annotate tools/maf/maf_split_by_species.xml @ 0:9071e359b9a3

Uploaded
author xuebing
date Fri, 09 Mar 2012 19:37:19 -0500
parents
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
0
9071e359b9a3 Uploaded
xuebing
parents:
diff changeset
1 <tool id="MAF_split_blocks_by_species1" name="Split MAF blocks" version="1.0.0">
9071e359b9a3 Uploaded
xuebing
parents:
diff changeset
2 <description>by Species</description>
9071e359b9a3 Uploaded
xuebing
parents:
diff changeset
3 <command interpreter="python">maf_split_by_species.py $input1 $out_file1 $collapse_columns</command>
9071e359b9a3 Uploaded
xuebing
parents:
diff changeset
4 <inputs>
9071e359b9a3 Uploaded
xuebing
parents:
diff changeset
5 <param format="maf" name="input1" type="data" label="MAF file to split"/>
9071e359b9a3 Uploaded
xuebing
parents:
diff changeset
6 <param name="collapse_columns" type="select" label="Collapse empty alignment columns" help="Removes columns that are gaps in all sequences">
9071e359b9a3 Uploaded
xuebing
parents:
diff changeset
7 <option value="True" selected="true">Yes</option>
9071e359b9a3 Uploaded
xuebing
parents:
diff changeset
8 <option value="False">No</option>
9071e359b9a3 Uploaded
xuebing
parents:
diff changeset
9 </param>
9071e359b9a3 Uploaded
xuebing
parents:
diff changeset
10 </inputs>
9071e359b9a3 Uploaded
xuebing
parents:
diff changeset
11 <outputs>
9071e359b9a3 Uploaded
xuebing
parents:
diff changeset
12 <data format="maf" name="out_file1" />
9071e359b9a3 Uploaded
xuebing
parents:
diff changeset
13 </outputs>
9071e359b9a3 Uploaded
xuebing
parents:
diff changeset
14 <tests>
9071e359b9a3 Uploaded
xuebing
parents:
diff changeset
15 <test>
9071e359b9a3 Uploaded
xuebing
parents:
diff changeset
16 <param name="input1" value="maf_split_by_species_in.maf"/>
9071e359b9a3 Uploaded
xuebing
parents:
diff changeset
17 <param name="collapse_columns" value="True"/>
9071e359b9a3 Uploaded
xuebing
parents:
diff changeset
18 <output name="out_file1" file="maf_split_by_species_collapsed_out.maf"/>
9071e359b9a3 Uploaded
xuebing
parents:
diff changeset
19 </test>
9071e359b9a3 Uploaded
xuebing
parents:
diff changeset
20 <test>
9071e359b9a3 Uploaded
xuebing
parents:
diff changeset
21 <param name="input1" value="maf_split_by_species_in.maf"/>
9071e359b9a3 Uploaded
xuebing
parents:
diff changeset
22 <param name="collapse_columns" value="False"/>
9071e359b9a3 Uploaded
xuebing
parents:
diff changeset
23 <output name="out_file1" file="maf_split_by_species_not_collapsed_out.maf"/>
9071e359b9a3 Uploaded
xuebing
parents:
diff changeset
24 </test>
9071e359b9a3 Uploaded
xuebing
parents:
diff changeset
25 </tests>
9071e359b9a3 Uploaded
xuebing
parents:
diff changeset
26 <help>
9071e359b9a3 Uploaded
xuebing
parents:
diff changeset
27
9071e359b9a3 Uploaded
xuebing
parents:
diff changeset
28 **What it does**
9071e359b9a3 Uploaded
xuebing
parents:
diff changeset
29
9071e359b9a3 Uploaded
xuebing
parents:
diff changeset
30 This tool examines each MAF block for multiple occurrences of a species in a single block. When this occurs, a block is split into multiple blocks where every combination of one sequence per species per block is represented.
9071e359b9a3 Uploaded
xuebing
parents:
diff changeset
31
9071e359b9a3 Uploaded
xuebing
parents:
diff changeset
32 The interface for this tool has two inputs:
9071e359b9a3 Uploaded
xuebing
parents:
diff changeset
33
9071e359b9a3 Uploaded
xuebing
parents:
diff changeset
34 * **MAF file to split**. Choose multiple alignments from history to be split by species.
9071e359b9a3 Uploaded
xuebing
parents:
diff changeset
35 * **Collapse empty alignment columns**. Should alignment columns containing only gaps in the new blocks be removed.
