diff run_seqsero_batch_galaxy.py @ 0:6895de35a263 draft

planemo upload commit 844a891e4eaf732830043204ac636907eefb011d-dirty

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/run_seqsero_batch_galaxy.py	Thu Oct 19 18:16:51 2017 -0400
@@ -0,0 +1,227 @@
+#!/usr/bin/python
+
+print 'monkey wonders where he is'
+
+import os
+
+# os.system('source /nfs/sw/apps/galaxy-dev/galaxy/.venv/bin/activate')
+
+import re, sys, time, datetime
+import subprocess, psycopg2, sqlalchemy
+from subprocess import Popen, PIPE
+from sqlalchemy import *
+from datetime import datetime
+
+print 'monkey found some files', sys.argv
+engine = create_engine('postgresql+psycopg2://galaxy:cF$[e-mail]:5432/galaxy')
+print 'monkey says "vroom vroom"'
+connection = engine.connect()
+print "monkey made a connection!"
+
+# database = '/nfs/sw/apps/galaxy-dev/galaxy/database/universe.sqlite'
+seqsero = '/nfs/sw/apps/galaxy-dev/galaxy/tools/seqsero/SeqSero.py'
+test_out = open("/nfs/sw/apps/galaxy-dev/galaxy/tools/seqsero/test.txt", 'w')
+out_path = '/nfs/sw/apps/galaxy-dev/galaxy/database/files/000'
+test_out2 = open("/nfs/sw/apps/galaxy-dev/galaxy/tools/seqsero/test2.txt", 'w')
+
+path2sample = '/nfs/sw/apps/galaxy-dev/galaxy/tools/seqsero/fastq_tmp'
+
+test_out.write("monkey ");
+test_out.write("\t".join(sys.argv)+'\n')
+
+fq_list1 = []
+
+test_out.write(str(len(sys.argv))+"\n")
+if len(sys.argv) >= 2:
+        test_out.write("\t".join(sys.argv)+'\n')
+        fq_list1 = sys.argv[1:]
+
+test_out.write(str(len(sys.argv))+"\n")
+
+fastq_files = re.split(",", fq_list1[0])	# fq_list1[0] is a string with commas between the path/filenames.
+
+def print_time():
+        test_out.write(time.asctime( time.localtime(time.time())))
+
+tmp_path = path2sample
+if not os.path.exists(tmp_path):
+        os.system('mkdir '+tmp_path)
+
+test_out.write(str(len(fastq_files))+"\n")
+
+def list_runs(fastq_files):
+        '''
+        Creates dict with runs as keys and list with filenames as values.
+        '''
+        run2fastqs = {}
+	is_fastq = 'yes'
+        for file in fastq_files:
+		print 'monkey found', file 
+		run = ''
+                try:
+                        fastq = open(file, 'r')
+                        i = 0
+                        for line in fastq:
+                                line = line.rstrip("\n")
+                                if i == 0:
+                                        run = re.split("\s", line)[0]
+                                        run = re.sub('@', '', run)
+					run = re.split("\.", run)[0]
+					if not re.search('^@', line):
+						is_fastq = 'no'
+                                else:
+                                        break
+                                i += 1
+                        file1 = re.split('/', file)[-1]
+			dataset_id = re.split('_', file1)
+			dataset_id = re.sub('.dat', '', dataset_id[-1])
+			print dataset_id, type(dataset_id)
+			result = connection.execute('SELECT name FROM history_dataset_association WHERE dataset_id = '+dataset_id+';')			
+			original_filename = ''
+			for row in result:
+				print 'monkey says the original_filename is something like', row[0]
+				original_filename = row[0]
+			if re.search('fasta$', original_filename):
+				if is_fastq == 'yes':
+					original_filename = re.sub('fasta', 'fastq', original_filename)
+				else:
+					print 'The input file is not a fastq file.'
+                        file2 = re.sub('.dat$', '_'+original_filename, file1)
+			print 'monkey renamed the file', file2
+                        new_path_file = tmp_path+'/'+file2
+                        if file2 not in os.listdir(tmp_path):
+				print file, new_path_file
+                                os.system('cp '+file+' '+new_path_file)
+                        if run in run2fastqs.keys():
+                                if file not in run2fastqs[run]:
+                                        run2fastqs[run].append(new_path_file)
+                        else:
+				run2fastqs[run] = [new_path_file]
+                except IOError:
+                        print "Data not found. It is possible for a deleted file to still be listed "\
+                                "in a Galaxy library. Please confirm that the data still exists on this "\
+                                "server. You may need to upload it again."
+        return run2fastqs
+
+def run_seqsero(run2fastqs):
+        '''
+        Takes files from run2fastqs and runs SeqSero.
