annotate splitStockholm.py @ 13:2a5defc09381 draft default tip

planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/GraphClust commit 4406735e44aba20859c252be39f4e99df28c7a92
author rnateam
date Sat, 27 Oct 2018 13:27:57 -0400
parents c0c9d19bc7b2
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
11
c0c9d19bc7b2 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust commit 746497a64b955f6b9afc1944d1c1d8d877e53267
rnateam
parents:
diff changeset
1 #!/usr/bin/env python
c0c9d19bc7b2 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust commit 746497a64b955f6b9afc1944d1c1d8d877e53267
rnateam
parents:
diff changeset
2
c0c9d19bc7b2 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust commit 746497a64b955f6b9afc1944d1c1d8d877e53267
rnateam
parents:
diff changeset
3 ########
c0c9d19bc7b2 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust commit 746497a64b955f6b9afc1944d1c1d8d877e53267
rnateam
parents:
diff changeset
4 # This script reads multiple alignments merged in single stockholm file
c0c9d19bc7b2 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust commit 746497a64b955f6b9afc1944d1c1d8d877e53267
rnateam
parents:
diff changeset
5 # and splits the alignment blocks according to data.names table
c0c9d19bc7b2 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust commit 746497a64b955f6b9afc1944d1c1d8d877e53267
rnateam
parents:
diff changeset
6 # The first sequence of each alignment file assumed to match to names table entries
c0c9d19bc7b2 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust commit 746497a64b955f6b9afc1944d1c1d8d877e53267
rnateam
parents:
diff changeset
7 # Author: M. Miladi
c0c9d19bc7b2 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust commit 746497a64b955f6b9afc1944d1c1d8d877e53267
rnateam
parents:
diff changeset
8 ########
c0c9d19bc7b2 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust commit 746497a64b955f6b9afc1944d1c1d8d877e53267
rnateam
parents:
diff changeset
9 import os
c0c9d19bc7b2 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust commit 746497a64b955f6b9afc1944d1c1d8d877e53267
rnateam
parents:
diff changeset
10 import re
c0c9d19bc7b2 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust commit 746497a64b955f6b9afc1944d1c1d8d877e53267
rnateam
parents:
diff changeset
11 import sys
c0c9d19bc7b2 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust commit 746497a64b955f6b9afc1944d1c1d8d877e53267
rnateam
parents:
diff changeset
12
c0c9d19bc7b2 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust commit 746497a64b955f6b9afc1944d1c1d8d877e53267
rnateam
parents:
diff changeset
13 from Bio import AlignIO, SeqIO
c0c9d19bc7b2 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust commit 746497a64b955f6b9afc1944d1c1d8d877e53267
rnateam
parents:
diff changeset
14 try:
c0c9d19bc7b2 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust commit 746497a64b955f6b9afc1944d1c1d8d877e53267
rnateam
parents:
diff changeset
15 from StringIO import StringIO
c0c9d19bc7b2 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust commit 746497a64b955f6b9afc1944d1c1d8d877e53267
rnateam
parents:
diff changeset
16 except ImportError:
c0c9d19bc7b2 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust commit 746497a64b955f6b9afc1944d1c1d8d877e53267
rnateam
parents:
diff changeset
17 from io import StringIO
c0c9d19bc7b2 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust commit 746497a64b955f6b9afc1944d1c1d8d877e53267
rnateam
parents:
diff changeset
18
c0c9d19bc7b2 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust commit 746497a64b955f6b9afc1944d1c1d8d877e53267
rnateam
parents:
diff changeset
19 stk_file = sys.argv[1]
c0c9d19bc7b2 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust commit 746497a64b955f6b9afc1944d1c1d8d877e53267
rnateam
parents:
diff changeset
20 print ("Parsing and splitting stk file:{}".format(stk_file))
c0c9d19bc7b2 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust commit 746497a64b955f6b9afc1944d1c1d8d877e53267
rnateam
parents:
diff changeset
21 target_f = "alignment_data_split.stk"
c0c9d19bc7b2 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust commit 746497a64b955f6b9afc1944d1c1d8d877e53267
