--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/pca.py	Fri Sep 28 11:57:18 2012 -0400
@@ -0,0 +1,258 @@
+#!/usr/bin/env python
+
+import errno
+import os
+import shutil
+import subprocess
+import sys
+from BeautifulSoup import BeautifulSoup
+import gd_composite
+
+################################################################################
+
+def mkdir_p(path):
+    try:
+        os.makedirs(path)
+    except OSError, e:
+        if e.errno <> errno.EEXIST:
+            raise
+
+################################################################################
+
+def run_program(prog, args, stdout_file=None):
+    #print "args: ", ' '.join(args)
+    p = subprocess.Popen(args, bufsize=-1, executable=prog, stdin=None, stdout=subprocess.PIPE, stderr=subprocess.PIPE)
+    (stdoutdata, stderrdata) = p.communicate()
+    rc = p.returncode
+
+    if stdout_file is not None:
+        with open(stdout_file, 'w') as ofh:
+            print >> ofh, stdoutdata
+
+    if rc != 0:
+        print >> sys.stderr, "FAILED: rc={0}: {1}".format(rc, ' '.join(args))
+        print >> sys.stderr, stderrdata
+        sys.exit(1)
+
+################################################################################
+
+def do_ped2geno(input, output):
+    lines = []
+    with open(input) as fh:
+        for line in fh:
+            line = line.rstrip('\r\n')
+            lines.append(line.split())
+
+    pair_map = {
+        '0':{ '0':'9', '1':'9', '2':'9' },
+        '1':{ '0':'1', '1':'2', '2':'1' },
+        '2':{ '0':'1', '1':'1', '2':'0' }
+    }
+    with open(output, 'w') as ofh:
+        for a_idx in xrange(6, len(lines[0]), 2):
+            b_idx = a_idx + 1
+            print >> ofh, ''.join(map(lambda line: pair_map[line[a_idx]][line[b_idx]], lines))
+
+def do_map2snp(input, output):
+    with open(output, 'w') as ofh:
+        with open(input) as fh:
+            for line in fh:
+                elems = line.split()
+                print >> ofh, '  {0} 11 0.002 2000 A T'.format(elems[1])
+
+def make_ind_file(ind_file, input):
+    pops = []
+
+    ofh = open(ind_file, 'w')
+
+    with open(input) as fh:
+        soup = BeautifulSoup(fh)
+        misc = soup.find('div', {'id': 'gd_misc'})
+        populations = misc('ul')[0]
+
+        i = 0
+        for entry in populations:
+            if i % 2 == 1:
+                population_name = entry.contents[0].encode('utf8').strip().replace(' ', '_')
+                pops.append(population_name)
+                individuals = entry.ol('li')
+                for individual in individuals:
+                    individual_name = individual.string.encode('utf8').strip()
+                    print >> ofh, individual_name, 'M', population_name
+            i += 1
+
+    ofh.close()
+    return pops
+
+def make_par_file(par_file, geno_file, snp_file, ind_file, evec_file, eval_file):
+    with open(par_file, 'w') as fh:
+        print >> fh, 'genotypename: {0}'.format(geno_file)
+        print >> fh, 'snpname: {0}'.format(snp_file)
+        print >> fh, 'indivname: {0}'.format(ind_file)
+        print >> fh, 'evecoutname: {0}'.format(evec_file)
+        print >> fh, 'evaloutname: {0}'.format(eval_file)
+        print >> fh, 'altnormstyle: NO'
+        print >> fh, 'numoutevec: 2'
+
+def do_smartpca(par_file):
+    prog = 'smartpca'
+
+    args = [ prog ]
+    args.append('-p')
+    args.append(par_file)
+
+    #print "args: ", ' '.join(args)
+    p = subprocess.Popen(args, bufsize=-1, stdin=None, stdout=subprocess.PIPE, stderr=sys.stderr)
+    (stdoutdata, stderrdata) = p.communicate()
+    rc = p.returncode
+
+    if rc != 0:
+        print >> sys.stderr, "FAILED: rc={0}: {1}".format(rc, ' '.join(args))
+        print >> sys.stderr, stderrdata
+        sys.exit(1)
+
+    stats = []
+
+    save_line = False
+    for line in stdoutdata.split('\n'):
+        if line.startswith(('## Average divergence', '## Anova statistics', '## Statistical significance')):
+            stats.append('')
+            save_line = True
+        if line.strip() == '':
+            save_line = False
+        if save_line:
+            stats.append(line)
+
+    return '\n'.join(stats[1:])
+
+def do_ploteig(evec_file, population_names):
+    prog = 'gd_ploteig'
+
+    args = [ prog ]
+    args.append('-i')
+    args.append(evec_file)
+    args.append('-c')
+    args.append('1:2')
+    args.append('-p')