9071e359b9a3 Uploaded
xuebing
parents:
diff changeset
36
9071e359b9a3 Uploaded
xuebing
parents:
diff changeset
37 -----
9071e359b9a3 Uploaded
xuebing
parents:
diff changeset
38
9071e359b9a3 Uploaded
xuebing
parents:
diff changeset
39 **Example 1**: **Collapse empty alignment columns is Yes**:
9071e359b9a3 Uploaded
xuebing
parents:
diff changeset
40
9071e359b9a3 Uploaded
xuebing
parents:
diff changeset
41 For the following alignment::
9071e359b9a3 Uploaded
xuebing
parents:
diff changeset
42
9071e359b9a3 Uploaded
xuebing
parents:
diff changeset
43 ##maf version=1
9071e359b9a3 Uploaded
xuebing
parents:
diff changeset
44 a score=2047408.0
9071e359b9a3 Uploaded
xuebing
parents:
diff changeset
45 s species1.chr1 147984545 85 + 245522847 ATGGCGTCGGCCTCCTCCGGGCCGTCGTCTTCGGTCGGTTTTTCATCCTTTGATCCCGCGGTCCCTTCCTGTACCTTGTCCTCAG
9071e359b9a3 Uploaded
xuebing
parents:
diff changeset
46 s species1.chr1 147984545 83 - 245522847 ATGGCGTCGGCCTCCTCCGGGCCGTCGTCTT--GTCGGTTTTTCATCCTTTGATCCCGCGGTCCCTTCCTGTACCTTGTCCTCAG
9071e359b9a3 Uploaded
xuebing
parents:
diff changeset
47 s species1.chr1 147984645 79 + 245522847 ATGGCGTCGGCCTCCTCCGGGCCGTCGTCTTCGGTCGGTTTTTCATCCTTTGATCCCGCGGTCCCTTCCTGTACCTT------AG
9071e359b9a3 Uploaded
xuebing
parents:
diff changeset
48 s species1.chr1 147984645 79 - 245522847 ATGGCGTCGGCCTCCTCCGGGCCGTCGTC---GGTCGGTTTTTCATCCTTTGATCCCGCGGTCCCTTCCTGTACCTTGTC---AG
9071e359b9a3 Uploaded
xuebing
parents:
diff changeset
49 s species2.chr1 129723125 85 + 229575298 ATGGCGTCGGCCTCCTCCGGGCCGTCGTCTTCGGTCGGTTTTTCATCCTTTGATCCCGCGGTCCCTTCCTGTACCTCGTCCTCAG
9071e359b9a3 Uploaded
xuebing
parents:
diff changeset
50 s species2.chr1 129723125 83 - 229575298 ATGGCGTCGGCCTCCTCCGGGCCGTCGTCT--GGTCGGTTTTTCATCCTTTGATCCCGCGGTCCCTTCCTGTACCTCGTCCTCAG
9071e359b9a3 Uploaded
xuebing
parents:
diff changeset
51 s species2.chr1 129723925 79 + 229575298 ATGGCGTCGGCCTCCTCCGGGCCGTCGTCTTCGGTCGGTTTTTCATCCTTTGATCCCGCGGTCCCTTCCTGTACCTC------AG
9071e359b9a3 Uploaded
xuebing
parents:
diff changeset
52 s species3.chr3 68255714 76 - 258222147 ATGGCGTCCGCCTCCTCAGGGCCAGCGGC---GGCGGGGTTTTCACCCCTTGATTCCGGGGTCCCTGCCGGTACCGC------AG
9071e359b9a3 Uploaded
xuebing
parents:
diff changeset
53
9071e359b9a3 Uploaded
xuebing
parents:
diff changeset
54 the tool will create **a single** history item containing 12 alignment blocks (notice that no columns contain only gaps)::
9071e359b9a3 Uploaded
xuebing
parents:
diff changeset
55
9071e359b9a3 Uploaded
xuebing
parents:
diff changeset
56 ##maf version=1
9071e359b9a3 Uploaded
xuebing
parents:
diff changeset
57 a score=2047408.0
9071e359b9a3 Uploaded
xuebing
parents:
diff changeset
58 s species1.chr1 147984545 85 + 245522847 ATGGCGTCGGCCTCCTCCGGGCCGTCGTCTTCGGTCGGTTTTTCATCCTTTGATCCCGCGGTCCCTTCCTGTACCTTGTCCTCAG
9071e359b9a3 Uploaded
xuebing
parents:
diff changeset
59 s species2.chr1 129723125 85 + 229575298 ATGGCGTCGGCCTCCTCCGGGCCGTCGTCTTCGGTCGGTTTTTCATCCTTTGATCCCGCGGTCCCTTCCTGTACCTCGTCCTCAG
9071e359b9a3 Uploaded
xuebing
parents:
diff changeset
60 s species3.chr3 68255714 76 - 258222147 ATGGCGTCCGCCTCCTCAGGGCCAGCGGC---GGCGGGGTTTTCACCCCTTGATTCCGGGGTCCCTGCCGGTACCGC------AG
9071e359b9a3 Uploaded
xuebing
parents:
diff changeset
61
9071e359b9a3 Uploaded
xuebing
parents:
diff changeset
62 a score=2047408.0
9071e359b9a3 Uploaded
xuebing
parents:
diff changeset
63 s species1.chr1 147984545 83 - 245522847 ATGGCGTCGGCCTCCTCCGGGCCGTCGTCTT--GTCGGTTTTTCATCCTTTGATCCCGCGGTCCCTTCCTGTACCTTGTCCTCAG