rnateam
parents:
diff changeset
22 pattern = re.compile("^>.*$")
c0c9d19bc7b2 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust commit 746497a64b955f6b9afc1944d1c1d8d877e53267
rnateam
parents:
diff changeset
23 toWriteID = ""
c0c9d19bc7b2 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust commit 746497a64b955f6b9afc1944d1c1d8d877e53267
rnateam
parents:
diff changeset
24
c0c9d19bc7b2 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust commit 746497a64b955f6b9afc1944d1c1d8d877e53267
rnateam
parents:
diff changeset
25 count_for_id = 1
c0c9d19bc7b2 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust commit 746497a64b955f6b9afc1944d1c1d8d877e53267
rnateam
parents:
diff changeset
26 seq_counter = 0
c0c9d19bc7b2 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust commit 746497a64b955f6b9afc1944d1c1d8d877e53267
rnateam
parents:
diff changeset
27 new_id = ""
c0c9d19bc7b2 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust commit 746497a64b955f6b9afc1944d1c1d8d877e53267
rnateam
parents:
diff changeset
28
c0c9d19bc7b2 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust commit 746497a64b955f6b9afc1944d1c1d8d877e53267
rnateam
parents:
diff changeset
29 seq_id = []
c0c9d19bc7b2 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust commit 746497a64b955f6b9afc1944d1c1d8d877e53267
rnateam
parents:
diff changeset
30 seq_string = []
c0c9d19bc7b2 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust commit 746497a64b955f6b9afc1944d1c1d8d877e53267
rnateam
parents:
diff changeset
31 orig_id = []
c0c9d19bc7b2 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust commit 746497a64b955f6b9afc1944d1c1d8d877e53267
rnateam
parents:
diff changeset
32 name_file = "FASTA/data.names"
c0c9d19bc7b2 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust commit 746497a64b955f6b9afc1944d1c1d8d877e53267
rnateam
parents:
diff changeset
33 array_all_chunks = []
c0c9d19bc7b2 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust commit 746497a64b955f6b9afc1944d1c1d8d877e53267
rnateam
parents:
diff changeset
34 with open(name_file, 'r') as f:
c0c9d19bc7b2 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust commit 746497a64b955f6b9afc1944d1c1d8d877e53267
rnateam
parents:
diff changeset
35 for line in f:
c0c9d19bc7b2 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust commit 746497a64b955f6b9afc1944d1c1d8d877e53267
rnateam
parents:
diff changeset
36 if len(line.strip()) == 0:
c0c9d19bc7b2 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust commit 746497a64b955f6b9afc1944d1c1d8d877e53267
rnateam
parents:
diff changeset
37 continue
c0c9d19bc7b2 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust commit 746497a64b955f6b9afc1944d1c1d8d877e53267
rnateam
parents:
diff changeset
38 seq_id.append(int(line.split()[0]))
c0c9d19bc7b2 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust commit 746497a64b955f6b9afc1944d1c1d8d877e53267
rnateam
parents:
diff changeset
39 seq_string.append(line.split()[1])
c0c9d19bc7b2 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust commit 746497a64b955f6b9afc1944d1c1d8d877e53267
rnateam
parents:
diff changeset
40 orig_id_srt = line.split()[3]
c0c9d19bc7b2 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust commit 746497a64b955f6b9afc1944d1c1d8d877e53267
rnateam
parents:
diff changeset
41 orig_id_srt = orig_id_srt.rsplit('_',1)[0]
c0c9d19bc7b2 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust commit 746497a64b955f6b9afc1944d1c1d8d877e53267
rnateam
parents:
diff changeset
42 orig_id.append(orig_id_srt)
c0c9d19bc7b2 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust commit 746497a64b955f6b9afc1944d1c1d8d877e53267
rnateam
parents:
diff changeset
43
c0c9d19bc7b2 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust commit 746497a64b955f6b9afc1944d1c1d8d877e53267
rnateam
parents:
diff changeset
44
c0c9d19bc7b2 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust commit 746497a64b955f6b9afc1944d1c1d8d877e53267
rnateam
parents:
diff changeset
45
c0c9d19bc7b2 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust commit 746497a64b955f6b9afc1944d1c1d8d877e53267
rnateam
parents:
diff changeset
