Mercurial > repos > charles_s_test > seqsero2
annotate run_seqsero.py @ 3:38ad1130d077 draft
planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty
| author | charles_s_test |
|---|---|
| date | Mon, 27 Nov 2017 11:21:07 -0500 |
| parents | 6895de35a263 |
| children | 3d6680af0bec |
| rev | line source |
|---|---|
|
0
6895de35a263
planemo upload commit 844a891e4eaf732830043204ac636907eefb011d-dirty
charles_s_test
parents:
diff
changeset
|
1 #!/usr/bin/python |
|
6895de35a263
planemo upload commit 844a891e4eaf732830043204ac636907eefb011d-dirty
charles_s_test
parents:
diff
changeset
|
2 |
|
6895de35a263
planemo upload commit 844a891e4eaf732830043204ac636907eefb011d-dirty
charles_s_test
parents:
diff
changeset
|
3 import os, re, sys, time, datetime |
|
6895de35a263
planemo upload commit 844a891e4eaf732830043204ac636907eefb011d-dirty
charles_s_test
parents:
diff
changeset
|
4 import subprocess |
|
6895de35a263
planemo upload commit 844a891e4eaf732830043204ac636907eefb011d-dirty
charles_s_test
parents:
diff
changeset
|
5 from subprocess import Popen, PIPE |
|
6895de35a263
planemo upload commit 844a891e4eaf732830043204ac636907eefb011d-dirty
charles_s_test
parents:
diff
changeset
|
6 |
|
3
38ad1130d077
planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty
charles_s_test
parents:
0
diff
changeset
|
7 |
|
38ad1130d077
planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty
charles_s_test
parents:
0
diff
changeset
|
8 # Declare Variables |
|
38ad1130d077
planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty
charles_s_test
parents:
0
diff
changeset
|
9 # paths to files and scripts |
|
38ad1130d077
planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty
charles_s_test
parents:
0
diff
changeset
|
10 |
|
38ad1130d077
planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty
charles_s_test
parents:
0
diff
changeset
|
11 fileDir = os.path.dirname(os.path.realpath('__file__')) |
|
38ad1130d077
planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty
charles_s_test
parents:
0
diff
changeset
|
12 print fileDir |
|
0
6895de35a263
planemo upload commit 844a891e4eaf732830043204ac636907eefb011d-dirty
charles_s_test
parents:
diff
changeset
|
13 |
|
3
38ad1130d077
planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty
charles_s_test
parents:
0
diff
changeset
|
14 fq_list1 = [] |
|
38ad1130d077
planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty
charles_s_test
parents:
0
diff
changeset
|
15 Tool_directory = sys.argv[2] |
|
38ad1130d077
planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty
charles_s_test
parents:
0
diff
changeset
|
16 database = Tool_directory + '/universe.sqlite' |
|
38ad1130d077
planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty
charles_s_test
parents:
0
diff
changeset
|
17 seqsero = Tool_directory + 'SeqSero.py' |
|
38ad1130d077
planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty
charles_s_test
parents:
0
diff
changeset
|
18 test_out = open(Tool_directory + "/test.txt", 'w') |
|
38ad1130d077
planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty
charles_s_test
parents:
0
diff
changeset
|
19 out_path = Tool_directory + '/files/000' |
|
38ad1130d077
planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty
charles_s_test
parents:
0
diff
changeset
|
20 test_out2 = open(Tool_directory + "/test2.txt", 'w') |
|
38ad1130d077
planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty
charles_s_test
parents:
0
diff
changeset
|
21 |
|
38ad1130d077
planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty
charles_s_test
parents:
0
diff
changeset
|
22 path2sample = Tool_directory + 'fastq_tmp' |
|
38ad1130d077
planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty
charles_s_test
parents:
0
diff
changeset
|
23 |
|
0
6895de35a263
planemo upload commit 844a891e4eaf732830043204ac636907eefb011d-dirty
charles_s_test
parents:
diff
changeset
|
24 |
|
6895de35a263
planemo upload commit 844a891e4eaf732830043204ac636907eefb011d-dirty
charles_s_test
parents:
diff
changeset
|
25 #test_out2.write(" Test test test"); |
|
6895de35a263
planemo upload commit 844a891e4eaf732830043204ac636907eefb011d-dirty
charles_s_test
parents:
diff
changeset
|
26 |
|
6895de35a263
planemo upload commit 844a891e4eaf732830043204ac636907eefb011d-dirty
charles_s_test
parents:
diff
changeset
|
27 test_out.write("monkey "); |
