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/tools/metag_tools/shrimp_color_wrapper.py

https://bitbucket.org/cistrome/cistrome-harvard/
Python | 116 lines | 87 code | 18 blank | 11 comment | 11 complexity | 9f6571f1d00b60b541de5d9590740854 MD5 | raw file
  1#!/usr/bin/env python
  2
  3"""
  4SHRiMP wrapper : Color space
  5"""
  6
  7import os, sys, tempfile, os.path, re
  8
  9assert sys.version_info[:2] >= (2.4)
 10
 11def stop_err( msg ):
 12    
 13    sys.stderr.write( "%s\n" % msg )
 14    sys.exit()
 15
 16
 17def __main__():
 18    
 19    # SHRiMP path
 20    shrimp = 'rmapper-cs'
 21    
 22    # I/O
 23    input_target_file = sys.argv[1]                  # fasta
 24    input_query_file = sys.argv[2]
 25    shrimp_outfile    = sys.argv[3]                # shrimp output
 26            
 27    # SHRiMP parameters
 28    spaced_seed = '1111001111'
 29    seed_matches_per_window = '2'
 30    seed_hit_taboo_length = '4'
 31    seed_generation_taboo_length = '0'
 32    seed_window_length = '115.0'
 33    max_hits_per_read = '100'
 34    max_read_length = '1000'
 35    kmer = '-1'
 36    sw_match_value = '100'
 37    sw_mismatch_value = '-150'
 38    sw_gap_open_ref = '-400'
 39    sw_gap_open_query = '-400'
 40    sw_gap_ext_ref = '-70'
 41    sw_gap_ext_query = '-70'
 42    sw_crossover_penalty = '-140'
 43    sw_full_hit_threshold = '68.0'
 44    sw_vector_hit_threshold = '60.0'
 45    
 46    # TODO: put the threshold on each of these parameters
 47    if len(sys.argv) > 4:
 48        
 49        try:
 50            if sys.argv[4].isdigit():
 51                spaced_seed = sys.argv[4]
 52            else:
 53                stop_err('Error in assigning parameter: Spaced seed.')
 54        except:
 55            stop_err('Spaced seed must be a combination of 1s and 0s.')
 56        
 57        seed_matches_per_window = sys.argv[5]
 58        seed_hit_taboo_length = sys.argv[6]
 59        seed_generation_taboo_length = sys.argv[7]
 60        seed_window_length = sys.argv[8]
 61        max_hits_per_read = sys.argv[9]
 62        max_read_length = sys.argv[10]
 63        kmer = sys.argv[11]
 64        sw_match_value = sys.argv[12]
 65        sw_mismatch_value = sys.argv[13]
 66        sw_gap_open_ref = sys.argv[14]
 67        sw_gap_open_query = sys.argv[15]
 68        sw_gap_ext_ref = sys.argv[16]
 69        sw_gap_ext_query = sys.argv[17]
 70        sw_crossover_penalty = sys.argv[18]
 71        sw_full_hit_threshold = sys.argv[19]
 72        sw_vector_hit_threshold = sys.argv[20]
 73        
 74    # temp file for shrimp log file
 75    shrimp_log = tempfile.NamedTemporaryFile().name
 76    
 77    # SHRiMP command
 78    command = ' '.join([shrimp,  '-s', spaced_seed, '-n', seed_matches_per_window, '-t', seed_hit_taboo_length, '-9', seed_generation_taboo_length, '-w', seed_window_length, '-o', max_hits_per_read, '-r', max_read_length, '-d', kmer, '-m', sw_match_value, '-i', sw_mismatch_value, '-g', sw_gap_open_ref, '-q', sw_gap_open_query, '-e', sw_gap_ext_ref, '-f', sw_gap_ext_query, '-x', sw_crossover_penalty, '-h', sw_full_hit_threshold, '-v', sw_vector_hit_threshold, input_query_file, input_target_file, '>', shrimp_outfile, '2>', shrimp_log])
 79    
 80    try:
 81        os.system(command)
 82    except Exception, e:
 83        if os.path.exists(query_fasta): os.remove(query_fasta)
 84        if os.path.exists(query_qual): os.remove(query_qual)
 85        stop_err(str(e))
 86    
 87    # check SHRiMP output: count number of lines
 88    num_hits = 0
 89    if shrimp_outfile:
 90        for i, line in enumerate(file(shrimp_outfile)):
 91            line = line.rstrip('\r\n')
 92            if not line or line.startswith('#'): continue
 93            try:
 94                fields = line.split()
 95                num_hits += 1
 96            except Exception, e:
 97                stop_err(str(e))
 98                
 99    if num_hits == 0:   # no hits generated
100        err_msg = ''
101        if shrimp_log:
102            for i, line in enumerate(file(shrimp_log)):
103                if line.startswith('error'):            # deal with memory error: 
104                    err_msg += line                     # error: realloc failed: Cannot allocate memory
105                if re.search('Reads Matched', line):    # deal with zero hits
106                    if int(line[8:].split()[2]) == 0:
107                        err_msg = 'Zero hits found.\n' 
108        stop_err('SHRiMP Failed due to:\n' + err_msg)
109        
110        
111    # remove temp. files
112    if os.path.exists(shrimp_log): os.remove(shrimp_log)
113
114    
115if __name__ == '__main__': __main__()
116