Mercurial > repos > devteam > blast_datatypes

annotate tools/ncbi_blast_plus/blastxml_to_tabular.xml @ 2:45ba7c750bc8 draft

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This update should have no functional effect. Renamed files (since xml.py will be inaccurate once BLAST databases are added in future update).
author peterjc
date Thu, 20 Sep 2012 10:12:43 -0400
parents
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
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2
45ba7c750bc8 This update should have no functional effect. Renamed files (since xml.py will be inaccurate once BLAST databases are added in future update).
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1 <tool id="blastxml_to_tabular" name="BLAST XML to tabular" version="0.0.8">
45ba7c750bc8 This update should have no functional effect. Renamed files (since xml.py will be inaccurate once BLAST databases are added in future update).
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2 <description>Convert BLAST XML output to tabular</description>
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3 <command interpreter="python">
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4 blastxml_to_tabular.py $blastxml_file $tabular_file $out_format
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5 </command>
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6 <inputs>
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7 <param name="blastxml_file" type="data" format="blastxml" label="BLAST results as XML"/>
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8 <param name="out_format" type="select" label="Output format">
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9 <option value="std" selected="True">Tabular (standard 12 columns)</option>
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10 <option value="ext">Tabular (extended 24 columns)</option>
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11 </param>
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12 </inputs>
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13 <outputs>
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14 <data name="tabular_file" format="tabular" label="BLAST results as tabular" />
45ba7c750bc8 This update should have no functional effect. Renamed files (since xml.py will be inaccurate once BLAST databases are added in future update).
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15 </outputs>
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16 <requirements>
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17 </requirements>
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18 <tests>
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19 <test>
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20 <param name="blastxml_file" value="blastp_four_human_vs_rhodopsin.xml" ftype="blastxml" />
45ba7c750bc8 This update should have no functional effect. Renamed files (since xml.py will be inaccurate once BLAST databases are added in future update).
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21 <param name="out_format" value="std" />
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22 <!-- Note this has some white space differences from the actual blastp output blast_four_human_vs_rhodopsin.tabluar -->
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23 <output name="tabular_file" file="blastp_four_human_vs_rhodopsin_converted.tabular" ftype="tabular" />
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24 </test>
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25 <test>
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26 <param name="blastxml_file" value="blastp_four_human_vs_rhodopsin.xml" ftype="blastxml" />
45ba7c750bc8 This update should have no functional effect. Renamed files (since xml.py will be inaccurate once BLAST databases are added in future update).
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27 <param name="out_format" value="ext" />
45ba7c750bc8 This update should have no functional effect. Renamed files (since xml.py will be inaccurate once BLAST databases are added in future update).
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28 <!-- Note this has some white space differences from the actual blastp output blast_four_human_vs_rhodopsin_22c.tabluar -->
45ba7c750bc8 This update should have no functional effect. Renamed files (since xml.py will be inaccurate once BLAST databases are added in future update).
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29 <output name="tabular_file" file="blastp_four_human_vs_rhodopsin_converted_ext.tabular" ftype="tabular" />
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30 </test>
45ba7c750bc8 This update should have no functional effect. Renamed files (since xml.py will be inaccurate once BLAST databases are added in future update).
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31 <test>
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32 <param name="blastxml_file" value="blastp_sample.xml" ftype="blastxml" />
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33 <param name="out_format" value="std" />
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34 <!-- Note this has some white space differences from the actual blastp output -->
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35 <output name="tabular_file" file="blastp_sample_converted.tabular" ftype="tabular" />
45ba7c750bc8 This update should have no functional effect. Renamed files (since xml.py will be inaccurate once BLAST databases are added in future update).
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36 </test>
45ba7c750bc8 This update should have no functional effect. Renamed files (since xml.py will be inaccurate once BLAST databases are added in future update).
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37 <test>
45ba7c750bc8 This update should have no functional effect. Renamed files (since xml.py will be inaccurate once BLAST databases are added in future update).
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38 <param name="blastxml_file" value="blastx_rhodopsin_vs_four_human.xml" ftype="blastxml" />
45ba7c750bc8 This update should have no functional effect. Renamed files (since xml.py will be inaccurate once BLAST databases are added in future update).
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39 <param name="out_format" value="std" />
45ba7c750bc8 This update should have no functional effect. Renamed files (since xml.py will be inaccurate once BLAST databases are added in future update).