|
6895de35a263
planemo upload commit 844a891e4eaf732830043204ac636907eefb011d-dirty
charles_s_test
parents:
diff
changeset
|
28 #test_out.write(""); |
|
6895de35a263
planemo upload commit 844a891e4eaf732830043204ac636907eefb011d-dirty
charles_s_test
parents:
diff
changeset
|
29 test_out.write("\t".join(sys.argv)+'\n') |
|
6895de35a263
planemo upload commit 844a891e4eaf732830043204ac636907eefb011d-dirty
charles_s_test
parents:
diff
changeset
|
30 |
|
3
38ad1130d077
planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty
charles_s_test
parents:
0
diff
changeset
|
31 |
|
38ad1130d077
planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty
charles_s_test
parents:
0
diff
changeset
|
32 |
|
38ad1130d077
planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty
charles_s_test
parents:
0
diff
changeset
|
33 |
|
38ad1130d077
planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty
charles_s_test
parents:
0
diff
changeset
|
34 print Tool_directory + ' path printed ' |
|
0
6895de35a263
planemo upload commit 844a891e4eaf732830043204ac636907eefb011d-dirty
charles_s_test
parents:
diff
changeset
|
35 |
|
6895de35a263
planemo upload commit 844a891e4eaf732830043204ac636907eefb011d-dirty
charles_s_test
parents:
diff
changeset
|
36 test_out.write(str(len(sys.argv))+"\n") |
|
6895de35a263
planemo upload commit 844a891e4eaf732830043204ac636907eefb011d-dirty
charles_s_test
parents:
diff
changeset
|
37 if len(sys.argv) >= 2: |
|
6895de35a263
planemo upload commit 844a891e4eaf732830043204ac636907eefb011d-dirty
charles_s_test
parents:
diff
changeset
|
38 test_out.write("\t".join(sys.argv)+'\n') |
|
6895de35a263
planemo upload commit 844a891e4eaf732830043204ac636907eefb011d-dirty
charles_s_test
parents:
diff
changeset
|
39 fq_list1 = sys.argv[1] |
|
6895de35a263
planemo upload commit 844a891e4eaf732830043204ac636907eefb011d-dirty
charles_s_test
parents:
diff
changeset
|
40 |
|
6895de35a263
planemo upload commit 844a891e4eaf732830043204ac636907eefb011d-dirty
charles_s_test
parents:
diff
changeset
|
41 test_out.write(str(len(sys.argv))+"\n") |
|
6895de35a263
planemo upload commit 844a891e4eaf732830043204ac636907eefb011d-dirty
charles_s_test
parents:
diff
changeset
|
42 |
|
6895de35a263
planemo upload commit 844a891e4eaf732830043204ac636907eefb011d-dirty
charles_s_test
parents:
diff
changeset
|
43 fastq_files = re.split(",", fq_list1) |
|
6895de35a263
planemo upload commit 844a891e4eaf732830043204ac636907eefb011d-dirty
charles_s_test
parents:
diff
changeset
|
44 |
|
6895de35a263
planemo upload commit 844a891e4eaf732830043204ac636907eefb011d-dirty
charles_s_test
parents:
diff
changeset
|
45 def print_time(): |
|
6895de35a263
planemo upload commit 844a891e4eaf732830043204ac636907eefb011d-dirty
charles_s_test
parents:
diff
changeset
|
46 test_out.write(time.asctime( time.localtime(time.time()))) |
|
6895de35a263
planemo upload commit 844a891e4eaf732830043204ac636907eefb011d-dirty
charles_s_test
parents:
diff
changeset
|
47 |
|
3
38ad1130d077
planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty
charles_s_test
parents:
0
diff
changeset
|
48 tmp_path = "fastq_tmp" |
|
0
6895de35a263
planemo upload commit 844a891e4eaf732830043204ac636907eefb011d-dirty
charles_s_test
parents:
diff
changeset
|
49 if not os.path.exists(tmp_path): |
|
6895de35a263
planemo upload commit 844a891e4eaf732830043204ac636907eefb011d-dirty
charles_s_test
parents:
diff
changeset
|
50 os.system('mkdir '+tmp_path) |
|
6895de35a263
planemo upload commit 844a891e4eaf732830043204ac636907eefb011d-dirty
charles_s_test
parents:
diff
changeset
|
51 |
|
6895de35a263
planemo upload commit 844a891e4eaf732830043204ac636907eefb011d-dirty
charles_s_test
parents:
diff
changeset
|
52 test_out.write(str(len(fastq_files))+"\n") |
|
6895de35a263
planemo upload commit 844a891e4eaf732830043204ac636907eefb011d-dirty
charles_s_test
parents:
diff
changeset
|
53 |
|
6895de35a263
planemo upload commit 844a891e4eaf732830043204ac636907eefb011d-dirty
charles_s_test
parents:
diff
changeset
|
54 def list_runs(fastq_files): |
|
6895de35a263
planemo upload commit 844a891e4eaf732830043204ac636907eefb011d-dirty
charles_s_test
parents:
diff
changeset
|
55 ''' |
|
6895de35a263
planemo upload commit 844a891e4eaf732830043204ac636907eefb011d-dirty
charles_s_test
parents:
diff
changeset
|
56 Creates dict with runs as keys and list with filenames as values. |
