diff raxml.py @ 0:66bcdd1ac9ca draft

planemo upload commit 2c71c5e5604b9c05648b883fddbb163a8e03c807

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/raxml.py	Tue Nov 03 16:27:41 2015 -0500
@@ -0,0 +1,360 @@
+#!/usr/bin/env python
+"""
+Runs RAxML on a sequence file.
+For use with RAxML version 8.2.4
+"""
+import os, shutil, subprocess, sys, optparse, fnmatch, glob
+
+def stop_err(msg):
+    sys.stderr.write("%s\n" % msg)
+    sys.exit()
+
+def getint(name):
+    basename = name.partition('RUN.')
+    if basename[2] != '':
+        num = basename[2]
+        return int(num)
+
+def __main__():
+    usage = "usage: %prog -T <threads> -s <input> -n <output> -m <model> [optional arguments]"
+
+    # Parse the primary wrapper's command line options
+    parser = optparse.OptionParser(usage = usage)
+    # raxml binary name, hardcoded in the xml file
+    parser.add_option("--binary", action="store", type="string", dest="binary", help="Command to run")
+    # (-a)
+    parser.add_option("--weightfile", action="store", type="string", dest="weightfile", help="Column weight file")
+    # (-A)
+    parser.add_option("--secondary_structure_model", action="store", type="string", dest="secondary_structure_model", help="Secondary structure model")
+    # (-b)
+    parser.add_option("--bootseed", action="store", type="int", dest="bootseed", help="Bootstrap random number seed")
+    # (-c)
+    parser.add_option("--numofcats", action="store", type="int", dest="numofcats", help="Number of distinct rate categories")
+    # (-d)
+    parser.add_option("--search_complete_random_tree", action="store_true", dest="search_complete_random_tree", help="Search with a complete random starting tree")
+    # (-D)
+    parser.add_option("--ml_search_convergence", action="store_true", dest="ml_search_convergence", help="ML search onvergence criterion")
+    # (-e)
+    parser.add_option("--model_opt_precision", action="store", type="float", dest="model_opt_precision", help="Model Optimization Precision (-e)")
+    # (-E)
+    parser.add_option("--excludefile", action="store", type="string", dest="excludefile", help="Exclude File Name")
+    # (-f)
+    parser.add_option("--search_algorithm", action="store", type="string", dest="search_algorithm", help="Search Algorithm")
+    # (-F)
+    parser.add_option("--save_memory_cat_model", action="store_true", dest="save_memory_cat_model", help="Save memory under CAT and GTRGAMMA models")
+    # (-g)
+    parser.add_option("--groupingfile", action="store", type="string", dest="groupingfile", help="Grouping File Name")
+    # (-G)
+    parser.add_option("--enable_evol_heuristics", action="store_true", dest="enable_evol_heuristics", help="Enable evol algo heuristics")
+    # (-i)
+    parser.add_option("--initial_rearrangement_setting", action="store", type="int", dest="initial_rearrangement_setting", help="Initial Rearrangement Setting")
+    # (-I)
+    parser.add_option("--posterior_bootstopping_analysis", action="store", type="string", dest="posterior_bootstopping_analysis", help="Posterior bootstopping analysis")
+    # (-J)
+    parser.add_option("--majority_rule_consensus", action="store", type="string", dest="majority_rule_consensus", help="Majority rule consensus")
+    # (-k)
+    parser.add_option("--print_branch_lengths", action="store_true", dest="print_branch_lengths", help="Print branch lengths")
+    # (-K)
+    parser.add_option("--multistate_sub_model", action="store", type="string", dest="multistate_sub_model", help="Multistate substitution model")
+    # (-m)
+    parser.add_option("--model_type", action="store", type="string", dest="model_type", help="Model Type")
+    parser.add_option("--base_model", action="store", type="string", dest="base_model", help="Base Model")
+    parser.add_option("--aa_empirical_freq", action="store_true", dest="aa_empirical_freq", help="Use AA Empirical base frequences")
+    parser.add_option("--aa_search_matrix", action="store", type="string", dest="aa_search_matrix", help="AA Search Matrix")
+    # (-n)