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40 <!-- Note this has some white space differences from the actual blastx output -->
45ba7c750bc8 This update should have no functional effect. Renamed files (since xml.py will be inaccurate once BLAST databases are added in future update).
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41 <output name="tabular_file" file="blastx_rhodopsin_vs_four_human_converted.tabular" ftype="tabular" />
45ba7c750bc8 This update should have no functional effect. Renamed files (since xml.py will be inaccurate once BLAST databases are added in future update).
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42 </test>
45ba7c750bc8 This update should have no functional effect. Renamed files (since xml.py will be inaccurate once BLAST databases are added in future update).
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43 <test>
45ba7c750bc8 This update should have no functional effect. Renamed files (since xml.py will be inaccurate once BLAST databases are added in future update).
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44 <param name="blastxml_file" value="blastx_rhodopsin_vs_four_human.xml" ftype="blastxml" />
45ba7c750bc8 This update should have no functional effect. Renamed files (since xml.py will be inaccurate once BLAST databases are added in future update).
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45 <param name="out_format" value="ext" />
45ba7c750bc8 This update should have no functional effect. Renamed files (since xml.py will be inaccurate once BLAST databases are added in future update).
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46 <!-- Note this has some white space and XXXX masking differences from the actual blastx output -->
45ba7c750bc8 This update should have no functional effect. Renamed files (since xml.py will be inaccurate once BLAST databases are added in future update).
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47 <output name="tabular_file" file="blastx_rhodopsin_vs_four_human_converted_ext.tabular" ftype="tabular" />
45ba7c750bc8 This update should have no functional effect. Renamed files (since xml.py will be inaccurate once BLAST databases are added in future update).
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48 </test>
45ba7c750bc8 This update should have no functional effect. Renamed files (since xml.py will be inaccurate once BLAST databases are added in future update).
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49 <test>
45ba7c750bc8 This update should have no functional effect. Renamed files (since xml.py will be inaccurate once BLAST databases are added in future update).
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50 <param name="blastxml_file" value="blastx_sample.xml" ftype="blastxml" />
45ba7c750bc8 This update should have no functional effect. Renamed files (since xml.py will be inaccurate once BLAST databases are added in future update).
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51 <param name="out_format" value="std" />
45ba7c750bc8 This update should have no functional effect. Renamed files (since xml.py will be inaccurate once BLAST databases are added in future update).
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52 <!-- Note this has some white space differences from the actual blastx output -->
45ba7c750bc8 This update should have no functional effect. Renamed files (since xml.py will be inaccurate once BLAST databases are added in future update).
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53 <output name="tabular_file" file="blastx_sample_converted.tabular" ftype="tabular" />
45ba7c750bc8 This update should have no functional effect. Renamed files (since xml.py will be inaccurate once BLAST databases are added in future update).
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54 </test>
45ba7c750bc8 This update should have no functional effect. Renamed files (since xml.py will be inaccurate once BLAST databases are added in future update).
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55 <test>
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56 <param name="blastxml_file" value="blastp_human_vs_pdb_seg_no.xml" ftype="blastxml" />
45ba7c750bc8 This update should have no functional effect. Renamed files (since xml.py will be inaccurate once BLAST databases are added in future update).
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57 <param name="out_format" value="std" />
45ba7c750bc8 This update should have no functional effect. Renamed files (since xml.py will be inaccurate once BLAST databases are added in future update).
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58 <!-- Note this has some white space differences from the actual blastp output -->
45ba7c750bc8 This update should have no functional effect. Renamed files (since xml.py will be inaccurate once BLAST databases are added in future update).
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59 <output name="tabular_file" file="blastp_human_vs_pdb_seg_no_converted_std.tabular" ftype="tabular" />
45ba7c750bc8 This update should have no functional effect. Renamed files (since xml.py will be inaccurate once BLAST databases are added in future update).
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60 </test>
45ba7c750bc8 This update should have no functional effect. Renamed files (since xml.py will be inaccurate once BLAST databases are added in future update).
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61 <test>
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62 <param name="blastxml_file" value="blastp_human_vs_pdb_seg_no.xml" ftype="blastxml" />
45ba7c750bc8 This update should have no functional effect. Renamed files (since xml.py will be inaccurate once BLAST databases are added in future update).