|
6895de35a263
planemo upload commit 844a891e4eaf732830043204ac636907eefb011d-dirty
charles_s_test
parents:
diff
changeset
|
57 ''' |
|
6895de35a263
planemo upload commit 844a891e4eaf732830043204ac636907eefb011d-dirty
charles_s_test
parents:
diff
changeset
|
58 # print "monkey" |
|
6895de35a263
planemo upload commit 844a891e4eaf732830043204ac636907eefb011d-dirty
charles_s_test
parents:
diff
changeset
|
59 run2fastqs = {} |
|
6895de35a263
planemo upload commit 844a891e4eaf732830043204ac636907eefb011d-dirty
charles_s_test
parents:
diff
changeset
|
60 for file in fastq_files: |
|
6895de35a263
planemo upload commit 844a891e4eaf732830043204ac636907eefb011d-dirty
charles_s_test
parents:
diff
changeset
|
61 run = '' |
|
6895de35a263
planemo upload commit 844a891e4eaf732830043204ac636907eefb011d-dirty
charles_s_test
parents:
diff
changeset
|
62 try: |
|
6895de35a263
planemo upload commit 844a891e4eaf732830043204ac636907eefb011d-dirty
charles_s_test
parents:
diff
changeset
|
63 fastq = open(file, 'r') |
|
6895de35a263
planemo upload commit 844a891e4eaf732830043204ac636907eefb011d-dirty
charles_s_test
parents:
diff
changeset
|
64 i = 0 |
|
6895de35a263
planemo upload commit 844a891e4eaf732830043204ac636907eefb011d-dirty
charles_s_test
parents:
diff
changeset
|
65 for line in fastq: |
|
6895de35a263
planemo upload commit 844a891e4eaf732830043204ac636907eefb011d-dirty
charles_s_test
parents:
diff
changeset
|
66 line = line.rstrip("\n") |
|
6895de35a263
planemo upload commit 844a891e4eaf732830043204ac636907eefb011d-dirty
charles_s_test
parents:
diff
changeset
|
67 if i == 0: |
|
6895de35a263
planemo upload commit 844a891e4eaf732830043204ac636907eefb011d-dirty
charles_s_test
parents:
diff
changeset
|
68 run = re.split("\s", line)[0] |
|
6895de35a263
planemo upload commit 844a891e4eaf732830043204ac636907eefb011d-dirty
charles_s_test
parents:
diff
changeset
|
69 run = re.sub('@', '', run) |
|
6895de35a263
planemo upload commit 844a891e4eaf732830043204ac636907eefb011d-dirty
charles_s_test
parents:
diff
changeset
|
70 run = re.sub("\.1", '', run) |
|
6895de35a263
planemo upload commit 844a891e4eaf732830043204ac636907eefb011d-dirty
charles_s_test
parents:
diff
changeset
|
71 else: |
|
6895de35a263
planemo upload commit 844a891e4eaf732830043204ac636907eefb011d-dirty
charles_s_test
parents:
diff
changeset
|
72 break |
|
6895de35a263
planemo upload commit 844a891e4eaf732830043204ac636907eefb011d-dirty
charles_s_test
parents:
diff
changeset
|
73 i += 1 |
|
6895de35a263
planemo upload commit 844a891e4eaf732830043204ac636907eefb011d-dirty
charles_s_test
parents:
diff
changeset
|
74 file1 = re.split('/', file)[-1] |
|
6895de35a263
planemo upload commit 844a891e4eaf732830043204ac636907eefb011d-dirty
charles_s_test
parents:
diff
changeset
|
75 file2 = re.sub('.dat$', '_'+run+'.fastq', file1) |
|
6895de35a263
planemo upload commit 844a891e4eaf732830043204ac636907eefb011d-dirty
charles_s_test
parents:
diff
changeset
|
76 new_path_file = tmp_path+'/'+file2 |
|
6895de35a263
planemo upload commit 844a891e4eaf732830043204ac636907eefb011d-dirty
charles_s_test
parents:
diff
changeset
|
77 # print run, new_path_file |
|
6895de35a263
planemo upload commit 844a891e4eaf732830043204ac636907eefb011d-dirty
charles_s_test
parents:
diff
changeset
|
78 if file2 not in os.listdir(tmp_path): |
|
6895de35a263
planemo upload commit 844a891e4eaf732830043204ac636907eefb011d-dirty
charles_s_test
parents:
diff
changeset
|
79 os.system('cp '+file+' '+new_path_file) |
|
6895de35a263
planemo upload commit 844a891e4eaf732830043204ac636907eefb011d-dirty
charles_s_test
parents:
diff
changeset
|
80 if run in run2fastqs.keys(): |
|
6895de35a263
planemo upload commit 844a891e4eaf732830043204ac636907eefb011d-dirty
charles_s_test
parents:
diff
changeset
|
81 if file not in run2fastqs[run]: |
|
6895de35a263
planemo upload commit 844a891e4eaf732830043204ac636907eefb011d-dirty
charles_s_test
parents:
diff
changeset
|
82 run2fastqs[run].append(new_path_file) |
|
6895de35a263
planemo upload commit 844a891e4eaf732830043204ac636907eefb011d-dirty
charles_s_test
parents:
diff
changeset
|
83 else: |
|
6895de35a263
planemo upload commit 844a891e4eaf732830043204ac636907eefb011d-dirty
charles_s_test
parents:
diff
changeset
|
84 run2fastqs[run] = [new_path_file] |
|
6895de35a263
