Bioutils - Revision history

imported>Weigang: /* Creative usage (with BASH) */

2014-10-08T20:47:41Z

Creative usage (with BASH)

← Older revision		Revision as of 20:47, 8 October 2014
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	echo -ne ">lookup\nATG\n" \| bioseq -t1 # Lookup a codon product		echo -ne ">lookup\nATG\n" \| bioseq -t1 # Lookup a codon product
	len=$(bioaln -l foo.aln); len_degap=$(bioaln -g foo.aln \| bioaln -l); echo "$len-$len_degap" \| bc -l # count alignment gaps		len=$(bioaln -l foo.aln); len_degap=$(bioaln -g foo.aln \| bioaln -l); echo "$len-$len_degap" \| bc -l # count alignment gaps
	for i in {1..100}; do bioaln -T foo.aln >> foo.boot; done # bootstrap an alignment (with replacement)		for i in {1..100}; do bioaln --boot foo.aln >> foo.boot; done # bootstrap an alignment (with replacement)
	</syntaxhighlight>		</syntaxhighlight>

imported>Weigang: /* Creative usage (with BASH) */

2014-10-08T20:42:52Z

Creative usage (with BASH)

← Older revision		Revision as of 20:42, 8 October 2014
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	echo -ne ">lookup\nATG\n" \| bioseq -t1 # Lookup a codon product		echo -ne ">lookup\nATG\n" \| bioseq -t1 # Lookup a codon product
	len=$(bioaln -l foo.aln); len_degap=$(bioaln -g foo.aln \| bioaln -l); echo "$len-$len_degap" \| bc -l # count alignment gaps		len=$(bioaln -l foo.aln); len_degap=$(bioaln -g foo.aln \| bioaln -l); echo "$len-$len_degap" \| bc -l # count alignment gaps
			for i in {1..100}; do bioaln -T foo.aln >> foo.boot; done # bootstrap an alignment (with replacement)
	</syntaxhighlight>		</syntaxhighlight>

imported>Weigang: /* Even-more powerful usage (with other applications) */

2014-10-07T17:36:44Z

Even-more powerful usage (with other applications)

← Older revision		Revision as of 17:36, 7 October 2014
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	# Permutation Trait Probability test for tree-ness:		# Permutation Trait Probability test for tree-ness:
	for i in {1..100); do		for i in {1..100); do
	bioaln -P -i'fasta' nt.fas > nt.permuted.fas;		bioaln -P -i'fasta' -o'fasta' nt.fas > nt.permuted.fas;
	FastTree -nt nt.permuted.fas 2> /dev/null \| biotree -l >> tree-length.txt # tree length of permuted alignment		FastTree -nt nt.permuted.fas 2> /dev/null \| biotree -l >> tree-length.txt # tree length of permuted alignment
	done;		done;

imported>Weigang: /* Live Demos */

2014-10-07T17:30:48Z

Live Demos

@@ Line 73: / Line 73: @@
 echo -ne ">lookup\nATG\n" | bioseq -t1 # Lookup a codon product
 len=$(bioaln -l foo.aln); len_degap=$(bioaln -g foo.aln | bioaln -l); echo "$len-$len_degap" | bc -l # count alignment gaps
 </syntaxhighlight>
 ----

imported>Weigang: /* Power usage (with pipes) */

2014-10-01T19:01:30Z

Power usage (with pipes)

← Older revision		Revision as of 19:01, 1 October 2014
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	bioaln -o'fasta' foo.aln \| bioseq -g # remove gaps within individual sequences		bioaln -o'fasta' foo.aln \| bioseq -g # remove gaps within individual sequences
	bioaln -o'fasta' foo.aln \| bioseq -t1 \| bioaln -i'fasta' # turn a nucleotide alignment into a peptide alignment		bioaln -o'fasta' foo.aln \| bioseq -t1 \| bioaln -i'fasta' # turn a nucleotide alignment into a peptide alignment
			biotree -s'otu1' -s'otu2' -s'otu3' foo.newick \| biotree -l # subset a large tree and get total tree length
	</syntaxhighlight>		</syntaxhighlight>

imported>Weigang: /* Power usage (with pipes) */

2014-10-01T12:48:36Z

Power usage (with pipes)