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63 <param name="out_format" value="ext" />
45ba7c750bc8 This update should have no functional effect. Renamed files (since xml.py will be inaccurate once BLAST databases are added in future update).
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64 <!-- Note this has some white space differences from the actual blastp output -->
45ba7c750bc8 This update should have no functional effect. Renamed files (since xml.py will be inaccurate once BLAST databases are added in future update).
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65 <output name="tabular_file" file="blastp_human_vs_pdb_seg_no_converted_ext.tabular" ftype="tabular" />
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66 </test>
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67 </tests>
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68 <help>
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69
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70 **What it does**
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71
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72 NCBI BLAST+ (and the older NCBI 'legacy' BLAST) can output in a range of
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73 formats including tabular and a more detailed XML format. A complex workflow
45ba7c750bc8 This update should have no functional effect. Renamed files (since xml.py will be inaccurate once BLAST databases are added in future update).
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74 may need both the XML and the tabular output - but running BLAST twice is
45ba7c750bc8 This update should have no functional effect. Renamed files (since xml.py will be inaccurate once BLAST databases are added in future update).
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75 slow and wasteful.
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76
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77 This tool takes the BLAST XML output and by default converts it into the
45ba7c750bc8 This update should have no functional effect. Renamed files (since xml.py will be inaccurate once BLAST databases are added in future update).
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78 standard 12 column tabular equivalent:
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79
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80 ====== ========= ============================================
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81 Column NCBI name Description
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82 ------ --------- --------------------------------------------
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83 1 qseqid Query Seq-id (ID of your sequence)
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84 2 sseqid Subject Seq-id (ID of the database hit)
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85 3 pident Percentage of identical matches
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86 4 length Alignment length
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87 5 mismatch Number of mismatches
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88 6 gapopen Number of gap openings
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89 7 qstart Start of alignment in query
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90 8 qend End of alignment in query
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91 9 sstart Start of alignment in subject (database hit)
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92 10 send End of alignment in subject (database hit)
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93 11 evalue Expectation value (E-value)
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94 12 bitscore Bit score
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95 ====== ========= ============================================
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96
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97 The BLAST+ tools can optionally output additional columns of information,
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98 but this takes longer to calculate. Most (but not all) of these columns are
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99 included by selecting the extended tabular output. The extra columns are
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100 included *after* the standard 12 columns. This is so that you can write
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101 workflow filtering steps that accept either the 12 or 22 column tabular
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102 BLAST output.
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103
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104 ====== ============= ===========================================
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105 Column NCBI name Description
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106 ------ ------------- -------------------------------------------
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107 13 sallseqid All subject Seq-id(s), separated by a ';'
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108 14 score Raw score
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109 15 nident Number of identical matches
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110 16 positive Number of positive-scoring matches
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111 17 gaps Total number of gaps
45ba7c750bc8 This update should have no functional effect. Renamed files (since xml.py will be inaccurate once BLAST databases are added in future update).
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112 18 ppos Percentage of positive-scoring matches
45ba7c750bc8 This update should have no functional effect. Renamed files (since xml.py will be inaccurate once BLAST databases are added in future update).
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113 19 qframe Query frame
45ba7c750bc8 This update should have no functional effect. Renamed files (since xml.py will be inaccurate once BLAST databases are added in future update).
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114 20 sframe Subject frame
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115 21 qseq Aligned part of query sequence
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116 22 sseq Aligned part of subject sequence
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117 23 qlen Query sequence length
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118 24 slen Subject sequence length
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119 ====== ============= ===========================================
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120
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121 Beware that the XML file (and thus the conversion) and the tabular output
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peterjc
parents:
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122 direct from BLAST+ may differ in the presence of XXXX masking on regions
45ba7c750bc8 This update should have no functional effect. Renamed files (since xml.py will be inaccurate once BLAST databases are added in future update).
peterjc
parents:
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123 low complexity (columns 21 and 22), and thus also calculated figures like
45ba7c750bc8 This update should have no functional effect. Renamed files (since xml.py will be inaccurate once BLAST databases are added in future update).
peterjc
parents:
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124 the percentage idenity (column 3).
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125
45ba7c750bc8 This update should have no functional effect. Renamed files (since xml.py will be inaccurate once BLAST databases are added in future update).
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126 </help>
45ba7c750bc8 This update should have no functional effect. Renamed files (since xml.py will be inaccurate once BLAST databases are added in future update).
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127 </tool>