planemo upload commit 844a891e4eaf732830043204ac636907eefb011d-dirty
charles_s_test
parents:
diff
changeset
|
85 except IOError: |
|
6895de35a263
planemo upload commit 844a891e4eaf732830043204ac636907eefb011d-dirty
charles_s_test
parents:
diff
changeset
|
86 print "Data not found. It is possible for a deleted file to still be listed "\ |
|
6895de35a263
planemo upload commit 844a891e4eaf732830043204ac636907eefb011d-dirty
charles_s_test
parents:
diff
changeset
|
87 "in a Galaxy library. Please confirm that the data still exists on this "\ |
|
6895de35a263
planemo upload commit 844a891e4eaf732830043204ac636907eefb011d-dirty
charles_s_test
parents:
diff
changeset
|
88 "server. You may need to upload it again." |
|
6895de35a263
planemo upload commit 844a891e4eaf732830043204ac636907eefb011d-dirty
charles_s_test
parents:
diff
changeset
|
89 return run2fastqs |
|
6895de35a263
planemo upload commit 844a891e4eaf732830043204ac636907eefb011d-dirty
charles_s_test
parents:
diff
changeset
|
90 |
|
6895de35a263
planemo upload commit 844a891e4eaf732830043204ac636907eefb011d-dirty
charles_s_test
parents:
diff
changeset
|
91 def run_seqsero(run2fastqs): |
|
6895de35a263
planemo upload commit 844a891e4eaf732830043204ac636907eefb011d-dirty
charles_s_test
parents:
diff
changeset
|
92 ''' |
|
6895de35a263
planemo upload commit 844a891e4eaf732830043204ac636907eefb011d-dirty
charles_s_test
parents:
diff
changeset
|
93 Takes files from run2fastqs and runs SeqSero. |
|
6895de35a263
planemo upload commit 844a891e4eaf732830043204ac636907eefb011d-dirty
charles_s_test
parents:
diff
changeset
|
94 ''' |
|
6895de35a263
planemo upload commit 844a891e4eaf732830043204ac636907eefb011d-dirty
charles_s_test
parents:
diff
changeset
|
95 outputs = [] |
|
6895de35a263
planemo upload commit 844a891e4eaf732830043204ac636907eefb011d-dirty
charles_s_test
parents:
diff
changeset
|
96 for run in run2fastqs: |
|
6895de35a263
planemo upload commit 844a891e4eaf732830043204ac636907eefb011d-dirty
charles_s_test
parents:
diff
changeset
|
97 seqsero_cmd = [] |
|
6895de35a263
planemo upload commit 844a891e4eaf732830043204ac636907eefb011d-dirty
charles_s_test
parents:
diff
changeset
|
98 if len(run2fastqs[run]) == 2: |
|
6895de35a263
planemo upload commit 844a891e4eaf732830043204ac636907eefb011d-dirty
charles_s_test
parents:
diff
changeset
|
99 seqsero_cmd = ['python', seqsero, '-m', '2', '-i', run2fastqs[run][0], run2fastqs[run][1]] |
|
6895de35a263
planemo upload commit 844a891e4eaf732830043204ac636907eefb011d-dirty
charles_s_test
parents:
diff
changeset
|
100 elif len(run2fastqs[run]) == 1: |
|
6895de35a263
planemo upload commit 844a891e4eaf732830043204ac636907eefb011d-dirty
charles_s_test
parents:
diff
changeset
|
101 seqsero_cmd = ['python', seqsero, '-m', '1', '-i', run2fastqs[run][0]] |
|
6895de35a263
planemo upload commit 844a891e4eaf732830043204ac636907eefb011d-dirty
charles_s_test
parents:
diff
changeset
|
102 p = Popen(seqsero_cmd, stdout=PIPE) |
|
6895de35a263
planemo upload commit 844a891e4eaf732830043204ac636907eefb011d-dirty
charles_s_test
parents:
diff
changeset
|
103 output = p.communicate() |
|
6895de35a263
planemo upload commit 844a891e4eaf732830043204ac636907eefb011d-dirty
charles_s_test
parents:
diff
changeset
|
104 outputs.append(output) |
|
6895de35a263
planemo upload commit 844a891e4eaf732830043204ac636907eefb011d-dirty
charles_s_test
parents:
diff
changeset
|
105 return outputs |
|
6895de35a263
planemo upload commit 844a891e4eaf732830043204ac636907eefb011d-dirty
charles_s_test
parents:
diff
changeset
|
106 |
|
6895de35a263
planemo upload commit 844a891e4eaf732830043204ac636907eefb011d-dirty
charles_s_test
parents:
diff
changeset
|
107 def get_serotypes(outputs): |
|
6895de35a263
planemo upload commit 844a891e4eaf732830043204ac636907eefb011d-dirty
charles_s_test
parents:
diff
changeset
|
108 ''' |
|
6895de35a263
planemo upload commit 844a891e4eaf732830043204ac636907eefb011d-dirty
charles_s_test
parents:
diff
changeset
|
109 ''' |
|
6895de35a263
planemo upload commit 844a891e4eaf732830043204ac636907eefb011d-dirty
charles_s_test
parents:
diff
changeset
|
110 fastq2comment = {} |
|
6895de35a263
planemo upload commit 844a891e4eaf732830043204ac636907eefb011d-dirty
charles_s_test
parents:
diff
changeset
|
111 fastq2serotype = {} |
|
6895de35a263
planemo upload commit 844a891e4eaf732830043204ac636907eefb011d-dirty