← Older revision		Revision as of 12:48, 1 October 2014
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	===Power usage (with pipes)===		===Power usage (with pipes)===
	<syntaxhighlight lang=bash">		<syntaxhighlight lang=bash">
	~~# Pipe with the same utility~~
	bioseq -p'order:5' foo.fasta \| bioseq -s'100,200' \| bioseq -r \| bioseq -t1 # pick, subseq, revcom, and translate		bioseq -p'order:5' foo.fasta \| bioseq -s'100,200' \| bioseq -r \| bioseq -t1 # pick, subseq, revcom, and translate
	~~# Pipe across utilities~~
	bioaln -o'fasta' foo.aln \| bioseq -g # remove gaps within individual sequences		bioaln -o'fasta' foo.aln \| bioseq -g # remove gaps within individual sequences
	bioaln -o'fasta' foo.aln \| bioseq -t1 \| bioaln -i'fasta' # turn nucleotide alignment into a peptide alignment		bioaln -o'fasta' foo.aln \| bioseq -t1 \| bioaln -i'fasta' # turn a nucleotide alignment into a peptide alignment
	</syntaxhighlight>		</syntaxhighlight>

imported>Weigang: /* Basic Usage */

2014-09-30T20:33:44Z

Basic Usage

← Older revision		Revision as of 20:33, 30 September 2014
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	bioseq -t6 foo.fasta # translate in all 6 frames		bioseq -t6 foo.fasta # translate in all 6 frames
	bioseq -p'id:seq_1' foo.fasta # pick a sequence by ID		bioseq -p'id:seq_1' foo.fasta # pick a sequence by ID
	bioseq -p'order:3' # pick the 3rd sequence		bioseq -p'order:3' foo.fasta # pick the 3rd sequence
	bioseq -p're:Human' foo.fasta # pick all sequences labeled as "Human" (by regular expression)		bioseq -p're:Human' foo.fasta # pick all sequences labeled as "Human" (by regular expression)
	bioseq -g foo.fasta # remove gaps		bioseq -g foo.fasta # remove gaps
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	<syntaxhighlight lang=bash">		<syntaxhighlight lang=bash">
	biotree -l foo.newick # total tree length		biotree -l foo.newick # total tree length
	biotree -e 'outgroup' newick # re-root on a "outgroup"		biotree -e 'outgroup' foo.newick # re-root on a "outgroup"
	biotree -z foo.newick # print pair-wise tree distances between leafs		biotree -z foo.newick # print pair-wise tree distances between leafs
	biotree -p 'node1' -p 'node2' foo.newick # remove "node1" and node2"		biotree -p 'node1' -p 'node2' foo.newick # remove "node1" and node2"
	biotree -s 'node1' -s 'node2' -s 'node3' -s'node4' # subtree consisting ONLY of these nodes		biotree -s 'node1' -s 'node2' -s 'node3' -s'node4' foo.newick # subtree consisting ONLY of these nodes
	</syntaxhighlight>		</syntaxhighlight>
	* biopop		* biopop

imported>Weigang: /* Power usage (with pipes) */

2014-09-30T20:31:46Z

Power usage (with pipes)

← Older revision		Revision as of 20:31, 30 September 2014
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	# Pipe with the same utility		# Pipe with the same utility
	bioseq -p'order:5' foo.fasta \| bioseq -s'100,200' \| bioseq -r \| bioseq -t1 # pick, subseq, revcom, and translate		bioseq -p'order:5' foo.fasta \| bioseq -s'100,200' \| bioseq -r \| bioseq -t1 # pick, subseq, revcom, and translate
	# Pipe ~~among~~ utilities		# Pipe across utilities
	bioaln -o'fasta' foo.aln \| bioseq -g # remove gaps within individual sequences		bioaln -o'fasta' foo.aln \| bioseq -g # remove gaps within individual sequences
			bioaln -o'fasta' foo.aln \| bioseq -t1 \| bioaln -i'fasta' # turn nucleotide alignment into a peptide alignment
	</syntaxhighlight>		</syntaxhighlight>

	===Creative usage (with BASH)===		===Creative usage (with BASH)===
	<syntaxhighlight lang=bash">		<syntaxhighlight lang=bash">