+    args.append(':'.join(population_names))
+    args.append('-x')
+
+    run_program(None, args)
+
+def do_eval2pct(eval_file, explained_file):
+    prog = 'eval2pct'
+
+    args = [ prog ]
+    args.append(eval_file)
+
+    with open(explained_file, 'w') as ofh:
+        #print "args:", ' '.join(args)
+        p = subprocess.Popen(args, bufsize=-1, stdin=None, stdout=ofh, stderr=subprocess.PIPE)
+        (stdoutdata, stderrdata) = p.communicate()
+        rc = p.returncode
+
+        if rc != 0:
+            print >> sys.stderr, "FAILED: rc={0}: {1}".format(rc, ' '.join(args))
+            print >> sys.stderr, stderrdata
+            sys.exit(1)
+
+def do_coords2admix(coords_file):
+    prog = 'coords2admix'
+
+    args = [ prog ]
+    args.append(coords_file)
+
+    with open('fake', 'w') as ofh:
+        #print "args:", ' '.join(args)
+        p = subprocess.Popen(args, bufsize=-1, stdin=None, stdout=ofh, stderr=subprocess.PIPE)
+        (stdoutdata, stderrdata) = p.communicate()
+        rc = p.returncode
+
+        if rc != 0:
+            print >> sys.stderr, "FAILED: rc={0}: {1}".format(rc, ' '.join(args))
+            print >> sys.stderr, stderrdata
+            sys.exit(1)
+
+    shutil.copy2('fake', coords_file)
+
+################################################################################
+
+if len(sys.argv) != 5:
+    print "usage"
+    sys.exit(1)
+
+input, input_files_path, output, output_files_path = sys.argv[1:5]
+
+mkdir_p(output_files_path)
+
+ped_file = os.path.join(input_files_path, 'admix.ped')
+geno_file = os.path.join(output_files_path, 'admix.geno')
+do_ped2geno(ped_file, geno_file)
+
+map_file = os.path.join(input_files_path, 'admix.map')
+snp_file = os.path.join(output_files_path, 'admix.snp')
+do_map2snp(map_file, snp_file)
+
+ind_file = os.path.join(output_files_path, 'admix.ind')
+population_names = make_ind_file(ind_file, input)
+
+par_file = os.path.join(output_files_path, 'par.admix')
+evec_file = os.path.join(output_files_path, 'coordinates.txt')
+eval_file = os.path.join(output_files_path, 'admix.eval')
+make_par_file(par_file, geno_file, snp_file, ind_file, evec_file, eval_file)
+
+smartpca_stats = do_smartpca(par_file)
+
+do_ploteig(evec_file, population_names)
+plot_file = 'coordinates.txt.1:2.{0}.pdf'.format(':'.join(population_names))
+output_plot_file = os.path.join(output_files_path, 'PCA.pdf')
+shutil.copy2(plot_file, output_plot_file)
+os.unlink(plot_file)
+
+do_eval2pct(eval_file, os.path.join(output_files_path, 'explained.txt'))
+os.unlink(eval_file)
+
+do_coords2admix(evec_file)
+
+################################################################################
+
+info_page = gd_composite.InfoPage()
+info_page.set_title('PCA Galaxy Composite Dataset')
+
+display_file = gd_composite.DisplayFile()
+display_value = gd_composite.DisplayValue()
+
+out_pdf = gd_composite.Parameter(name='PCA.pdf', value='PCA.pdf', display_type=display_file)
+out_evec = gd_composite.Parameter(name='coordinates.txt', value='coordinates.txt', display_type=display_file)
+out_explained = gd_composite.Parameter(name='explained.txt', value='explained.txt', display_type=display_file)
+
+evec_prefix = 'coordinates.txt.1:2.{0}'.format(':'.join(population_names))
+ps_file = '{0}.ps'.format(evec_prefix)
+xtxt_file = '{0}.xtxt'.format(evec_prefix)
+
+os.unlink(os.path.join(output_files_path, ps_file))
+os.unlink(os.path.join(output_files_path, xtxt_file))
+
+info_page.add_output_parameter(out_pdf)
+info_page.add_output_parameter(out_evec)
+info_page.add_output_parameter(out_explained)
+
+in_admix = gd_composite.Parameter(name='par.admix', value='par.admix', display_type=display_file)
+in_geno = gd_composite.Parameter(name='admix.geno', value='admix.geno', display_type=display_file)
+in_snp = gd_composite.Parameter(name='admix.snp', value='admix.snp', display_type=display_file)
+in_ind = gd_composite.Parameter(name='admix.ind', value='admix.ind', display_type=display_file)
+
+info_page.add_input_parameter(in_admix)
+info_page.add_input_parameter(in_geno)
+info_page.add_input_parameter(in_snp)
+info_page.add_input_parameter(in_ind)
+
+misc_stats = gd_composite.Parameter(description='Stats<p/><pre>\n{0}\n</pre>'.format(smartpca_stats), display_type=display_value)
+
+info_page.add_misc(misc_stats)
+
+with open (output, 'w') as ofh:
+    print >> ofh, info_page.render()
+
+sys.exit(0)
+