charles_s_test
parents:
diff
changeset
|
112 for sample in outputs: |
|
6895de35a263
planemo upload commit 844a891e4eaf732830043204ac636907eefb011d-dirty
charles_s_test
parents:
diff
changeset
|
113 fastqs = '' |
|
6895de35a263
planemo upload commit 844a891e4eaf732830043204ac636907eefb011d-dirty
charles_s_test
parents:
diff
changeset
|
114 lines_used = [] |
|
6895de35a263
planemo upload commit 844a891e4eaf732830043204ac636907eefb011d-dirty
charles_s_test
parents:
diff
changeset
|
115 for line in sample: # line is actually the entire seqsero output. |
|
6895de35a263
planemo upload commit 844a891e4eaf732830043204ac636907eefb011d-dirty
charles_s_test
parents:
diff
changeset
|
116 line = str(line) |
|
6895de35a263
planemo upload commit 844a891e4eaf732830043204ac636907eefb011d-dirty
charles_s_test
parents:
diff
changeset
|
117 linel = re.split("\n", line) |
|
6895de35a263
planemo upload commit 844a891e4eaf732830043204ac636907eefb011d-dirty
charles_s_test
parents:
diff
changeset
|
118 # print linel |
|
6895de35a263
planemo upload commit 844a891e4eaf732830043204ac636907eefb011d-dirty
charles_s_test
parents:
diff
changeset
|
119 #lines_used = [] |
|
6895de35a263
planemo upload commit 844a891e4eaf732830043204ac636907eefb011d-dirty
charles_s_test
parents:
diff
changeset
|
120 for element in linel: # element is a line of seqsero output. |
|
6895de35a263
planemo upload commit 844a891e4eaf732830043204ac636907eefb011d-dirty
charles_s_test
parents:
diff
changeset
|
121 element = element.rstrip("\n") |
|
6895de35a263
planemo upload commit 844a891e4eaf732830043204ac636907eefb011d-dirty
charles_s_test
parents:
diff
changeset
|
122 test_out.write(element+"\n") |
|
6895de35a263
planemo upload commit 844a891e4eaf732830043204ac636907eefb011d-dirty
charles_s_test
parents:
diff
changeset
|
123 elementl = re.split("\t", element) |
|
6895de35a263
planemo upload commit 844a891e4eaf732830043204ac636907eefb011d-dirty
charles_s_test
parents:
diff
changeset
|
124 if elementl[0] == 'Input files:': |
|
6895de35a263
planemo upload commit 844a891e4eaf732830043204ac636907eefb011d-dirty
charles_s_test
parents:
diff
changeset
|
125 fastqs = elementl[1] |
|
6895de35a263
planemo upload commit 844a891e4eaf732830043204ac636907eefb011d-dirty
charles_s_test
parents:
diff
changeset
|
126 lines_used.append(element) |
|
6895de35a263
planemo upload commit 844a891e4eaf732830043204ac636907eefb011d-dirty
charles_s_test
parents:
diff
changeset
|
127 if elementl[1] not in fastq2serotype.keys(): |
|
6895de35a263
planemo upload commit 844a891e4eaf732830043204ac636907eefb011d-dirty
charles_s_test
parents:
diff
changeset
|
128 fastq2serotype[fastqs] = ['']*5 |
|
6895de35a263
planemo upload commit 844a891e4eaf732830043204ac636907eefb011d-dirty
charles_s_test
parents:
diff
changeset
|
129 fastq2comment[fastqs] = [] |
|
6895de35a263
planemo upload commit 844a891e4eaf732830043204ac636907eefb011d-dirty
charles_s_test
parents:
diff
changeset
|
130 elif elementl[0] == 'O antigen prediction:': |
|
6895de35a263
planemo upload commit 844a891e4eaf732830043204ac636907eefb011d-dirty
charles_s_test
parents:
diff
changeset
|
131 lines_used.append(element) |
|
6895de35a263
planemo upload commit 844a891e4eaf732830043204ac636907eefb011d-dirty
charles_s_test
parents:
diff
changeset
|
132 fastq2serotype[fastqs][0] = elementl[1] # add predicted profile |
|
6895de35a263
planemo upload commit 844a891e4eaf732830043204ac636907eefb011d-dirty
charles_s_test
parents:
diff
changeset
|
133 elif elementl[0] == 'H1 antigen prediction(fliC):': |
|
6895de35a263
planemo upload commit 844a891e4eaf732830043204ac636907eefb011d-dirty
charles_s_test
parents:
diff
changeset
|
134 lines_used.append(element) |
|
6895de35a263
planemo upload commit 844a891e4eaf732830043204ac636907eefb011d-dirty
charles_s_test
parents:
diff
changeset
|
135 fastq2serotype[fastqs][1] = elementl[1] # add predicted profile |
|
6895de35a263
planemo upload commit 844a891e4eaf732830043204ac636907eefb011d-dirty
charles_s_test
parents:
diff
changeset
|
136 elif elementl[0] == 'H2 antigen prediction(fljB):': |
|
6895de35a263
planemo upload commit 844a891e4eaf732830043204ac636907eefb011d-dirty
charles_s_test
parents:
diff
changeset
|
137 lines_used.append(element) |
|
6895de35a263
planemo upload commit 844a891e4eaf732830043204ac636907eefb011d-dirty