+        '''
+        outputs = []
+        for run in run2fastqs:
+		print run, run2fastqs[run]
+                seqsero_cmd = []
+                if len(run2fastqs[run]) == 2:
+                        seqsero_cmd = ['python', seqsero, '-m', '2', '-i', run2fastqs[run][0], run2fastqs[run][1]]
+                elif len(run2fastqs[run]) == 1:
+                        seqsero_cmd = ['python', seqsero, '-m', '1', '-i', run2fastqs[run][0]]
+		print seqsero_cmd
+                p = Popen(seqsero_cmd, stdout=PIPE)
+                output = p.communicate()
+                outputs.append(output)
+        return outputs
+
+def get_serotypes(outputs):
+        '''
+        '''
+	fastq2comment = {}
+        fastq2serotype = {}
+        for sample in outputs:
+		fastqs = ''
+		lines_used = []
+                for line in sample:	# line is actually the entire seqsero output.
+                        line = str(line)
+                        linel = re.split("\n", line)
+#                       print linel
+			#lines_used = []
+                        for element in linel:	# element is a line of seqsero output.
+				element = element.rstrip("\n")
+				test_out.write(element+"\n")
+                                elementl = re.split("\t", element)
+                                if elementl[0] == 'Input files:':
+                                        fastqs = elementl[1]
+					lines_used.append(element)
+                                        if elementl[1] not in fastq2serotype.keys():
+                                                fastq2serotype[fastqs] = ['']*5
+						fastq2comment[fastqs] = []
+                                elif elementl[0] == 'O antigen prediction:':
+					lines_used.append(element)
+                                        fastq2serotype[fastqs][0] = elementl[1] # add predicted profile
+                                elif elementl[0] == 'H1 antigen prediction(fliC):':
+					lines_used.append(element)
+                                        fastq2serotype[fastqs][1] = elementl[1] # add predicted profile
+                                elif elementl[0] == 'H2 antigen prediction(fljB):':
+					lines_used.append(element)
+                                        fastq2serotype[fastqs][2] = elementl[1] # add predicted profile                    
+                                elif elementl[0] == 'Predicted antigenic profile:':
+					lines_used.append(element)
+                                        fastq2serotype[fastqs][3] = elementl[1] # add predicted profile
+                                elif elementl[0] == 'Predicted serotype(s):':
+					lines_used.append(element)
+                                        fastq2serotype[fastqs][4] = elementl[1] # add predicted serotype
+				if element not in lines_used and re.search("\w", fastqs) and len(element) > 7:
+					fastq2comment[fastqs].append(element)
+                #print "\n"
+        return fastq2serotype, fastq2comment
+
+def print_html(fastq2serotype, fastq2comment):
+        '''
+        Takes dict and prints to html file.
+        '''
+	tab_out = open('Seqsero_result.txt', 'w');
+        html_out = open('Seqsero_result.html', 'w')
+        html_out.write('<!DOCTYPE html>\n')
+        html_out.write('<html>\n')
+        html_out.write('<head>\n')
+        html_out.write('<title>SeqSero Results</title>\n')
+        html_out.write('</head>\n')
+        html_out.write('<body>\n')
+        html_out.write('<body style="font-family:Helvetica;">\n')
+        html_out.write('<p style="font-size:10px">\n')
+        html_out.write('<table border=1>\n')
+        header = 'Input Files\tO antigen prediction\tH1 antigen prediction(fliC)\tH2 antigen prediction(fljB)\tPredicted antigenic profile\tPredicted serotype(s)'
+        header = re.sub(' ', '_', header)
+        header_l = ['Input Files', 'O antigen prediction', 'H1 antigen prediction(fliC)', 'H2 antigen prediction(fljB)', 'Predicted antigenic profile', 'Predicted serotype(s)']
+        html_out.write('<tr>\n')
+        for element in header_l:
+                html_out.write('<td>'+element+'</td>\n')
+        html_out.write('</tr>\n')
+        tab_out.write(header+"\n")
+        print "\n\n", header
+        for fastq in fastq2serotype:
+#               print fastq, fastq2serotype[fastq]
+                line_to_print = fastq+'\t'+"\t".join(fastq2serotype[fastq])
+                tab_out.write(line_to_print+"\n")
+                html_out.write('<tr>\n')
+                html_out.write('<td>'+fastq+'</td>\n')
+                for antigen in fastq2serotype[fastq]:
+                        html_out.write('<td>'+antigen+'</td>\n')
+                html_out.write('</tr>\n')
+                print line_to_print
+        html_out.write('</table>\n')
+	print "\n"
+        for fastq in fastq2comment:
+                tab_out.write("\n"+fastq+"\n")
+                html_out.write('<tr>\n')
+		html_out.write('<p>\n')
+                html_out.write('<td>'+fastq+"<br></td>\n")
+                for line in fastq2comment[fastq]:
+			#if len(line) > 7:
+                        html_out.write('<td>'+line+'</td>\n')
+                        tab_out.write(line+"\n")
+			print line
+		print "\n"
+		html_out.write('</p>\n')
+                html_out.write('</tr>\n')
+        html_out.write('</body>\n')
+        html_out.write('</html>\n')
+        html_out.close()
+
+run2fastqs = list_runs(fastq_files)
+#print run2fastqs
+outputs = run_seqsero(run2fastqs)
+fastq2serotype, fastq2comment = get_serotypes(outputs)
+print_html(fastq2serotype, fastq2comment)
+print_time()
+                                                                                                                                                                                                                          
+