46 with open(stk_file) as stk_in:
c0c9d19bc7b2 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust commit 746497a64b955f6b9afc1944d1c1d8d877e53267
rnateam
parents:
diff changeset
47 alignments = AlignIO.parse(stk_in, "stockholm")#, alphabet=IUPAC.ambiguous_rna)
c0c9d19bc7b2 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust commit 746497a64b955f6b9afc1944d1c1d8d877e53267
rnateam
parents:
diff changeset
48 alignments_dic = {(a[0].id):a for a in alignments}
c0c9d19bc7b2 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust commit 746497a64b955f6b9afc1944d1c1d8d877e53267
rnateam
parents:
diff changeset
49
c0c9d19bc7b2 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust commit 746497a64b955f6b9afc1944d1c1d8d877e53267
rnateam
parents:
diff changeset
50
c0c9d19bc7b2 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust commit 746497a64b955f6b9afc1944d1c1d8d877e53267
rnateam
parents:
diff changeset
51 regx_gaps = '[-.~_]' # valid gap symbols all be converted to "-"
c0c9d19bc7b2 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust commit 746497a64b955f6b9afc1944d1c1d8d877e53267
rnateam
parents:
diff changeset
52 str_gaps = '-.~_' # valid gap symbols all be converted to "-"
c0c9d19bc7b2 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust commit 746497a64b955f6b9afc1944d1c1d8d877e53267
rnateam
parents:
diff changeset
53
c0c9d19bc7b2 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust commit 746497a64b955f6b9afc1944d1c1d8d877e53267
rnateam
parents:
diff changeset
54
c0c9d19bc7b2 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust commit 746497a64b955f6b9afc1944d1c1d8d877e53267
rnateam
parents:
diff changeset
55 chunks = []
c0c9d19bc7b2 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust commit 746497a64b955f6b9afc1944d1c1d8d877e53267
rnateam
parents:
diff changeset
56 with open(target_f, 'w') as out_stk_handle:
c0c9d19bc7b2 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust commit 746497a64b955f6b9afc1944d1c1d8d877e53267
rnateam
parents:
diff changeset
57 for i in range(len(orig_id)):
c0c9d19bc7b2 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust commit 746497a64b955f6b9afc1944d1c1d8d877e53267
rnateam
parents:
diff changeset
58
c0c9d19bc7b2 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust commit 746497a64b955f6b9afc1944d1c1d8d877e53267
rnateam
parents:
diff changeset
59 #----------------------
c0c9d19bc7b2 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust commit 746497a64b955f6b9afc1944d1c1d8d877e53267
rnateam
parents:
diff changeset
60 # We need to map ungapped positions of the chunks to gapped positions of first sequence
c0c9d19bc7b2 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust commit 746497a64b955f6b9afc1944d1c1d8d877e53267
rnateam
parents:
diff changeset
61 gap_count = 0
c0c9d19bc7b2 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust commit 746497a64b955f6b9afc1944d1c1d8d877e53267
rnateam
parents:
diff changeset
62 ungap_ind = 0
c0c9d19bc7b2 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust commit 746497a64b955f6b9afc1944d1c1d8d877e53267
rnateam
parents:
diff changeset
63 dic_gap_counts = dict()
c0c9d19bc7b2 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust commit 746497a64b955f6b9afc1944d1c1d8d877e53267
rnateam
parents:
diff changeset
64 cur_alignment = alignments_dic[orig_id[i]]
c0c9d19bc7b2 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust commit 746497a64b955f6b9afc1944d1c1d8d877e53267
rnateam
parents:
diff changeset
65 for c in cur_alignment[0].seq:
c0c9d19bc7b2 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust commit 746497a64b955f6b9afc1944d1c1d8d877e53267
rnateam
parents:
diff changeset
66 #print ungap_ind
c0c9d19bc7b2 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust commit 746497a64b955f6b9afc1944d1c1d8d877e53267
rnateam
parents:
diff changeset
67 if c in str_gaps:
c0c9d19bc7b2 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust commit 746497a64b955f6b9afc1944d1c1d8d877e53267
rnateam
parents:
diff changeset
68 gap_count += 1
c0c9d19bc7b2 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust commit 746497a64b955f6b9afc1944d1c1d8d877e53267