9071e359b9a3 Uploaded
xuebing
parents:
diff changeset
64 s species2.chr1 129723125 85 + 229575298 ATGGCGTCGGCCTCCTCCGGGCCGTCGTCTTCGGTCGGTTTTTCATCCTTTGATCCCGCGGTCCCTTCCTGTACCTCGTCCTCAG
9071e359b9a3 Uploaded
xuebing
parents:
diff changeset
65 s species3.chr3 68255714 76 - 258222147 ATGGCGTCCGCCTCCTCAGGGCCAGCGGC---GGCGGGGTTTTCACCCCTTGATTCCGGGGTCCCTGCCGGTACCGC------AG
9071e359b9a3 Uploaded
xuebing
parents:
diff changeset
66
9071e359b9a3 Uploaded
xuebing
parents:
diff changeset
67 a score=2047408.0
9071e359b9a3 Uploaded
xuebing
parents:
diff changeset
68 s species1.chr1 147984645 79 + 245522847 ATGGCGTCGGCCTCCTCCGGGCCGTCGTCTTCGGTCGGTTTTTCATCCTTTGATCCCGCGGTCCCTTCCTGTACCTT------AG
9071e359b9a3 Uploaded
xuebing
parents:
diff changeset
69 s species2.chr1 129723125 85 + 229575298 ATGGCGTCGGCCTCCTCCGGGCCGTCGTCTTCGGTCGGTTTTTCATCCTTTGATCCCGCGGTCCCTTCCTGTACCTCGTCCTCAG
9071e359b9a3 Uploaded
xuebing
parents:
diff changeset
70 s species3.chr3 68255714 76 - 258222147 ATGGCGTCCGCCTCCTCAGGGCCAGCGGC---GGCGGGGTTTTCACCCCTTGATTCCGGGGTCCCTGCCGGTACCGC------AG
9071e359b9a3 Uploaded
xuebing
parents:
diff changeset
71
9071e359b9a3 Uploaded
xuebing
parents:
diff changeset
72 a score=2047408.0
9071e359b9a3 Uploaded
xuebing
parents:
diff changeset
73 s species1.chr1 147984645 79 - 245522847 ATGGCGTCGGCCTCCTCCGGGCCGTCGTC---GGTCGGTTTTTCATCCTTTGATCCCGCGGTCCCTTCCTGTACCTTGTC---AG
9071e359b9a3 Uploaded
xuebing
parents:
diff changeset
74 s species2.chr1 129723125 85 + 229575298 ATGGCGTCGGCCTCCTCCGGGCCGTCGTCTTCGGTCGGTTTTTCATCCTTTGATCCCGCGGTCCCTTCCTGTACCTCGTCCTCAG
9071e359b9a3 Uploaded
xuebing
parents:
diff changeset
75 s species3.chr3 68255714 76 - 258222147 ATGGCGTCCGCCTCCTCAGGGCCAGCGGC---GGCGGGGTTTTCACCCCTTGATTCCGGGGTCCCTGCCGGTACCGC------AG
9071e359b9a3 Uploaded
xuebing
parents:
diff changeset
76
9071e359b9a3 Uploaded
xuebing
parents:
diff changeset
77 a score=2047408.0
9071e359b9a3 Uploaded
xuebing
parents:
diff changeset
78 s species1.chr1 147984545 85 + 245522847 ATGGCGTCGGCCTCCTCCGGGCCGTCGTCTTCGGTCGGTTTTTCATCCTTTGATCCCGCGGTCCCTTCCTGTACCTTGTCCTCAG
9071e359b9a3 Uploaded
xuebing
parents:
diff changeset
79 s species2.chr1 129723125 83 - 229575298 ATGGCGTCGGCCTCCTCCGGGCCGTCGTCT--GGTCGGTTTTTCATCCTTTGATCCCGCGGTCCCTTCCTGTACCTCGTCCTCAG
9071e359b9a3 Uploaded
xuebing
parents:
diff changeset
80 s species3.chr3 68255714 76 - 258222147 ATGGCGTCCGCCTCCTCAGGGCCAGCGGC---GGCGGGGTTTTCACCCCTTGATTCCGGGGTCCCTGCCGGTACCGC------AG
9071e359b9a3 Uploaded
xuebing
parents:
diff changeset
81
9071e359b9a3 Uploaded
xuebing
parents:
diff changeset
82 a score=2047408.0
9071e359b9a3 Uploaded
xuebing
parents:
diff changeset
83 s species1.chr1 147984545 83 - 245522847 ATGGCGTCGGCCTCCTCCGGGCCGTCGTCTT-GTCGGTTTTTCATCCTTTGATCCCGCGGTCCCTTCCTGTACCTTGTCCTCAG
9071e359b9a3 Uploaded
xuebing
parents:
diff changeset
84 s species2.chr1 129723125 83 - 229575298 ATGGCGTCGGCCTCCTCCGGGCCGTCGTCT-GGTCGGTTTTTCATCCTTTGATCCCGCGGTCCCTTCCTGTACCTCGTCCTCAG
9071e359b9a3 Uploaded
xuebing
parents:
diff changeset
85 s species3.chr3 68255714 76 - 258222147 ATGGCGTCCGCCTCCTCAGGGCCAGCGGC--GGCGGGGTTTTCACCCCTTGATTCCGGGGTCCCTGCCGGTACCGC------AG
9071e359b9a3 Uploaded
xuebing
parents:
diff changeset
86
9071e359b9a3 Uploaded
xuebing
parents:
diff changeset
87 a score=2047408.0
9071e359b9a3 Uploaded
xuebing
parents:
diff changeset
88 s species1.chr1 147984645 79 + 245522847 ATGGCGTCGGCCTCCTCCGGGCCGTCGTCTTCGGTCGGTTTTTCATCCTTTGATCCCGCGGTCCCTTCCTGTACCTT------AG
9071e359b9a3 Uploaded
xuebing
