/tools/maf/maf_to_fasta.xml

https://bitbucket.org/cistrome/cistrome-harvard/ · XML · 199 lines · 156 code · 43 blank · 0 comment · 0 complexity · 6070ce5f2311016787b776b577d7eff0 MD5 · raw file 

    

  1. <tool id="MAF_To_Fasta1" name="MAF to FASTA" version="1.0.1">

    2. 

  2.   <description>Converts a MAF formatted file to FASTA format</description>

    3. 

  3.   <command interpreter="python">

    4. 

  4.     #if $fasta_target_type.fasta_type == "multiple" #maf_to_fasta_multiple_sets.py $input1 $out_file1 $fasta_target_type.species $fasta_target_type.complete_blocks

    5. 

  5.     #else                                           #maf_to_fasta_concat.py $fasta_target_type.species $input1 $out_file1

    6. 

  6.     #end if#

    7. 

  7.   </command>

    8. 

  8.   <inputs>

    9. 

  9.     <param format="maf" name="input1" type="data" label="MAF file to convert"/>

    10. 

  10.     <conditional name="fasta_target_type">

    11. 

  11.       <param name="fasta_type" type="select" label="Type of FASTA Output">

    12. 

  12.         <option value="multiple" selected="true">Multiple Blocks</option>

    13. 

  13.         <option value="concatenated">One Sequence per Species</option>

    14. 

  14.       </param>

    15. 

  15.       <when value="multiple">

    16. 

  16.         <param name="species" type="select" label="Select species" display="checkboxes" multiple="true" help="checked taxa will be included in the output">

    17. 

  17.           <options>

    18. 

  18.             <filter type="data_meta" ref="input1" key="species" />

    19. 

  19.           </options>

    20. 

  20.         </param>

    21. 

  21. 	    <param name="complete_blocks" type="select" label="Choose to">

    22. 

  22. 	      <option value="partial_allowed">include blocks with missing species</option>

    23. 

  23. 	      <option value="partial_disallowed">exclude blocks with missing species</option>

    24. 

  24. 	    </param>

    25. 

  25.       </when>

    26. 

  26.       <when value="concatenated">

    27. 

  27.         <param name="species" type="select" label="Species to extract" display="checkboxes" multiple="true">

    28. 

  28.           <options>

    29. 

  29.             <filter type="data_meta" ref="input1" key="species" />

    30. 

  30.           </options>

    31. 

  31.         </param>

    32. 

  32.       </when>

    33. 

  33.     </conditional>

    34. 

  34.   </inputs>

    35. 

  35.   <outputs>

    36. 

  36.     <data format="fasta" name="out_file1" />

    37. 

  37.   </outputs>

    38. 

  38.   <tests>

    39. 

  39.     <test>

    40. 

  40.       <param name="input1" value="3.maf" ftype="maf"/>

    41. 

  41.       <param name="fasta_type" value="concatenated"/>

    42. 

  42.       <param name="species" value="canFam1"/>

    43. 

  43.       <output name="out_file1" file="cf_maf2fasta_concat.dat" ftype="fasta"/>

    44. 

  44.     </test>

    45. 

  45.     <test>

    46. 

  46.       <param name="input1" value="4.maf" ftype="maf"/>

    47. 

  47.       <param name="fasta_type" value="multiple"/>

    48. 

  48.       <param name="species" value="hg17,panTro1,rheMac2,rn3,mm7,canFam2,bosTau2,dasNov1"/>

    49. 

  49.       <param name="complete_blocks" value="partial_allowed"/>

    50. 

  50.       <output name="out_file1" file="cf_maf2fasta_new.dat" ftype="fasta"/>

    51. 

  51.     </test>

    52. 

  52.   </tests>

    53. 

  53.   <help>

    54. 

  54. 

    55. 

  55. **Types of MAF to FASTA conversion**

    56. 

  56. 

    57. 

  57.  * **Multiple Blocks** converts a single MAF block to a single FASTA block. For example, if you have 6 MAF blocks, they will be converted to 6 FASTA blocks.

    58. 

  58.  * **One Sequence per Species** converts MAF blocks to a single aggregated FASTA block. For example, if you have 6 MAF blocks, they will be converted and concatenated into a single FASTA block.

    59. 

  59. 

    60. 

  60. -------

    61. 

  61. 

    62. 

  62. **What it does**

    63. 

  63. 

    64. 

  64. This tool converts MAF blocks to FASTA format and concatenates them into a single FASTA block or outputs multiple FASTA blocks separated by empty lines.