charles_s_test
parents:
diff
changeset
|
138 fastq2serotype[fastqs][2] = elementl[1] # add predicted profile |
|
6895de35a263
planemo upload commit 844a891e4eaf732830043204ac636907eefb011d-dirty
charles_s_test
parents:
diff
changeset
|
139 elif elementl[0] == 'Predicted antigenic profile:': |
|
6895de35a263
planemo upload commit 844a891e4eaf732830043204ac636907eefb011d-dirty
charles_s_test
parents:
diff
changeset
|
140 lines_used.append(element) |
|
6895de35a263
planemo upload commit 844a891e4eaf732830043204ac636907eefb011d-dirty
charles_s_test
parents:
diff
changeset
|
141 fastq2serotype[fastqs][3] = elementl[1] # add predicted profile |
|
6895de35a263
planemo upload commit 844a891e4eaf732830043204ac636907eefb011d-dirty
charles_s_test
parents:
diff
changeset
|
142 elif elementl[0] == 'Predicted serotype(s):': |
|
6895de35a263
planemo upload commit 844a891e4eaf732830043204ac636907eefb011d-dirty
charles_s_test
parents:
diff
changeset
|
143 lines_used.append(element) |
|
6895de35a263
planemo upload commit 844a891e4eaf732830043204ac636907eefb011d-dirty
charles_s_test
parents:
diff
changeset
|
144 fastq2serotype[fastqs][4] = elementl[1] # add predicted serotype |
|
6895de35a263
planemo upload commit 844a891e4eaf732830043204ac636907eefb011d-dirty
charles_s_test
parents:
diff
changeset
|
145 if element not in lines_used and re.search("\w", fastqs) and len(element) > 7: |
|
6895de35a263
planemo upload commit 844a891e4eaf732830043204ac636907eefb011d-dirty
charles_s_test
parents:
diff
changeset
|
146 fastq2comment[fastqs].append(element) |
|
6895de35a263
planemo upload commit 844a891e4eaf732830043204ac636907eefb011d-dirty
charles_s_test
parents:
diff
changeset
|
147 #print "\n" |
|
6895de35a263
planemo upload commit 844a891e4eaf732830043204ac636907eefb011d-dirty
charles_s_test
parents:
diff
changeset
|
148 return fastq2serotype, fastq2comment |
|
6895de35a263
planemo upload commit 844a891e4eaf732830043204ac636907eefb011d-dirty
charles_s_test
parents:
diff
changeset
|
149 |
|
6895de35a263
planemo upload commit 844a891e4eaf732830043204ac636907eefb011d-dirty
charles_s_test
parents:
diff
changeset
|
150 def print_html(fastq2serotype, fastq2comment): |
|
6895de35a263
planemo upload commit 844a891e4eaf732830043204ac636907eefb011d-dirty
charles_s_test
parents:
diff
changeset
|
151 ''' |
|
6895de35a263
planemo upload commit 844a891e4eaf732830043204ac636907eefb011d-dirty
charles_s_test
parents:
diff
changeset
|
152 Takes dict and prints to html file. |
|
6895de35a263
planemo upload commit 844a891e4eaf732830043204ac636907eefb011d-dirty
charles_s_test
parents:
diff
changeset
|
153 ''' |
|
6895de35a263
planemo upload commit 844a891e4eaf732830043204ac636907eefb011d-dirty
charles_s_test
parents:
diff
changeset
|
154 tab_out = open('Seqsero_result.txt', 'w'); |
|
6895de35a263
planemo upload commit 844a891e4eaf732830043204ac636907eefb011d-dirty
charles_s_test
parents:
diff
changeset
|
155 html_out = open('Seqsero_result.html', 'w') |
|
6895de35a263
planemo upload commit 844a891e4eaf732830043204ac636907eefb011d-dirty
charles_s_test
parents:
diff
changeset
|
156 html_out.write('<!DOCTYPE html>\n') |
|
6895de35a263
planemo upload commit 844a891e4eaf732830043204ac636907eefb011d-dirty
charles_s_test
parents:
diff
changeset
|
157 html_out.write('<html>\n') |
|
6895de35a263
planemo upload commit 844a891e4eaf732830043204ac636907eefb011d-dirty
charles_s_test
parents:
diff
changeset
|
158 html_out.write('<head>\n') |
|
6895de35a263
planemo upload commit 844a891e4eaf732830043204ac636907eefb011d-dirty
charles_s_test
parents:
diff
changeset
|
159 html_out.write('<title>SeqSero Results</title>\n') |
|
6895de35a263
planemo upload commit 844a891e4eaf732830043204ac636907eefb011d-dirty
charles_s_test
parents:
diff
changeset
|
160 html_out.write('</head>\n') |
|
6895de35a263
planemo upload commit 844a891e4eaf732830043204ac636907eefb011d-dirty
charles_s_test
parents:
diff
changeset
|
161 html_out.write('<body>\n') |
|
6895de35a263
planemo upload commit 844a891e4eaf732830043204ac636907eefb011d-dirty
charles_s_test
parents:
diff
changeset
|
162 html_out.write('<body style="font-family:Helvetica;">\n') |
|
6895de35a263
planemo upload commit 844a891e4eaf732830043204ac636907eefb011d-dirty
charles_s_test
parents:
diff
changeset
|
163 html_out.write('<p style="font-size:10px">\n') |
|
6895de35a263