parents:
diff changeset
89 s species2.chr1 129723125 83 - 229575298 ATGGCGTCGGCCTCCTCCGGGCCGTCGTCT--GGTCGGTTTTTCATCCTTTGATCCCGCGGTCCCTTCCTGTACCTCGTCCTCAG
9071e359b9a3 Uploaded
xuebing
parents:
diff changeset
90 s species3.chr3 68255714 76 - 258222147 ATGGCGTCCGCCTCCTCAGGGCCAGCGGC---GGCGGGGTTTTCACCCCTTGATTCCGGGGTCCCTGCCGGTACCGC------AG
9071e359b9a3 Uploaded
xuebing
parents:
diff changeset
91
9071e359b9a3 Uploaded
xuebing
parents:
diff changeset
92 a score=2047408.0
9071e359b9a3 Uploaded
xuebing
parents:
diff changeset
93 s species1.chr1 147984645 79 - 245522847 ATGGCGTCGGCCTCCTCCGGGCCGTCGTC-GGTCGGTTTTTCATCCTTTGATCCCGCGGTCCCTTCCTGTACCTTGTC---AG
9071e359b9a3 Uploaded
xuebing
parents:
diff changeset
94 s species2.chr1 129723125 83 - 229575298 ATGGCGTCGGCCTCCTCCGGGCCGTCGTCTGGTCGGTTTTTCATCCTTTGATCCCGCGGTCCCTTCCTGTACCTCGTCCTCAG
9071e359b9a3 Uploaded
xuebing
parents:
diff changeset
95 s species3.chr3 68255714 76 - 258222147 ATGGCGTCCGCCTCCTCAGGGCCAGCGGC-GGCGGGGTTTTCACCCCTTGATTCCGGGGTCCCTGCCGGTACCGC------AG
9071e359b9a3 Uploaded
xuebing
parents:
diff changeset
96
9071e359b9a3 Uploaded
xuebing
parents:
diff changeset
97 a score=2047408.0
9071e359b9a3 Uploaded
xuebing
parents:
diff changeset
98 s species1.chr1 147984545 85 + 245522847 ATGGCGTCGGCCTCCTCCGGGCCGTCGTCTTCGGTCGGTTTTTCATCCTTTGATCCCGCGGTCCCTTCCTGTACCTTGTCCTCAG
9071e359b9a3 Uploaded
xuebing
parents:
diff changeset
99 s species2.chr1 129723925 79 + 229575298 ATGGCGTCGGCCTCCTCCGGGCCGTCGTCTTCGGTCGGTTTTTCATCCTTTGATCCCGCGGTCCCTTCCTGTACCTC------AG
9071e359b9a3 Uploaded
xuebing
parents:
diff changeset
100 s species3.chr3 68255714 76 - 258222147 ATGGCGTCCGCCTCCTCAGGGCCAGCGGC---GGCGGGGTTTTCACCCCTTGATTCCGGGGTCCCTGCCGGTACCGC------AG
9071e359b9a3 Uploaded
xuebing
parents:
diff changeset
101
9071e359b9a3 Uploaded
xuebing
parents:
diff changeset
102 a score=2047408.0
9071e359b9a3 Uploaded
xuebing
parents:
diff changeset
103 s species1.chr1 147984545 83 - 245522847 ATGGCGTCGGCCTCCTCCGGGCCGTCGTCTT--GTCGGTTTTTCATCCTTTGATCCCGCGGTCCCTTCCTGTACCTTGTCCTCAG
9071e359b9a3 Uploaded
xuebing
parents:
diff changeset
104 s species2.chr1 129723925 79 + 229575298 ATGGCGTCGGCCTCCTCCGGGCCGTCGTCTTCGGTCGGTTTTTCATCCTTTGATCCCGCGGTCCCTTCCTGTACCTC------AG
9071e359b9a3 Uploaded
xuebing
parents:
diff changeset
105 s species3.chr3 68255714 76 - 258222147 ATGGCGTCCGCCTCCTCAGGGCCAGCGGC---GGCGGGGTTTTCACCCCTTGATTCCGGGGTCCCTGCCGGTACCGC------AG
9071e359b9a3 Uploaded
xuebing
parents:
diff changeset
106
9071e359b9a3 Uploaded
xuebing
parents:
diff changeset
107 a score=2047408.0
9071e359b9a3 Uploaded
xuebing
parents:
diff changeset
108 s species1.chr1 147984645 79 + 245522847 ATGGCGTCGGCCTCCTCCGGGCCGTCGTCTTCGGTCGGTTTTTCATCCTTTGATCCCGCGGTCCCTTCCTGTACCTTAG
9071e359b9a3 Uploaded
xuebing
parents:
diff changeset
109 s species2.chr1 129723925 79 + 229575298 ATGGCGTCGGCCTCCTCCGGGCCGTCGTCTTCGGTCGGTTTTTCATCCTTTGATCCCGCGGTCCCTTCCTGTACCTCAG
9071e359b9a3 Uploaded
xuebing
parents:
diff changeset
110 s species3.chr3 68255714 76 - 258222147 ATGGCGTCCGCCTCCTCAGGGCCAGCGGC---GGCGGGGTTTTCACCCCTTGATTCCGGGGTCCCTGCCGGTACCGCAG
9071e359b9a3 Uploaded
xuebing
parents:
diff changeset
111
9071e359b9a3 Uploaded
xuebing
parents:
diff changeset
112 a score=2047408.0
9071e359b9a3 Uploaded
xuebing
parents:
diff changeset
113 s species1.chr1 147984645 79 - 245522847 ATGGCGTCGGCCTCCTCCGGGCCGTCGTC---GGTCGGTTTTTCATCCTTTGATCCCGCGGTCCCTTCCTGTACCTTGTCAG
9071e359b9a3 Uploaded
xuebing
parents:
diff changeset