    65. 

  65. 

    66. 

  66. The interface for this tool contains two pages (steps): 

    67. 

  67. 

    68. 

  68.  * **Step 1 of 2**. Choose multiple alignments from history to be converted to FASTA format.

    69. 

  69.  * **Step 2 of 2**. Choose the type of output as well as the species from the alignment to be included in the output.

    70. 

  70.  

    71. 

  71.    Multiple Block output has additional options:

    72. 

  72.    

    73. 

  73.    *  **Choose species** - the tool reads the alignment provided during Step 1 and generates a list of species contained within that alignment. Using checkboxes you can specify taxa to be included in the output (all species are selected by default). 

    74. 

  74.    *  **Choose to include/exclude blocks with missing species** - if an alignment block does not contain any one of the species you selected within **Choose species** menu and this option is set to **exclude blocks with missing species**, then such a block **will not** be included in the output (see **Example 2** below).  For example, if you want to extract human, mouse, and rat from a series of alignments and one of the blocks does not contain mouse sequence, then this block will not be converted to FASTA and will not be returned.

    75. 

  75. 

    76. 

  76. 

    77. 

  77. -----

    78. 

  78. 

    79. 

  79. **Example 1**:

    80. 

  80. 

    81. 

  81. In the concatenated approach, the following alignment::

    82. 

  82. 

    83. 

  83.   ##maf version=1

    84. 

  84.   a score=68686.000000

    85. 

  85.   s hg18.chr20     56827368 75 +  62435964 GACAGGGTGCATCTGGGAGGG---CCTGCCGGGCCTTTA-TTCAACACTAGATACGCCCCATCTCCAATTCTAATGGAC- 

    86. 

  86.   s panTro2.chr20  56528685 75 +  62293572 GACAGGGTGCATCTGAGAGGG---CCTGCCAGGCCTTTA-TTCAACACTAGATACGCCCCATCTCCAATTCTAATGGAC- 

    87. 

  87.   s rheMac2.chr10  89144112 69 -  94855758 GACAGGGTGCATCTGAGAGGG---CCTGCTGGGCCTTTG-TTCAAAACTAGATATGCCCCAACTCCAATTCTA------- 

    88. 

  88.   s mm8.chr2      173910832 61 + 181976762 AGAAGGATCCACCT------------TGCTGGGCCTCTGCTCCAGCAAGACCCACCTCCCAACTCAAATGCCC------- 

    89. 

  89.   s canFam2.chr24  46551822 67 +  50763139 CG------GCGTCTGTAAGGGGCCACCGCCCGGCCTGTG-CTCAAAGCTACAAATGACTCAACTCCCAACCGA------C 

    90. 

  90. 

    91. 

  91.   a score=10289.000000

    92. 

  92.   s hg18.chr20    56827443 37 + 62435964 ATGTGCAGAAAATGTGATACAGAAACCTGCAGAGCAG 

    93. 

  93.   s panTro2.chr20 56528760 37 + 62293572 ATGTGCAGAAAATGTGATACAGAAACCTGCAGAGCAG 

    94. 

  94.   s rheMac2.chr10 89144181 37 - 94855758 ATGTGCGGAAAATGTGATACAGAAACCTGCAGAGCAG 

    95. 

  95. 

    96. 

  96. will be converted to (**note** that because mm8 (mouse) and canFam2 (dog) are absent from the second block, they are replaced with gaps after concatenation)::

    97. 

  97. 

    98. 

  98.   &gt;canFam2

    99. 

  99.   CG------GCGTCTGTAAGGGGCCACCGCCCGGCCTGTG-CTCAAAGCTACAAATGACTCAACTCCCAACCGA------C-------------------------------------

    100. 

  100.   &gt;hg18

    101. 

  101.   GACAGGGTGCATCTGGGAGGG---CCTGCCGGGCCTTTA-TTCAACACTAGATACGCCCCATCTCCAATTCTAATGGAC-ATGTGCAGAAAATGTGATACAGAAACCTGCAGAGCAG

    102. 

  102.   &gt;mm8

    103. 

  103.   AGAAGGATCCACCT------------TGCTGGGCCTCTGCTCCAGCAAGACCCACCTCCCAACTCAAATGCCC--------------------------------------------

    104. 

  104.   &gt;panTro2

    105. 