imported>Weigang: /* Basic Usage */

2014-09-30T02:33:57Z

Basic Usage

← Older revision		Revision as of 02:33, 30 September 2014
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	bioseq -p'order:3' # pick the 3rd sequence		bioseq -p'order:3' # pick the 3rd sequence
	bioseq -p're:Human' foo.fasta # pick all sequences labeled as "Human" (by regular expression)		bioseq -p're:Human' foo.fasta # pick all sequences labeled as "Human" (by regular expression)
	bioseq -g foo.fasta # remove ~~all~~ gaps		bioseq -g foo.fasta # remove gaps
	bioseq -z'CP003201' -o'genbank' # retrieve a GenBank file with accession		bioseq -z'CP003201' -o'genbank' # retrieve a GenBank file with accession
	bioseq -z'CP003201' -o'fasta' # same file in FASTA		bioseq -z'CP003201' -o'fasta' # same file in FASTA
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	* bioaln		* bioaln
	<syntaxhighlight lang=bash">		<syntaxhighlight lang=bash">
	bioaln -i'fasta' -o'phylip' foo.fasta # convert a FASTA alignment to PHYLIP		bioaln -i'fasta' -o'phylip' foo.fasta # convert FASTA alignment to PHYLIP
	bioaln -l foo.aln # print alignment length of a CLUSTALW (default format) file		bioaln -l foo.aln # print alignment length of a CLUSTALW (default format) file
	bioaln -s'100, 200' foo.aln # obtain an alignment slice		bioaln -s'100, 200' foo.aln # obtain an alignment slice
	bioaln -m foo.aln # show only variable sites		bioaln -m foo.aln # show only variable sites
	bioaln -r'seq_2' foo.aln # ~~use~~ "seq_2" as reference (first) sequence		bioaln -r'seq_2' foo.aln # set "seq_2" as reference (first) sequence
	bioaln -g foo.aln # remove gapped sites		bioaln -g foo.aln # remove gapped sites
	bioaln -p'seq_1,seq_3,seq_6' foo.aln # pick a subset of sequences		bioaln -p'seq_1,seq_3,seq_6' foo.aln # pick a subset of sequences
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	* biotree		* biotree
	<syntaxhighlight lang=bash">		<syntaxhighlight lang=bash">
			biotree -l foo.newick # total tree length
			biotree -e 'outgroup' newick # re-root on a "outgroup"
			biotree -z foo.newick # print pair-wise tree distances between leafs
			biotree -p 'node1' -p 'node2' foo.newick # remove "node1" and node2"
			biotree -s 'node1' -s 'node2' -s 'node3' -s'node4' # subtree consisting ONLY of these nodes
	</syntaxhighlight>		</syntaxhighlight>
	* biopop		* biopop
	<syntaxhighlight lang=bash">		<syntaxhighlight lang=bash">
			biopop --stats 'pi,theta' foo.aln # print pi and theta of population (default: CLUSTALW alignment)
			biopop -m foo.aln # print mismatch distribution
			biopop -d foo.aln # print distance matrix (default: Jukes-Cantor model; should be back-tracked into "bioaln")
			biopop -s foo.aln # obtain number of segregating sites (i.e., SNPs)
			biopop -a foo.aln # get heterozygosity for each SNP site
	</syntaxhighlight>		</syntaxhighlight>

imported>Weigang at 02:18, 30 September 2014

2014-09-30T02:18:05Z

← Older revision		Revision as of 02:18, 30 September 2014
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	<span style="color: Seagreen;font-weight:bold;font-size:large;"><u>~~Bio~~</u>~~Perl~~-based Sequence <u>Util</u>ities<span>		<span style="color: Seagreen;font-weight:bold;font-size:large;"><u>B</u>io<u>P</u>erl-based Sequence <u>Util</u>ities<span>
	[[File:Seq-util.png\|thumbnail\|600px\|right\|'''Figure 1'''. Design and Methods of ''~~bioutils~~'']]		[[File:Seq-util.png\|thumbnail\|600px\|right\|'''Figure 1'''. Design and Methods of ''bputils'']]
	==What is ''~~bioutils~~''?==		==What is ''bputils''?==
	''~~bioutils~~'' is a suite of Perl scripts that provide convenient command-line access to popular BioPerl methods. Designed as UNIX utilities, these tools aim to circumvent a constant need (and urge) to compose one-off BioPerl scripts for routine manipulations of sequences, alignments and trees.		''bputils'' is a suite of Perl scripts that provide convenient command-line access to popular BioPerl methods. Designed as UNIX utilities, these tools aim to circumvent a constant need (and urge) to compose one-off BioPerl scripts for routine manipulations of sequences, alignments and trees.

	The initial release of ''~~bioutils~~'' consists of four inter-connected utilities ('''Figure 1'''):		The initial release of ''bputils'' consists of four inter-connected utilities ('''Figure 1'''):
	* '''bioseq''': a wrapper of BioPerl class Bio::Seq (with additional methods)		* '''bioseq''': a wrapper of BioPerl class Bio::Seq (with additional methods)
	* '''bioaln''': a wrapper of Bio::SimpleAlign (which inherits Bio::Seq; with additional methods)		* '''bioaln''': a wrapper of Bio::SimpleAlign (which inherits Bio::Seq; with additional methods)