+    parser.add_option("--name", action="store", type="string", dest="name", help="Run Name")
+    # (-N/#)
+    parser.add_option("--number_of_runs", action="store", type="int", dest="number_of_runs", help="Number of alternative runs")
+    parser.add_option("--number_of_runs_bootstop", action="store", type="string", dest="number_of_runs_bootstop", help="Number of alternative runs based on the bootstop criteria")
+    # (-M)
+    parser.add_option("--estimate_individual_branch_lengths", action="store_true", dest="estimate_individual_branch_lengths", help="Estimate individual branch lengths")
+    # (-o)
+    parser.add_option("--outgroup_name", action="store", type="string", dest="outgroup_name", help="Outgroup Name")
+    # (-O)
+    parser.add_option("--disable_undetermined_seq_check", action="store_true", dest="disable_undetermined_seq_check", help="Disable undetermined sequence check")
+    # (-p)
+    parser.add_option("--random_seed", action="store", type="int", dest="random_seed", help="Random Number Seed")
+    # (-P)
+    parser.add_option("--external_protein_model", action="store", type="string", dest="external_protein_model", help="External Protein Model")
+    # (-q)
+    parser.add_option("--multiple_model", action="store", type="string", dest="multiple_model", help="Multiple Model File")
+    # (-r)
+    parser.add_option("--constraint_file", action="store", type="string", dest="constraint_file", help="Constraint File")
+    # (-R)
+    parser.add_option("--bin_model_parameter_file", action="store", type="string", dest="bin_model_parameter_file", help="Constraint File")
+    # (-s)
+    parser.add_option("--source", action="store", type="string", dest="source", help="Input file")
+    # (-S)
+    parser.add_option("--secondary_structure_file", action="store", type="string", dest="secondary_structure_file", help="Secondary structure file")
+    # (-t)
+    parser.add_option("--starting_tree", action="store", type="string", dest="starting_tree", help="Starting Tree")
+    # (-T)
+    parser.add_option("--threads", action="store", type="int", dest="threads", help="Number of threads to use")
+    # (-u)
+    parser.add_option("--use_median_approximation", action="store_true", dest="use_median_approximation", help="Use median approximation")
+    # (-U)
+    parser.add_option("--save_memory_gappy_alignments", action="store_true", dest="save_memory_gappy_alignments", help="Save memory in large gapped alignments")
+    # (-V)
+    parser.add_option("--disable_rate_heterogeneity", action="store_true", dest="disable_rate_heterogeneity", help="Disable rate heterogeneity")
+    # (-W)
+    parser.add_option("--sliding_window_size", action="store", type="string", dest="sliding_window_size", help="Sliding window size")
+    # (-x)
+    parser.add_option("--rapid_bootstrap_random_seed", action="store", type="int", dest="rapid_bootstrap_random_seed", help="Rapid Boostrap Random Seed")
+    # (-y)
+    parser.add_option("--parsimony_starting_tree_only", action="store_true", dest="parsimony_starting_tree_only", help="Generate a parsimony starting tree only")
+    # (-z)
+    parser.add_option("--file_multiple_trees", action="store", type="string", dest="file_multiple_trees", help="Multiple Trees File")
+
+    (options, args) = parser.parse_args()
+    cmd = []
+
+    # Required parameters
+    binary = options.binary
+    cmd.append(binary)
+    # Threads
+    threads = "-T %d" % options.threads
+    cmd.append(threads)
+    # Source
+    source = "-s %s" % options.source
+    cmd.append(source)
+    #Hardcode to "galaxy" first to simplify the output part of the wrapper
+    #name = "-n %s" % options.name
+    name = "-n galaxy"
+    cmd.append(name)
+    ## Model
+    model_type = options.model_type
+    base_model = options.base_model
+    aa_search_matrix = options.aa_search_matrix
+    aa_empirical_freq = options.aa_empirical_freq
+    if model_type == 'aminoacid':
+        model = "-m %s%s" % (base_model, aa_search_matrix)
+        if aa_empirical_freq:
+            model = "-m %s%s%s" % (base_model, aa_search_matrix, 'F')
+        # (-P)
+        if options.external_protein_model:
+            external_protein_model = "-P %s" % options.external_protein_model
+            cmd.append(external_protein_model)
+    else:
+        model = "-m %s" % base_model
+    cmd.append(model)
+    if model == "GTRCAT":
+        # (-c)
+        if options.numofcats:
+            numofcats = "-c %d" % options.numofcats
+            cmd.append(numofcats)
+    # Optional parameters
+    if options.number_of_runs_bootstop:
+        number_of_runs_bootstop = "-N %s" % options.number_of_runs_bootstop
+        cmd.append(number_of_runs_bootstop)
+    else:
+        number_of_runs_bootstop = ''
+    if options.number_of_runs:
+        number_of_runs_opt = "-N %d" % options.number_of_runs
+        cmd.append(number_of_runs_opt)
+    else:
+        number_of_runs_opt = 0
+    # (-a)
+    if options.weightfile:
+        weightfile = "-a %s" % options.weightfile
+        cmd.append(weightfile)
+    # (-A)
+    if options.secondary_structure_model:
+        secondary_structure_model  = "-A %s" % options.secondary_structure_model
+        cmd.append(secondary_structure_model )
+    # (-b)
+    if options.bootseed:
+        bootseed = "-b %d" % options.bootseed
+        cmd.append(bootseed)
+    else:
+        bootseed = 0
+    # -C - doesn't work in pthreads version, skipped
+    if options.search_complete_random_tree:
+        cmd.append("-d")
+    if options.ml_search_convergence:
+        cmd.append("-D" )
+    if options.model_opt_precision:
+        model_opt_precision = "-e %f" % options.model_opt_precision
+        cmd.append(model_opt_precision)
+    if options.excludefile:
+        excludefile = "-E %s" % options.excludefile
+        cmd.append(excludefile)
+    if options.search_algorithm:
+        search_algorithm = "-f %s" % options.search_algorithm
+        cmd.append(search_algorithm)
+    if options.save_memory_cat_model:
+        cmd.append("-F")
+    if options.groupingfile:
+        groupingfile = "-g %s" % options.groupingfile
+        cmd.append(groupingfile)
+    if options.enable_evol_heuristics:
+        enable_evol_heuristics = "-G %f" % options.enable_evol_heuristics
+        cmd.append(enable_evol_heuristics )
+    if options.initial_rearrangement_setting:
+        initial_rearrangement_setting  = "-i %s" % options.initial_rearrangement_setting
+        cmd.append(initial_rearrangement_setting)
+    if options.posterior_bootstopping_analysis:
+        posterior_bootstopping_analysis = "-I %s" % options.posterior_bootstopping_analysis
+        cmd.append(posterior_bootstopping_analysis)
+    if options.majority_rule_consensus:
+        majority_rule_consensus = "-J %s" % options.majority_rule_consensus
+        cmd.append(majority_rule_consensus)
+    if options.print_branch_lengths:
+        cmd.append("-k")
+    if options.multistate_sub_model:
+        multistate_sub_model = "-K %s" % options.multistate_sub_model
+        cmd.append(multistate_sub_model)
+    if options.estimate_individual_branch_lengths:
+        cmd.append("-M")
+    if options.outgroup_name:
+        outgroup_name = "-o %s" % options.outgroup_name
+        cmd.append(outgroup_name)
+    if options.disable_undetermined_seq_check:
+        cmd.append("-O")
+    if options.random_seed:
+        random_seed = "-p %d" % options.random_seed
+        cmd.append(random_seed)
+    multiple_model = None
+    if options.multiple_model:
+        multiple_model = "-q %s" % options.multiple_model
+        cmd.append(multiple_model)
+    if options.constraint_file:
+        constraint_file = "-r %s" % options.constraint_file
+        cmd.append(constraint_file)
+    if options.bin_model_parameter_file:
+        bin_model_parameter_file_name = "RAxML_binaryModelParameters.galaxy"
+        os.symlink(options.bin_model_parameter_file, bin_model_parameter_file_name )
+        bin_model_parameter_file = "-R %s" % options.bin_model_parameter_file
+        #Needs testing. Is the hardcoded name or the real path needed?
