Difference between revisions of "GBrowse syn Scripts"
From GMOD
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Example: | Example: | ||
perl aln2hit -f clustalw -i my_alignments.aln >my_alignments.txt | perl aln2hit -f clustalw -i my_alignments.aln >my_alignments.txt | ||
− | + | ===Options=== | |
{|class=wikitable | {|class=wikitable | ||
!argument | !argument | ||
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<span class=pops>[http://gmod.svn.sourceforge.net/viewvc/gmod/Generic-Genome-Browser/branches/stable/bin/gbrowse_syn/clustal2hit.pl clustal2hit.pl] is a CLUSTALW format alignment data parser. | <span class=pops>[http://gmod.svn.sourceforge.net/viewvc/gmod/Generic-Genome-Browser/branches/stable/bin/gbrowse_syn/clustal2hit.pl clustal2hit.pl] is a CLUSTALW format alignment data parser. | ||
+ | ;Purpose | ||
+ | :Use this script in cases where you have a one or more clustal alignment files and want to convert them to the [[GBrowse_syn_Database#alignment_data_loading_format|tab-delimited format]] that is used to load the GBrowse_syn alignment database. | ||
+ | Example: | ||
+ | perl clustal2hit.pl *.aln >my_alignments.txt | ||
− | + | ===Options=== | |
− | + | None. | |
− | + | ||
− | + | ||
− | + | ||
− | + | ||
− | + | ||
− | + | ||
− | + | ||
==mercatoraln_to_synhits.pl== | ==mercatoraln_to_synhits.pl== | ||
+ | [http://gmod.svn.sourceforge.net/viewvc/gmod/Generic-Genome-Browser/branches/stable/bin/gbrowse_syn/mercatoraln_to_synhits.pl] is a data parser for multiple sequence alignments generated by mercator. | ||
+ | ;Purpose | ||
+ | :This script will process alignments generated by the MERCATOR pipeline | ||
+ | |||
+ | Example: | ||
+ | Usage example here | ||
+ | |||
+ | ===Options=== | ||
{|class=wikitable | {|class=wikitable | ||
!argument | !argument | ||
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!description | !description | ||
|- | |- | ||
− | | | + | !a|aln|i|input |
− | | | + | |None |
− | | | + | |Specified the name of the alignment file |
+ | |- | ||
+ | !v|verbose | ||
+ | |None | ||
+ | |Print progress reports while running | ||
+ | |- | ||
+ | !f|format | ||
+ | |fasta | ||
+ | |Specifies format of the input alignment files | ||
+ | |- | ||
+ | !d|dir | ||
+ | |None | ||
+ | |Specifies the containing directory for the genome and map files | ||
|} | |} | ||
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Revision as of 15:27, 5 December 2009
This page describes helper scripts for processing alignment data for loading into GBrowse_syn.
Contents
Parsing Multiple Sequence Alignment Data
The scripts in this section process multiple sequence alignment data in various formats and convert them to the tab-delimited format used to load the GBRowse_syn database.
aln2hit.pl
aln2hit.pl is a generic alignment data parser that reads alignment data into the GBrowse_syn database loading format.
- Purpose
- Use this script in cases where you have a single alignment file and want to convert it to the tab-delimited format that is used to load the GBrowse_syn alignment database.
Example:
perl aln2hit -f clustalw -i my_alignments.aln >my_alignments.txt
Options
argument | default | description |
---|---|---|
f | clustalw | Specifies the alignment file format. MOst common formats recongnized by BioPerl's AlignIO parsers are supported. Use clustalw or fasta for best results. |
i | Specifies the name of the input alignment file |
clustal2hit.pl
clustal2hit.pl is a CLUSTALW format alignment data parser.
- Purpose
- Use this script in cases where you have a one or more clustal alignment files and want to convert them to the tab-delimited format that is used to load the GBrowse_syn alignment database.
Example:
perl clustal2hit.pl *.aln >my_alignments.txt
Options
None.
mercatoraln_to_synhits.pl
[1] is a data parser for multiple sequence alignments generated by mercator.
- Purpose
- This script will process alignments generated by the MERCATOR pipeline
Example:
Usage example here
Options
argument | default | description |
---|---|---|
a|aln|i|input | None | Specified the name of the alignment file |
v|verbose | None | Print progress reports while running |
f|format | fasta | Specifies format of the input alignment files |
d|dir | None | Specifies the containing directory for the genome and map files |
Direct Database Loading Scripts
The scripts in this section load data from multiple sequence alignment files into the GBrowse_syn alignment database
load_alignment_database.pl
argument | default | description |
---|---|---|
load_alignments_gff3.pl
argument | default | description |
---|---|---|
load_alignments_msa.pl
argument | default | description |
---|---|---|
split_clustal.pl
argument | default | description |
---|---|---|