114 s species2.chr1 129723925 79 + 229575298 ATGGCGTCGGCCTCCTCCGGGCCGTCGTCTTCGGTCGGTTTTTCATCCTTTGATCCCGCGGTCCCTTCCTGTACCTC---AG
9071e359b9a3 Uploaded
xuebing
parents:
diff changeset
115 s species3.chr3 68255714 76 - 258222147 ATGGCGTCCGCCTCCTCAGGGCCAGCGGC---GGCGGGGTTTTCACCCCTTGATTCCGGGGTCCCTGCCGGTACCGC---AG
9071e359b9a3 Uploaded
xuebing
parents:
diff changeset
116
9071e359b9a3 Uploaded
xuebing
parents:
diff changeset
117 -----
9071e359b9a3 Uploaded
xuebing
parents:
diff changeset
118
9071e359b9a3 Uploaded
xuebing
parents:
diff changeset
119 **Example 2**: **Collapse empty alignment columns is No**:
9071e359b9a3 Uploaded
xuebing
parents:
diff changeset
120
9071e359b9a3 Uploaded
xuebing
parents:
diff changeset
121 For the following alignment::
9071e359b9a3 Uploaded
xuebing
parents:
diff changeset
122
9071e359b9a3 Uploaded
xuebing
parents:
diff changeset
123 ##maf version=1
9071e359b9a3 Uploaded
xuebing
parents:
diff changeset
124 a score=2047408.0
9071e359b9a3 Uploaded
xuebing
parents:
diff changeset
125 s species1.chr1 147984545 85 + 245522847 ATGGCGTCGGCCTCCTCCGGGCCGTCGTCTTCGGTCGGTTTTTCATCCTTTGATCCCGCGGTCCCTTCCTGTACCTTGTCCTCAG
9071e359b9a3 Uploaded
xuebing
parents:
diff changeset
126 s species1.chr1 147984545 83 - 245522847 ATGGCGTCGGCCTCCTCCGGGCCGTCGTCTT--GTCGGTTTTTCATCCTTTGATCCCGCGGTCCCTTCCTGTACCTTGTCCTCAG
9071e359b9a3 Uploaded
xuebing
parents:
diff changeset
127 s species1.chr1 147984645 79 + 245522847 ATGGCGTCGGCCTCCTCCGGGCCGTCGTCTTCGGTCGGTTTTTCATCCTTTGATCCCGCGGTCCCTTCCTGTACCTT------AG
9071e359b9a3 Uploaded
xuebing
parents:
diff changeset
128 s species1.chr1 147984645 79 - 245522847 ATGGCGTCGGCCTCCTCCGGGCCGTCGTC---GGTCGGTTTTTCATCCTTTGATCCCGCGGTCCCTTCCTGTACCTTGTC---AG
9071e359b9a3 Uploaded
xuebing
parents:
diff changeset
129 s species2.chr1 129723125 85 + 229575298 ATGGCGTCGGCCTCCTCCGGGCCGTCGTCTTCGGTCGGTTTTTCATCCTTTGATCCCGCGGTCCCTTCCTGTACCTCGTCCTCAG
9071e359b9a3 Uploaded
xuebing
parents:
diff changeset
130 s species2.chr1 129723125 83 - 229575298 ATGGCGTCGGCCTCCTCCGGGCCGTCGTCT--GGTCGGTTTTTCATCCTTTGATCCCGCGGTCCCTTCCTGTACCTCGTCCTCAG
9071e359b9a3 Uploaded
xuebing
parents:
diff changeset
131 s species2.chr1 129723925 79 + 229575298 ATGGCGTCGGCCTCCTCCGGGCCGTCGTCTTCGGTCGGTTTTTCATCCTTTGATCCCGCGGTCCCTTCCTGTACCTC------AG
9071e359b9a3 Uploaded
xuebing
parents:
diff changeset
132 s species3.chr3 68255714 76 - 258222147 ATGGCGTCCGCCTCCTCAGGGCCAGCGGC---GGCGGGGTTTTCACCCCTTGATTCCGGGGTCCCTGCCGGTACCGC------AG
9071e359b9a3 Uploaded
xuebing
parents:
diff changeset
133
9071e359b9a3 Uploaded
xuebing
parents:
diff changeset
134 the tool will create **a single** history item containing 12 alignment blocks (notice that some columns contain only gaps)::
9071e359b9a3 Uploaded
xuebing
parents:
diff changeset
135
9071e359b9a3 Uploaded
xuebing
parents:
diff changeset
136 ##maf version=1
9071e359b9a3 Uploaded
xuebing
parents:
diff changeset
137 a score=2047408.0
9071e359b9a3 Uploaded
xuebing
parents:
diff changeset
138 s species1.chr1 147984545 85 + 245522847 ATGGCGTCGGCCTCCTCCGGGCCGTCGTCTTCGGTCGGTTTTTCATCCTTTGATCCCGCGGTCCCTTCCTGTACCTTGTCCTCAG
9071e359b9a3 Uploaded
xuebing
parents:
diff changeset
139 s species2.chr1 129723125 85 + 229575298 ATGGCGTCGGCCTCCTCCGGGCCGTCGTCTTCGGTCGGTTTTTCATCCTTTGATCCCGCGGTCCCTTCCTGTACCTCGTCCTCAG
9071e359b9a3 Uploaded
xuebing
parents:
diff changeset
140 s species3.chr3 68255714 76 - 258222147 ATGGCGTCCGCCTCCTCAGGGCCAGCGGC---GGCGGGGTTTTCACCCCTTGATTCCGGGGTCCCTGCCGGTACCGC------AG