rnateam
parents:
diff changeset
69 else:
c0c9d19bc7b2 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust commit 746497a64b955f6b9afc1944d1c1d8d877e53267
rnateam
parents:
diff changeset
70 dic_gap_counts[ungap_ind] = gap_count
c0c9d19bc7b2 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust commit 746497a64b955f6b9afc1944d1c1d8d877e53267
rnateam
parents:
diff changeset
71 ungap_ind += 1
c0c9d19bc7b2 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust commit 746497a64b955f6b9afc1944d1c1d8d877e53267
rnateam
parents:
diff changeset
72 ID = str(seq_id[i]) + " " + seq_string[i]
c0c9d19bc7b2 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust commit 746497a64b955f6b9afc1944d1c1d8d877e53267
rnateam
parents:
diff changeset
73 chunks = re.findall(r'\d+', seq_string[i])
c0c9d19bc7b2 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust commit 746497a64b955f6b9afc1944d1c1d8d877e53267
rnateam
parents:
diff changeset
74 print (ID,chunks)
c0c9d19bc7b2 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust commit 746497a64b955f6b9afc1944d1c1d8d877e53267
rnateam
parents:
diff changeset
75
c0c9d19bc7b2 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust commit 746497a64b955f6b9afc1944d1c1d8d877e53267
rnateam
parents:
diff changeset
76 index_start, index_end =int(chunks[1])-1, int(chunks[2])-1
c0c9d19bc7b2 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust commit 746497a64b955f6b9afc1944d1c1d8d877e53267
rnateam
parents:
diff changeset
77 subalign = cur_alignment[:, index_start + dic_gap_counts[index_start]:
c0c9d19bc7b2 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust commit 746497a64b955f6b9afc1944d1c1d8d877e53267
rnateam
parents:
diff changeset
78 index_end+dic_gap_counts[index_end]+1]
c0c9d19bc7b2 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust commit 746497a64b955f6b9afc1944d1c1d8d877e53267
rnateam
parents:
diff changeset
79
c0c9d19bc7b2 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust commit 746497a64b955f6b9afc1944d1c1d8d877e53267
rnateam
parents:
diff changeset
80 #----------------------
c0c9d19bc7b2 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust commit 746497a64b955f6b9afc1944d1c1d8d877e53267
rnateam
parents:
diff changeset
81 # BioPython does not handel the GF ID entry for alignment
c0c9d19bc7b2 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust commit 746497a64b955f6b9afc1944d1c1d8d877e53267
rnateam
parents:
diff changeset
82 # So we add entry in the second line manually
c0c9d19bc7b2 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust commit 746497a64b955f6b9afc1944d1c1d8d877e53267
rnateam
parents:
diff changeset
83 siotmp = StringIO()
c0c9d19bc7b2 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust commit 746497a64b955f6b9afc1944d1c1d8d877e53267
rnateam
parents:
diff changeset
84 AlignIO.write(subalign, siotmp, format="stockholm")
c0c9d19bc7b2 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust commit 746497a64b955f6b9afc1944d1c1d8d877e53267
rnateam
parents:
diff changeset
85 stk_lines = siotmp.getvalue().split('\n')
c0c9d19bc7b2 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust commit 746497a64b955f6b9afc1944d1c1d8d877e53267
rnateam
parents:
diff changeset
86 out_stk_handle.write('{}\n'.format(stk_lines[0]))
c0c9d19bc7b2 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust commit 746497a64b955f6b9afc1944d1c1d8d877e53267
rnateam
parents:
diff changeset
87 out_stk_handle.write('#=GF ID {}\n'.format(ID))
c0c9d19bc7b2 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust commit 746497a64b955f6b9afc1944d1c1d8d877e53267
rnateam
parents:
diff changeset
88 out_stk_handle.writelines('\n'.join(stk_lines[1:]))
c0c9d19bc7b2 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust commit 746497a64b955f6b9afc1944d1c1d8d877e53267
rnateam
parents:
diff changeset
89 #print out_stk_handle.getvalue()
c0c9d19bc7b2 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust commit 746497a64b955f6b9afc1944d1c1d8d877e53267
rnateam
parents:
diff changeset
90
c0c9d19bc7b2 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust commit 746497a64b955f6b9afc1944d1c1d8d877e53267
rnateam
parents:
diff changeset
91