root/galaxy-central/tools/metag_tools/shrimp_color_wrapper.py @ 2

#!/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__()