9071e359b9a3 Uploaded
xuebing
parents:
diff changeset
141
9071e359b9a3 Uploaded
xuebing
parents:
diff changeset
142 a score=2047408.0
9071e359b9a3 Uploaded
xuebing
parents:
diff changeset
143 s species1.chr1 147984545 83 - 245522847 ATGGCGTCGGCCTCCTCCGGGCCGTCGTCTT--GTCGGTTTTTCATCCTTTGATCCCGCGGTCCCTTCCTGTACCTTGTCCTCAG
9071e359b9a3 Uploaded
xuebing
parents:
diff changeset
144 s species2.chr1 129723125 85 + 229575298 ATGGCGTCGGCCTCCTCCGGGCCGTCGTCTTCGGTCGGTTTTTCATCCTTTGATCCCGCGGTCCCTTCCTGTACCTCGTCCTCAG
9071e359b9a3 Uploaded
xuebing
parents:
diff changeset
145 s species3.chr3 68255714 76 - 258222147 ATGGCGTCCGCCTCCTCAGGGCCAGCGGC---GGCGGGGTTTTCACCCCTTGATTCCGGGGTCCCTGCCGGTACCGC------AG
9071e359b9a3 Uploaded
xuebing
parents:
diff changeset
146
9071e359b9a3 Uploaded
xuebing
parents:
diff changeset
147 a score=2047408.0
9071e359b9a3 Uploaded
xuebing
parents:
diff changeset
148 s species1.chr1 147984645 79 + 245522847 ATGGCGTCGGCCTCCTCCGGGCCGTCGTCTTCGGTCGGTTTTTCATCCTTTGATCCCGCGGTCCCTTCCTGTACCTT------AG
9071e359b9a3 Uploaded
xuebing
parents:
diff changeset
149 s species2.chr1 129723125 85 + 229575298 ATGGCGTCGGCCTCCTCCGGGCCGTCGTCTTCGGTCGGTTTTTCATCCTTTGATCCCGCGGTCCCTTCCTGTACCTCGTCCTCAG
9071e359b9a3 Uploaded
xuebing
parents:
diff changeset
150 s species3.chr3 68255714 76 - 258222147 ATGGCGTCCGCCTCCTCAGGGCCAGCGGC---GGCGGGGTTTTCACCCCTTGATTCCGGGGTCCCTGCCGGTACCGC------AG
9071e359b9a3 Uploaded
xuebing
parents:
diff changeset
151
9071e359b9a3 Uploaded
xuebing
parents:
diff changeset
152 a score=2047408.0
9071e359b9a3 Uploaded
xuebing
parents:
diff changeset
153 s species1.chr1 147984645 79 - 245522847 ATGGCGTCGGCCTCCTCCGGGCCGTCGTC---GGTCGGTTTTTCATCCTTTGATCCCGCGGTCCCTTCCTGTACCTTGTC---AG
9071e359b9a3 Uploaded
xuebing
parents:
diff changeset
154 s species2.chr1 129723125 85 + 229575298 ATGGCGTCGGCCTCCTCCGGGCCGTCGTCTTCGGTCGGTTTTTCATCCTTTGATCCCGCGGTCCCTTCCTGTACCTCGTCCTCAG
9071e359b9a3 Uploaded
xuebing
parents:
diff changeset
155 s species3.chr3 68255714 76 - 258222147 ATGGCGTCCGCCTCCTCAGGGCCAGCGGC---GGCGGGGTTTTCACCCCTTGATTCCGGGGTCCCTGCCGGTACCGC------AG
9071e359b9a3 Uploaded
xuebing
parents:
diff changeset
156
9071e359b9a3 Uploaded
xuebing
parents:
diff changeset
157 a score=2047408.0
9071e359b9a3 Uploaded
xuebing
parents:
diff changeset
158 s species1.chr1 147984545 85 + 245522847 ATGGCGTCGGCCTCCTCCGGGCCGTCGTCTTCGGTCGGTTTTTCATCCTTTGATCCCGCGGTCCCTTCCTGTACCTTGTCCTCAG
9071e359b9a3 Uploaded
xuebing
parents:
diff changeset
159 s species2.chr1 129723125 83 - 229575298 ATGGCGTCGGCCTCCTCCGGGCCGTCGTCT--GGTCGGTTTTTCATCCTTTGATCCCGCGGTCCCTTCCTGTACCTCGTCCTCAG
9071e359b9a3 Uploaded
xuebing
parents:
diff changeset
160 s species3.chr3 68255714 76 - 258222147 ATGGCGTCCGCCTCCTCAGGGCCAGCGGC---GGCGGGGTTTTCACCCCTTGATTCCGGGGTCCCTGCCGGTACCGC------AG
9071e359b9a3 Uploaded
xuebing
parents:
diff changeset
161
9071e359b9a3 Uploaded
xuebing
parents:
diff changeset
162 a score=2047408.0
9071e359b9a3 Uploaded
xuebing
parents:
diff changeset
163 s species1.chr1 147984545 83 - 245522847 ATGGCGTCGGCCTCCTCCGGGCCGTCGTCTT--GTCGGTTTTTCATCCTTTGATCCCGCGGTCCCTTCCTGTACCTTGTCCTCAG
9071e359b9a3 Uploaded
xuebing
parents:
diff changeset
164 s species2.chr1 129723125 83 - 229575298 ATGGCGTCGGCCTCCTCCGGGCCGTCGTCT--GGTCGGTTTTTCATCCTTTGATCCCGCGGTCCCTTCCTGTACCTCGTCCTCAG
9071e359b9a3 Uploaded
xuebing
parents:
diff changeset
165 s species3.chr3 68255714 76 - 258222147 ATGGCGTCCGCCTCCTCAGGGCCAGCGGC---GGCGGGGTTTTCACCCCTTGATTCCGGGGTCCCTGCCGGTACCGC------AG
