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Difference between revisions of "GBrowse syn Scripts"
From GMOD
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!description | !description | ||
|- | |- | ||
| − | + | |'''f''' | |
|clustalw | |clustalw | ||
|Specifies the alignment file format. MOst common formats recongnized by BioPerl's [http://doc.bioperl.org/releases/bioperl-1.0/Bio/AlignIO.html AlignIO parsers] are supported, but use clustalw or fasta for best results. This argument is optional and | |Specifies the alignment file format. MOst common formats recongnized by BioPerl's [http://doc.bioperl.org/releases/bioperl-1.0/Bio/AlignIO.html AlignIO parsers] are supported, but use clustalw or fasta for best results. This argument is optional and | ||
| + | |- | ||
| + | |'''i''' | ||
| + | | | ||
| + | |Specifies the name of the input alignment file | ||
|} | |} | ||
| + | |||
* Take care to format the sequence IDs as described [http://gmod.org/wiki/GBrowse_syn_Database#Note_on_the_sequence_ID_syntax here]. | * Take care to format the sequence IDs as described [http://gmod.org/wiki/GBrowse_syn_Database#Note_on_the_sequence_ID_syntax here]. | ||
Revision as of 12:13, 5 December 2009
Contents
aln2hit.pl
aln2hit.pl is a generic alignment data parser that will generate a tab-delimited file suitable for loading into the GBrowse_syn alignment database.
Example:
perl aln2hit -f clustalw -i my_alignments.aln >my_alignments.txt
| argument | default | description |
|---|---|---|
| f | clustalw | Specifies the alignment file format. MOst common formats recongnized by BioPerl's AlignIO parsers are supported, but use clustalw or fasta for best results. This argument is optional and |
| i | Specifies the name of the input alignment file |
- Take care to format the sequence IDs as described here.