+        cmd.append(bin_model_parameter_file)
+    if options.secondary_structure_file:
+        secondary_structure_file = "-S %s" % options.secondary_structure_file
+        cmd.append(secondary_structure_file)
+    if options.starting_tree:
+        starting_tree = "-t %s" % options.starting_tree
+        cmd.append(starting_tree)
+    if options.use_median_approximation:
+        cmd.append("-u")
+    if options.save_memory_gappy_alignments:
+        cmd.append("-U")
+    if options.disable_rate_heterogeneity:
+        cmd.append("-V")
+    if options.sliding_window_size:
+        sliding_window_size = "-W %d" % options.sliding_window_size
+        cmd.append(sliding_window_size)
+    if options.rapid_bootstrap_random_seed:
+        rapid_bootstrap_random_seed = "-x %d" % options.rapid_bootstrap_random_seed
+        cmd.append(rapid_bootstrap_random_seed)
+    else:
+        rapid_bootstrap_random_seed = 0
+    if options.parsimony_starting_tree_only:
+        cmd.append("-y")
+    if options.file_multiple_trees:
+        file_multiple_trees = "-z %s" % options.file_multiple_trees
+        cmd.append(file_multiple_trees)
+
+    print "cmd list: ", cmd, "\n"
+
+    full_cmd = " ".join(cmd)
+    print "Command string: %s" % full_cmd
+
+    try:
+        proc = subprocess.Popen(args=full_cmd, shell=True, stdout=subprocess.PIPE, stderr=subprocess.PIPE)
+    except Exception, err:
+        sys.stderr.write("Error invoking command: \n%s\n\n%s\n" % (cmd, err))
+        sys.exit(1)
+    stdout, stderr = proc.communicate()
+    return_code = proc.returncode
+    if return_code:
+        sys.stdout.write(stdout)
+        sys.stderr.write(stderr)
+        sys.stderr.write("Return error code %i from command:\n" % return_code)
+        sys.stderr.write("%s\n" % cmd)
+    else:
+        sys.stdout.write(stdout)
+        sys.stdout.write(stderr)
+
+    #Multiple runs - concatenate
+    if number_of_runs_opt > 0:
+        if (bootseed == 0) and (rapid_bootstrap_random_seed == 0 ):
+            runfiles = glob.glob('RAxML*RUN*')
+            runfiles.sort(key=getint)
+        # Logs
+            outfile = open('RAxML_log.galaxy','w')
+            for filename in runfiles:
+                if fnmatch.fnmatch(filename, 'RAxML_log.galaxy.RUN.*'):
+                    infile = open(filename, 'r')
+                    filename_line = "%s\n" % filename
+                    outfile.write(filename_line)
+                    for line in infile:
+                        outfile.write(line)
+                    infile.close()
+            outfile.close()
+        # Parsimony Trees
+            outfile = open('RAxML_parsimonyTree.galaxy','w')
+            for filename in runfiles:
+                if fnmatch.fnmatch(filename, 'RAxML_parsimonyTree.galaxy.RUN.*'):
+                    infile = open(filename, 'r')
+                    filename_line = "%s\n" % filename
+                    outfile.write(filename_line)
+                    for line in infile:
+                        outfile.write(line)
+                    infile.close()
+            outfile.close()
+        # Results
+            outfile = open('RAxML_result.galaxy','w')
+            for filename in runfiles:
+                if fnmatch.fnmatch(filename, 'RAxML_result.galaxy.RUN.*'):
+                    infile = open(filename, 'r')
+                    filename_line = "%s\n" % filename
+                    outfile.write(filename_line)
+                    for line in infile:
+                        outfile.write(line)
+                    infile.close()
+            outfile.close()
+    # Multiple Model Partition Files
+    if multiple_model:
+        files = glob.glob('RAxML_bestTree.galaxy.PARTITION.*')
+        if len(files) > 0:
+            files.sort(key=getint)
+            outfile = open('RAxML_bestTreePartitions.galaxy','w')
+            # Best Tree Partitions
+            for filename in files:
+                if fnmatch.fnmatch(filename, 'RAxML_bestTree.galaxy.PARTITION.*'):
+                    infile = open(filename, 'r')
+                    filename_line = "%s\n" % filename
+                    outfile.write(filename_line)
+                    for line in infile:
+                        outfile.write(line)
+                    infile.close()
+            outfile.close()
+        else:
+            outfile = open('RAxML_bestTreePartitions.galaxy','w')
+            outfile.write("No partition files were produced.\n")
+            outfile.close()
+
+        # Result Partitions
+        files = glob.glob('RAxML_result.galaxy.PARTITION.*')
+        if len(files) > 0:
+            files.sort(key=getint)
+            outfile = open('RAxML_resultPartitions.galaxy','w')
+            for filename in files:
+                if fnmatch.fnmatch(filename, 'RAxML_result.galaxy.PARTITION.*'):
+                    infile = open(filename, 'r')
+                    filename_line = "%s\n" % filename
+                    outfile.write(filename_line)
+                    for line in infile:
+                        outfile.write(line)
+                    infile.close()
+            outfile.close()
+        else:
+            outfile = open('RAxML_resultPartitions.galaxy','w')
+            outfile.write("No partition files were produced.\n")
+            outfile.close()
+
+    # DEBUG options
+    infof = open('RAxML_info.galaxy','a')
+    infof.write('\nOM: CLI options DEBUG START:\n')
+    infof.write(options.__repr__())
+    infof.write('\nOM: CLI options DEBUG END\n')
+
+if __name__=="__main__": __main__()