9071e359b9a3 Uploaded
xuebing
parents:
diff changeset
166
9071e359b9a3 Uploaded
xuebing
parents:
diff changeset
167 a score=2047408.0
9071e359b9a3 Uploaded
xuebing
parents:
diff changeset
168 s species1.chr1 147984645 79 + 245522847 ATGGCGTCGGCCTCCTCCGGGCCGTCGTCTTCGGTCGGTTTTTCATCCTTTGATCCCGCGGTCCCTTCCTGTACCTT------AG
9071e359b9a3 Uploaded
xuebing
parents:
diff changeset
169 s species2.chr1 129723125 83 - 229575298 ATGGCGTCGGCCTCCTCCGGGCCGTCGTCT--GGTCGGTTTTTCATCCTTTGATCCCGCGGTCCCTTCCTGTACCTCGTCCTCAG
9071e359b9a3 Uploaded
xuebing
parents:
diff changeset
170 s species3.chr3 68255714 76 - 258222147 ATGGCGTCCGCCTCCTCAGGGCCAGCGGC---GGCGGGGTTTTCACCCCTTGATTCCGGGGTCCCTGCCGGTACCGC------AG
9071e359b9a3 Uploaded
xuebing
parents:
diff changeset
171
9071e359b9a3 Uploaded
xuebing
parents:
diff changeset
172 a score=2047408.0
9071e359b9a3 Uploaded
xuebing
parents:
diff changeset
173 s species1.chr1 147984645 79 - 245522847 ATGGCGTCGGCCTCCTCCGGGCCGTCGTC---GGTCGGTTTTTCATCCTTTGATCCCGCGGTCCCTTCCTGTACCTTGTC---AG
9071e359b9a3 Uploaded
xuebing
parents:
diff changeset
174 s species2.chr1 129723125 83 - 229575298 ATGGCGTCGGCCTCCTCCGGGCCGTCGTCT--GGTCGGTTTTTCATCCTTTGATCCCGCGGTCCCTTCCTGTACCTCGTCCTCAG
9071e359b9a3 Uploaded
xuebing
parents:
diff changeset
175 s species3.chr3 68255714 76 - 258222147 ATGGCGTCCGCCTCCTCAGGGCCAGCGGC---GGCGGGGTTTTCACCCCTTGATTCCGGGGTCCCTGCCGGTACCGC------AG
9071e359b9a3 Uploaded
xuebing
parents:
diff changeset
176
9071e359b9a3 Uploaded
xuebing
parents:
diff changeset
177 a score=2047408.0
9071e359b9a3 Uploaded
xuebing
parents:
diff changeset
178 s species1.chr1 147984545 85 + 245522847 ATGGCGTCGGCCTCCTCCGGGCCGTCGTCTTCGGTCGGTTTTTCATCCTTTGATCCCGCGGTCCCTTCCTGTACCTTGTCCTCAG
9071e359b9a3 Uploaded
xuebing
parents:
diff changeset
179 s species2.chr1 129723925 79 + 229575298 ATGGCGTCGGCCTCCTCCGGGCCGTCGTCTTCGGTCGGTTTTTCATCCTTTGATCCCGCGGTCCCTTCCTGTACCTC------AG
9071e359b9a3 Uploaded
xuebing
parents:
diff changeset
180 s species3.chr3 68255714 76 - 258222147 ATGGCGTCCGCCTCCTCAGGGCCAGCGGC---GGCGGGGTTTTCACCCCTTGATTCCGGGGTCCCTGCCGGTACCGC------AG
9071e359b9a3 Uploaded
xuebing
parents:
diff changeset
181
9071e359b9a3 Uploaded
xuebing
parents:
diff changeset
182 a score=2047408.0
9071e359b9a3 Uploaded
xuebing
parents:
diff changeset
183 s species1.chr1 147984545 83 - 245522847 ATGGCGTCGGCCTCCTCCGGGCCGTCGTCTT--GTCGGTTTTTCATCCTTTGATCCCGCGGTCCCTTCCTGTACCTTGTCCTCAG
9071e359b9a3 Uploaded
xuebing
parents:
diff changeset
184 s species2.chr1 129723925 79 + 229575298 ATGGCGTCGGCCTCCTCCGGGCCGTCGTCTTCGGTCGGTTTTTCATCCTTTGATCCCGCGGTCCCTTCCTGTACCTC------AG
9071e359b9a3 Uploaded
xuebing
parents:
diff changeset
185 s species3.chr3 68255714 76 - 258222147 ATGGCGTCCGCCTCCTCAGGGCCAGCGGC---GGCGGGGTTTTCACCCCTTGATTCCGGGGTCCCTGCCGGTACCGC------AG
9071e359b9a3 Uploaded
xuebing
parents:
diff changeset
186
9071e359b9a3 Uploaded
xuebing
parents:
diff changeset
187 a score=2047408.0
9071e359b9a3 Uploaded
xuebing
parents:
diff changeset
188 s species1.chr1 147984645 79 + 245522847 ATGGCGTCGGCCTCCTCCGGGCCGTCGTCTTCGGTCGGTTTTTCATCCTTTGATCCCGCGGTCCCTTCCTGTACCTT------AG
9071e359b9a3 Uploaded
xuebing
parents:
diff changeset
189 s species2.chr1 129723925 79 + 229575298 ATGGCGTCGGCCTCCTCCGGGCCGTCGTCTTCGGTCGGTTTTTCATCCTTTGATCCCGCGGTCCCTTCCTGTACCTC------AG
9071e359b9a3 Uploaded
xuebing
parents:
diff changeset
190 s species3.chr3 68255714 76 - 258222147 ATGGCGTCCGCCTCCTCAGGGCCAGCGGC---GGCGGGGTTTTCACCCCTTGATTCCGGGGTCCCTGCCGGTACCGC------AG
