 draft

Imported from capsule None

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/rmapq_wrapper.py	Mon May 19 12:34:22 2014 -0400
@@ -0,0 +1,100 @@
+#!/usr/bin/env python
+
+import os, sys, tempfile
+
+assert sys.version_info[:2] >= (2.4)
+
+def stop_err( msg ):
+    
+    sys.stderr.write( "%s\n" % msg )
+    sys.exit()
+    
+
+def __main__():
+    
+    # I/O
+    target_path = sys.argv[1]
+    infile = sys.argv[2]
+    scorefile = sys.argv[3]
+    high_score = sys.argv[4]            # -q
+    high_len = sys.argv[5]              # -M
+    read_len = sys.argv[6]              # -w
+    align_len = sys.argv[7]             # -h
+    mismatch = sys.argv[8]              # -m
+    output_file = sys.argv[9]
+    
+    try: 
+        float(high_score)
+    except:
+        stop_err('Invalid value for minimal quality score.')
+
+    try:
+        int(high_len)
+    except:
+        stop_err('Invalid value for minimal high quality bases.')
+            
+    # first guess the read length
+    guess_read_len = 0
+    seq = ''
+    for i, line in enumerate(open(infile)):
+        line = line.rstrip('\r\n')
+        if line.startswith('>'):
+            if seq:
+                guess_read_len = len(seq)
+                break
+        else:
+            seq += line
+            
+    try: 
+        test = int(read_len)
+        if test == 0:
+            read_len = str(guess_read_len)
+        else:
+            assert test >= 20 and test <= 64
+    except:
+        stop_err('Invalid value for read length. Must be between 20 and 64.')
+
+    
+    try:
+        int(align_len)    
+    except:
+        stop_err('Invalid value for minimal length of a hit.')
+    
+    try:
+        int(mismatch)
+    except:
+        stop_err('Invalid value for mismatch numbers in an alignment.')
+    
+    all_files = []
+    if os.path.isdir(target_path):
+        # check target genome
+        fa_files = os.listdir(target_path)
+            
+        for file in fa_files:
+            file = "%s/%s" % ( target_path, file )
+            file = os.path.normpath(file)
+            all_files.append(file)
+    else:
+        stop_err("No sequences for %s are available for search, please report this error." %(target_path))
+   
+    for detail_file_path in all_files:
+        output_tempfile = tempfile.NamedTemporaryFile().name
+        command = "rmapq -q %s -M %s -h %s -w %s -m %s -Q %s -c %s %s -o %s 2>&1" % ( high_score, high_len, align_len, read_len, mismatch, scorefile, detail_file_path, infile, output_tempfile )
+        #print command
+        try:
+            os.system( command )
+        except Exception, e:
+            stop_err( str( e ) )
+
+        try:
+            assert os.system( 'cat %s >> %s' % ( output_tempfile, output_file ) ) == 0
+        except Exception, e:
+            stop_err( str( e ) )
+        
+        try:
+            os.remove( output_tempfile )
+        except:
+            pass
+
+            
+if __name__ == '__main__': __main__()