planemo upload commit 844a891e4eaf732830043204ac636907eefb011d-dirty
charles_s_test
parents:
diff
changeset
|
164 html_out.write('<table border=1>\n') |
|
6895de35a263
planemo upload commit 844a891e4eaf732830043204ac636907eefb011d-dirty
charles_s_test
parents:
diff
changeset
|
165 header = 'Input Files\tO antigen prediction\tH1 antigen prediction(fliC)\tH2 antigen prediction(fljB)\tPredicted antigenic profile\tPredicted serotype(s)' |
|
6895de35a263
planemo upload commit 844a891e4eaf732830043204ac636907eefb011d-dirty
charles_s_test
parents:
diff
changeset
|
166 header = re.sub(' ', '_', header) |
|
6895de35a263
planemo upload commit 844a891e4eaf732830043204ac636907eefb011d-dirty
charles_s_test
parents:
diff
changeset
|
167 header_l = ['Input Files', 'O antigen prediction', 'H1 antigen prediction(fliC)', 'H2 antigen prediction(fljB)', 'Predicted antigenic profile', 'Predicted serotype(s)'] |
|
6895de35a263
planemo upload commit 844a891e4eaf732830043204ac636907eefb011d-dirty
charles_s_test
parents:
diff
changeset
|
168 html_out.write('<tr>\n') |
|
6895de35a263
planemo upload commit 844a891e4eaf732830043204ac636907eefb011d-dirty
charles_s_test
parents:
diff
changeset
|
169 for element in header_l: |
|
6895de35a263
planemo upload commit 844a891e4eaf732830043204ac636907eefb011d-dirty
charles_s_test
parents:
diff
changeset
|
170 html_out.write('<td>'+element+'</td>\n') |
|
6895de35a263
planemo upload commit 844a891e4eaf732830043204ac636907eefb011d-dirty
charles_s_test
parents:
diff
changeset
|
171 html_out.write('</tr>\n') |
|
6895de35a263
planemo upload commit 844a891e4eaf732830043204ac636907eefb011d-dirty
charles_s_test
parents:
diff
changeset
|
172 tab_out.write(header+"\n") |
|
6895de35a263
planemo upload commit 844a891e4eaf732830043204ac636907eefb011d-dirty
charles_s_test
parents:
diff
changeset
|
173 print "\n\n", header |
|
6895de35a263
planemo upload commit 844a891e4eaf732830043204ac636907eefb011d-dirty
charles_s_test
parents:
diff
changeset
|
174 for fastq in fastq2serotype: |
|
6895de35a263
planemo upload commit 844a891e4eaf732830043204ac636907eefb011d-dirty
charles_s_test
parents:
diff
changeset
|
175 # print fastq, fastq2serotype[fastq] |
|
6895de35a263
planemo upload commit 844a891e4eaf732830043204ac636907eefb011d-dirty
charles_s_test
parents:
diff
changeset
|
176 line_to_print = fastq+'\t'+"\t".join(fastq2serotype[fastq]) |
|
6895de35a263
planemo upload commit 844a891e4eaf732830043204ac636907eefb011d-dirty
charles_s_test
parents:
diff
changeset
|
177 tab_out.write(line_to_print+"\n") |
|
6895de35a263
planemo upload commit 844a891e4eaf732830043204ac636907eefb011d-dirty
charles_s_test
parents:
diff
changeset
|
178 html_out.write('<tr>\n') |
|
6895de35a263
planemo upload commit 844a891e4eaf732830043204ac636907eefb011d-dirty
charles_s_test
parents:
diff
changeset
|
179 html_out.write('<td>'+fastq+'</td>\n') |
|
6895de35a263
planemo upload commit 844a891e4eaf732830043204ac636907eefb011d-dirty
charles_s_test
parents:
diff
changeset
|
180 for antigen in fastq2serotype[fastq]: |
|
6895de35a263
planemo upload commit 844a891e4eaf732830043204ac636907eefb011d-dirty
charles_s_test
parents:
diff
changeset
|
181 html_out.write('<td>'+antigen+'</td>\n') |
|
6895de35a263
planemo upload commit 844a891e4eaf732830043204ac636907eefb011d-dirty
charles_s_test
parents:
diff
changeset
|
182 html_out.write('</tr>\n') |
|
6895de35a263
planemo upload commit 844a891e4eaf732830043204ac636907eefb011d-dirty
charles_s_test
parents:
diff
changeset
|
183 print line_to_print |
|
6895de35a263
planemo upload commit 844a891e4eaf732830043204ac636907eefb011d-dirty
charles_s_test
parents:
diff
changeset
|
184 html_out.write('</table>\n') |
|
6895de35a263
planemo upload commit 844a891e4eaf732830043204ac636907eefb011d-dirty
charles_s_test
parents:
diff
changeset
|
185 print "\n" |
|
6895de35a263
planemo upload commit 844a891e4eaf732830043204ac636907eefb011d-dirty
charles_s_test
parents:
diff
changeset
|
186 for fastq in fastq2comment: |
|
6895de35a263
planemo upload commit 844a891e4eaf732830043204ac636907eefb011d-dirty
charles_s_test
parents:
diff
changeset
|
187 tab_out.write("\n"+fastq+"\n") |
|
6895de35a263
planemo upload commit 844a891e4eaf732830043204ac636907eefb011d-dirty
charles_s_test
parents:
diff
changeset
|
188 html_out.write('<tr>\n') |
|
6895de35a263