9071e359b9a3 Uploaded
xuebing
parents:
diff changeset
191
9071e359b9a3 Uploaded
xuebing
parents:
diff changeset
192 a score=2047408.0
9071e359b9a3 Uploaded
xuebing
parents:
diff changeset
193 s species1.chr1 147984645 79 - 245522847 ATGGCGTCGGCCTCCTCCGGGCCGTCGTC---GGTCGGTTTTTCATCCTTTGATCCCGCGGTCCCTTCCTGTACCTTGTC---AG
9071e359b9a3 Uploaded
xuebing
parents:
diff changeset
194 s species2.chr1 129723925 79 + 229575298 ATGGCGTCGGCCTCCTCCGGGCCGTCGTCTTCGGTCGGTTTTTCATCCTTTGATCCCGCGGTCCCTTCCTGTACCTC------AG
9071e359b9a3 Uploaded
xuebing
parents:
diff changeset
195 s species3.chr3 68255714 76 - 258222147 ATGGCGTCCGCCTCCTCAGGGCCAGCGGC---GGCGGGGTTTTCACCCCTTGATTCCGGGGTCCCTGCCGGTACCGC------AG
9071e359b9a3 Uploaded
xuebing
parents:
diff changeset
196
9071e359b9a3 Uploaded
xuebing
parents:
diff changeset
197 -------
9071e359b9a3 Uploaded
xuebing
parents:
diff changeset
198
9071e359b9a3 Uploaded
xuebing
parents:
diff changeset
199 .. class:: infomark
9071e359b9a3 Uploaded
xuebing
parents:
diff changeset
200
9071e359b9a3 Uploaded
xuebing
parents:
diff changeset
201 **About formats**
9071e359b9a3 Uploaded
xuebing
parents:
diff changeset
202
9071e359b9a3 Uploaded
xuebing
parents:
diff changeset
203 **MAF format** multiple alignment format file. This format stores multiple alignments at the DNA level between entire genomes.
9071e359b9a3 Uploaded
xuebing
parents:
diff changeset
204
9071e359b9a3 Uploaded
xuebing
parents:
diff changeset
205 - The .maf format is line-oriented. Each multiple alignment ends with a blank line.
9071e359b9a3 Uploaded
xuebing
parents:
diff changeset
206 - Each sequence in an alignment is on a single line.
9071e359b9a3 Uploaded
xuebing
parents:
diff changeset
207 - Lines starting with # are considered to be comments.
9071e359b9a3 Uploaded
xuebing
parents:
diff changeset
208 - Each multiple alignment is in a separate paragraph that begins with an "a" line and contains an "s" line for each sequence in the multiple alignment.
9071e359b9a3 Uploaded
xuebing
parents:
diff changeset
209 - Some MAF files may contain two optional line types:
9071e359b9a3 Uploaded
xuebing
parents:
diff changeset
210
9071e359b9a3 Uploaded
xuebing
parents:
diff changeset
211 - An "i" line containing information about what is in the aligned species DNA before and after the immediately preceding "s" line;
9071e359b9a3 Uploaded
xuebing
parents:
diff changeset
212 - An "e" line containing information about the size of the gap between the alignments that span the current block.
9071e359b9a3 Uploaded
xuebing
parents:
diff changeset
213
9071e359b9a3 Uploaded
xuebing
parents:
diff changeset
214 ------
9071e359b9a3 Uploaded
xuebing
parents:
diff changeset
215
9071e359b9a3 Uploaded
xuebing
parents:
diff changeset
216 **Citation**
9071e359b9a3 Uploaded
xuebing
parents:
diff changeset
217
9071e359b9a3 Uploaded
xuebing
parents:
diff changeset
218 If you use this tool, please cite `Blankenberg D, Taylor J, Nekrutenko A; The Galaxy Team. Making whole genome multiple alignments usable for biologists. Bioinformatics. 2011 Sep 1;27(17):2426-2428. &lt;http://www.ncbi.nlm.nih.gov/pubmed/21775304&gt;`_
9071e359b9a3 Uploaded
xuebing
parents:
diff changeset
219
9071e359b9a3 Uploaded
xuebing
parents:
diff changeset
220
9071e359b9a3 Uploaded
xuebing
parents:
diff changeset
221 </help>
9071e359b9a3 Uploaded
xuebing
parents:
diff changeset
222 </tool>
9071e359b9a3 Uploaded
xuebing
parents:
diff changeset
223