/tools/metag_tools/shrimp_color_wrapper.py
https://bitbucket.org/cistrome/cistrome-harvard/ · Python · 116 lines · 81 code · 23 blank · 12 comment · 22 complexity · 9f6571f1d00b60b541de5d9590740854 MD5 · raw file
- #!/usr/bin/env python
- """
- SHRiMP wrapper : Color space
- """
- import os, sys, tempfile, os.path, re
- assert sys.version_info[:2] >= (2.4)
- def stop_err( msg ):
-
- sys.stderr.write( "%s\n" % msg )
- sys.exit()
- def __main__():
-
- # SHRiMP path
- shrimp = 'rmapper-cs'
-
- # I/O
- input_target_file = sys.argv[1] # fasta
- input_query_file = sys.argv[2]
- shrimp_outfile = sys.argv[3] # shrimp output
-
- # SHRiMP parameters
- spaced_seed = '1111001111'
- seed_matches_per_window = '2'
- seed_hit_taboo_length = '4'
- seed_generation_taboo_length = '0'
- seed_window_length = '115.0'
- max_hits_per_read = '100'
- max_read_length = '1000'
- kmer = '-1'
- sw_match_value = '100'
- sw_mismatch_value = '-150'
- sw_gap_open_ref = '-400'
- sw_gap_open_query = '-400'
- sw_gap_ext_ref = '-70'
- sw_gap_ext_query = '-70'
- sw_crossover_penalty = '-140'
- sw_full_hit_threshold = '68.0'
- sw_vector_hit_threshold = '60.0'
-
- # TODO: put the threshold on each of these parameters
- if len(sys.argv) > 4:
-
- try:
- if sys.argv[4].isdigit():
- spaced_seed = sys.argv[4]
- else:
- stop_err('Error in assigning parameter: Spaced seed.')
- except:
- stop_err('Spaced seed must be a combination of 1s and 0s.')
-
- seed_matches_per_window = sys.argv[5]
- seed_hit_taboo_length = sys.argv[6]
- seed_generation_taboo_length = sys.argv[7]
- seed_window_length = sys.argv[8]
- max_hits_per_read = sys.argv[9]
- max_read_length = sys.argv[10]
- kmer = sys.argv[11]
- sw_match_value = sys.argv[12]
- sw_mismatch_value = sys.argv[13]
- sw_gap_open_ref = sys.argv[14]
- sw_gap_open_query = sys.argv[15]
- sw_gap_ext_ref = sys.argv[16]
- sw_gap_ext_query = sys.argv[17]
- sw_crossover_penalty = sys.argv[18]
- sw_full_hit_threshold = sys.argv[19]
- sw_vector_hit_threshold = sys.argv[20]
-
- # temp file for shrimp log file
- shrimp_log = tempfile.NamedTemporaryFile().name
-
- # SHRiMP command
- 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])
-
- try:
- os.system(command)
- except Exception, e:
- if os.path.exists(query_fasta): os.remove(query_fasta)
- if os.path.exists(query_qual): os.remove(query_qual)
- stop_err(str(e))
-
- # check SHRiMP output: count number of lines
- num_hits = 0
- if shrimp_outfile:
- for i, line in enumerate(file(shrimp_outfile)):
- line = line.rstrip('\r\n')
- if not line or line.startswith('#'): continue
- try:
- fields = line.split()
- num_hits += 1
- except Exception, e:
- stop_err(str(e))
-
- if num_hits == 0: # no hits generated
- err_msg = ''
- if shrimp_log:
- for i, line in enumerate(file(shrimp_log)):
- if line.startswith('error'): # deal with memory error:
- err_msg += line # error: realloc failed: Cannot allocate memory
- if re.search('Reads Matched', line): # deal with zero hits
- if int(line[8:].split()[2]) == 0:
- err_msg = 'Zero hits found.\n'
- stop_err('SHRiMP Failed due to:\n' + err_msg)
-
-
- # remove temp. files
- if os.path.exists(shrimp_log): os.remove(shrimp_log)
-
- if __name__ == '__main__': __main__()