  105.   GACAGGGTGCATCTGAGAGGG---CCTGCCAGGCCTTTA-TTCAACACTAGATACGCCCCATCTCCAATTCTAATGGAC-ATGTGCAGAAAATGTGATACAGAAACCTGCAGAGCAG

    106. 

  106.   &gt;rheMac2

    107. 

  107.   GACAGGGTGCATCTGAGAGGG---CCTGCTGGGCCTTTG-TTCAAAACTAGATATGCCCCAACTCCAATTCTA-------ATGTGCGGAAAATGTGATACAGAAACCTGCAGAGCAG

    108. 

  108. 

    109. 

  109. ------

    110. 

  110. 

    111. 

  111. **Example 2a**: Multiple Block Approach **Include all species** and **include blocks with missing species**:

    112. 

  112. 

    113. 

  113. The following alignment::

    114. 

  114. 

    115. 

  115.   ##maf version=1

    116. 

  116.   a score=68686.000000

    117. 

  117.   s hg18.chr20     56827368 75 +  62435964 GACAGGGTGCATCTGGGAGGG---CCTGCCGGGCCTTTA-TTCAACACTAGATACGCCCCATCTCCAATTCTAATGGAC- 

    118. 

  118.   s panTro2.chr20  56528685 75 +  62293572 GACAGGGTGCATCTGAGAGGG---CCTGCCAGGCCTTTA-TTCAACACTAGATACGCCCCATCTCCAATTCTAATGGAC- 

    119. 

  119.   s rheMac2.chr10  89144112 69 -  94855758 GACAGGGTGCATCTGAGAGGG---CCTGCTGGGCCTTTG-TTCAAAACTAGATATGCCCCAACTCCAATTCTA------- 

    120. 

  120.   s mm8.chr2      173910832 61 + 181976762 AGAAGGATCCACCT------------TGCTGGGCCTCTGCTCCAGCAAGACCCACCTCCCAACTCAAATGCCC------- 

    121. 

  121.   s canFam2.chr24  46551822 67 +  50763139 CG------GCGTCTGTAAGGGGCCACCGCCCGGCCTGTG-CTCAAAGCTACAAATGACTCAACTCCCAACCGA------C 

    122. 

  122. 

    123. 

  123.   a score=10289.000000

    124. 

  124.   s hg18.chr20    56827443 37 + 62435964 ATGTGCAGAAAATGTGATACAGAAACCTGCAGAGCAG 

    125. 

  125.   s panTro2.chr20 56528760 37 + 62293572 ATGTGCAGAAAATGTGATACAGAAACCTGCAGAGCAG 

    126. 

  126.   s rheMac2.chr10 89144181 37 - 94855758 ATGTGCGGAAAATGTGATACAGAAACCTGCAGAGCAG 

    127. 

  127. 

    128. 

  128. will be converted to::

    129. 

  129. 

    130. 

  130.   &gt;hg18.chr20(+):56827368-56827443|hg18_0

    131. 

  131.   GACAGGGTGCATCTGGGAGGG---CCTGCCGGGCCTTTA-TTCAACACTAGATACGCCCCATCTCCAATTCTAATGGAC-

    132. 

  132.   &gt;panTro2.chr20(+):56528685-56528760|panTro2_0

    133. 

  133.   GACAGGGTGCATCTGAGAGGG---CCTGCCAGGCCTTTA-TTCAACACTAGATACGCCCCATCTCCAATTCTAATGGAC-

    134. 

  134.   &gt;rheMac2.chr10(-):89144112-89144181|rheMac2_0

    135. 

  135.   GACAGGGTGCATCTGAGAGGG---CCTGCTGGGCCTTTG-TTCAAAACTAGATATGCCCCAACTCCAATTCTA-------

    136. 

  136.   &gt;mm8.chr2(+):173910832-173910893|mm8_0

    137. 

  137.   AGAAGGATCCACCT------------TGCTGGGCCTCTGCTCCAGCAAGACCCACCTCCCAACTCAAATGCCC-------

    138. 

  138.   &gt;canFam2.chr24(+):46551822-46551889|canFam2_0

    139. 

  139.   CG------GCGTCTGTAAGGGGCCACCGCCCGGCCTGTG-CTCAAAGCTACAAATGACTCAACTCCCAACCGA------C

    140. 

  140. 

    141. 

  141.   &gt;hg18.chr20(+):56827443-56827480|hg18_1

    142. 

  142.   ATGTGCAGAAAATGTGATACAGAAACCTGCAGAGCAG

    143. 

  143.   &gt;panTro2.chr20(+):56528760-56528797|panTro2_1

    144. 