planemo upload commit 844a891e4eaf732830043204ac636907eefb011d-dirty
charles_s_test
parents:
diff
changeset
|
189 html_out.write('<p>\n') |
|
6895de35a263
planemo upload commit 844a891e4eaf732830043204ac636907eefb011d-dirty
charles_s_test
parents:
diff
changeset
|
190 html_out.write('<td>'+fastq+"<br></td>\n") |
|
6895de35a263
planemo upload commit 844a891e4eaf732830043204ac636907eefb011d-dirty
charles_s_test
parents:
diff
changeset
|
191 for line in fastq2comment[fastq]: |
|
6895de35a263
planemo upload commit 844a891e4eaf732830043204ac636907eefb011d-dirty
charles_s_test
parents:
diff
changeset
|
192 #if len(line) > 7: |
|
6895de35a263
planemo upload commit 844a891e4eaf732830043204ac636907eefb011d-dirty
charles_s_test
parents:
diff
changeset
|
193 html_out.write('<td>'+line+'</td>\n') |
|
6895de35a263
planemo upload commit 844a891e4eaf732830043204ac636907eefb011d-dirty
charles_s_test
parents:
diff
changeset
|
194 tab_out.write(line+"\n") |
|
6895de35a263
planemo upload commit 844a891e4eaf732830043204ac636907eefb011d-dirty
charles_s_test
parents:
diff
changeset
|
195 print line |
|
6895de35a263
planemo upload commit 844a891e4eaf732830043204ac636907eefb011d-dirty
charles_s_test
parents:
diff
changeset
|
196 print "\n" |
|
6895de35a263
planemo upload commit 844a891e4eaf732830043204ac636907eefb011d-dirty
charles_s_test
parents:
diff
changeset
|
197 html_out.write('</p>\n') |
|
6895de35a263
planemo upload commit 844a891e4eaf732830043204ac636907eefb011d-dirty
charles_s_test
parents:
diff
changeset
|
198 html_out.write('</tr>\n') |
|
6895de35a263
planemo upload commit 844a891e4eaf732830043204ac636907eefb011d-dirty
charles_s_test
parents:
diff
changeset
|
199 html_out.write('</body>\n') |
|
6895de35a263
planemo upload commit 844a891e4eaf732830043204ac636907eefb011d-dirty
charles_s_test
parents:
diff
changeset
|
200 html_out.write('</html>\n') |
|
6895de35a263
planemo upload commit 844a891e4eaf732830043204ac636907eefb011d-dirty
charles_s_test
parents:
diff
changeset
|
201 html_out.close() |
|
6895de35a263
planemo upload commit 844a891e4eaf732830043204ac636907eefb011d-dirty
charles_s_test
parents:
diff
changeset
|
202 |
|
3
38ad1130d077
planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty
charles_s_test
parents:
0
diff
changeset
|
203 |
|
38ad1130d077
planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty
charles_s_test
parents:
0
diff
changeset
|
204 def readFile(filename): |
|
38ad1130d077
planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty
charles_s_test
parents:
0
diff
changeset
|
205 filehandle = open(filename) |
|
38ad1130d077
planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty
charles_s_test
parents:
0
diff
changeset
|
206 print filehandle.read() |
|
38ad1130d077
planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty
charles_s_test
parents:
0
diff
changeset
|
207 filehandle.close() |
|
38ad1130d077
planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty
charles_s_test
parents:
0
diff
changeset
|
208 |
|
38ad1130d077
planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty
charles_s_test
parents:
0
diff
changeset
|
209 |
|
0
6895de35a263
planemo upload commit 844a891e4eaf732830043204ac636907eefb011d-dirty
charles_s_test
parents:
diff
changeset
|
210 run2fastqs = list_runs(fastq_files) |
|
6895de35a263
planemo upload commit 844a891e4eaf732830043204ac636907eefb011d-dirty
charles_s_test
parents:
diff
changeset
|
211 outputs = run_seqsero(run2fastqs) |
|
6895de35a263
planemo upload commit 844a891e4eaf732830043204ac636907eefb011d-dirty
charles_s_test
parents:
diff
changeset
|
212 fastq2serotype, fastq2comment = get_serotypes(outputs) |
|
6895de35a263
planemo upload commit 844a891e4eaf732830043204ac636907eefb011d-dirty
charles_s_test
parents:
diff
changeset
|
213 print_html(fastq2serotype, fastq2comment) |
|
6895de35a263
planemo upload commit 844a891e4eaf732830043204ac636907eefb011d-dirty
charles_s_test
parents:
diff
changeset
|
214 |
|
6895de35a263
planemo upload commit 844a891e4eaf732830043204ac636907eefb011d-dirty
charles_s_test
parents:
diff
changeset
|
215 print_time() |
|
6895de35a263
planemo upload commit 844a891e4eaf732830043204ac636907eefb011d-dirty
charles_s_test
parents:
diff
changeset
|
216 |
|
6895de35a263
planemo upload commit 844a891e4eaf732830043204ac636907eefb011d-dirty
charles_s_test
parents:
diff
changeset
|
217 |