  144.   ATGTGCAGAAAATGTGATACAGAAACCTGCAGAGCAG

    145. 

  145.   &gt;rheMac2.chr10(-):89144181-89144218|rheMac2_1

    146. 

  146.   ATGTGCGGAAAATGTGATACAGAAACCTGCAGAGCAG

    147. 

  147. 

    148. 

  148. -----

    149. 

  149. 

    150. 

  150. **Example 2b**: Multiple Block Approach **Include hg18 and mm8** and **exclude blocks with missing species**:

    151. 

  151. 

    152. 

  152. The following alignment::

    153. 

  153. 

    154. 

  154.   ##maf version=1

    155. 

  155.   a score=68686.000000

    156. 

  156.   s hg18.chr20     56827368 75 +  62435964 GACAGGGTGCATCTGGGAGGG---CCTGCCGGGCCTTTA-TTCAACACTAGATACGCCCCATCTCCAATTCTAATGGAC- 

    157. 

  157.   s panTro2.chr20  56528685 75 +  62293572 GACAGGGTGCATCTGAGAGGG---CCTGCCAGGCCTTTA-TTCAACACTAGATACGCCCCATCTCCAATTCTAATGGAC- 

    158. 

  158.   s rheMac2.chr10  89144112 69 -  94855758 GACAGGGTGCATCTGAGAGGG---CCTGCTGGGCCTTTG-TTCAAAACTAGATATGCCCCAACTCCAATTCTA------- 

    159. 

  159.   s mm8.chr2      173910832 61 + 181976762 AGAAGGATCCACCT------------TGCTGGGCCTCTGCTCCAGCAAGACCCACCTCCCAACTCAAATGCCC------- 

    160. 

  160.   s canFam2.chr24  46551822 67 +  50763139 CG------GCGTCTGTAAGGGGCCACCGCCCGGCCTGTG-CTCAAAGCTACAAATGACTCAACTCCCAACCGA------C 

    161. 

  161. 

    162. 

  162.   a score=10289.000000

    163. 

  163.   s hg18.chr20    56827443 37 + 62435964 ATGTGCAGAAAATGTGATACAGAAACCTGCAGAGCAG 

    164. 

  164.   s panTro2.chr20 56528760 37 + 62293572 ATGTGCAGAAAATGTGATACAGAAACCTGCAGAGCAG 

    165. 

  165.   s rheMac2.chr10 89144181 37 - 94855758 ATGTGCGGAAAATGTGATACAGAAACCTGCAGAGCAG 

    166. 

  166. 

    167. 

  167. will be converted to (**note** that the second MAF block, which does not have mm8, is not included in the output)::

    168. 

  168. 

    169. 

  169.   &gt;hg18.chr20(+):56827368-56827443|hg18_0

    170. 

  170.   GACAGGGTGCATCTGGGAGGGCCTGCCGGGCCTTTA-TTCAACACTAGATACGCCCCATCTCCAATTCTAATGGAC

    171. 

  171.   &gt;mm8.chr2(+):173910832-173910893|mm8_0

    172. 

  172.   AGAAGGATCCACCT---------TGCTGGGCCTCTGCTCCAGCAAGACCCACCTCCCAACTCAAATGCCC------

    173. 

  173. 

    174. 

  174. ------

    175. 

  175. 

    176. 

  176. .. class:: infomark

    177. 

  177. 

    178. 

  178. **About formats**

    179. 

  179. 

    180. 

  180.  **MAF format** multiple alignment format file. This format stores multiple alignments at the DNA level between entire genomes. 

    181. 

  181. 

    182. 

  182.  - The .maf format is line-oriented. Each multiple alignment ends with a blank line.

    183. 

  183.  - Each sequence in an alignment is on a single line.

    184. 

  184.  - Lines starting with # are considered to be comments.

    185. 

  185.  - 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.

    186. 

  186.  - Some MAF files may contain two optional line types: 

    187. 

  187. 

    188. 

  188.    - An "i" line containing information about what is in the aligned species DNA before and after the immediately preceding "s" line; 

    189. 

  189.    - An "e" line containing information about the size of the gap between the alignments that span the current block.

    190. 

  190. 

    191. 

  191. ------

    192. 

  192. 

    193. 

  193. **Citation**

    194. 

  194. 

    195. 

  195. 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;`_

    196. 

  196. 

    197. 

  197. 

    198. 

  198.   </help>

    199. 

  199. </tool>
    200.