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More clean up and modification of FASTA tools

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This commit is contained in:
Anton Nekrutenko
2008-04-29 14:36:04 +00:00
parent 70dce8172e
commit a3ee9be735
9 changed files with 77 additions and 44 deletions
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tool_conf.xml.main
+7
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@@ -56,6 +56,13 @@
<tool file="maf/maf_to_fasta.xml" />
<tool file="fasta_tools/tabular_to_fasta.xml" />
</section>
<section name="FASTA manipulation" id="fasta_manipulation">
<tool file="fasta_tools/fasta_compute_length.xml" />
<tool file="fasta_tools/fasta_filter_by_length.xml" />
<tool file="fasta_tools/fasta_concatenate_by_species.xml" />
<tool file="fasta_tools/fasta_to_tabular.xml" />
<tool file="fasta_tools/tabular_to_fasta.xml" />
</section>
<section name="Extract Features" id="features">
<tool file="filters/ucsc_gene_bed_to_exon_bed.xml" />
<tool file="extract/extract_GFF_Features.xml" />
tool_conf.xml.sample
+2
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@@ -264,6 +264,8 @@
<tool file="fasta_tools/fasta_compute_length.xml" />
<tool file="fasta_tools/fasta_filter_by_length.xml" />
<tool file="fasta_tools/fasta_concatenate_by_species.xml" />
<tool file="fasta_tools/fasta_to_tabular.xml" />
<tool file="fasta_tools/tabular_to_fasta.xml" />
</section>
<section name="Short Read Analysis" id="short_read_analysis">
<tool file="metag_tools/short_reads_figure_score.xml" />
tools/fasta_tools/fasta_compute_length.py
+5 -1
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@@ -12,10 +12,14 @@ assert sys.version_info[:2] >= ( 2, 4 )
def __main__():
input_filename = sys.argv[1]
output_filename = sys.argv[2]
keep_first = int( sys.argv[3] ) + 1
tmp_title = tmp_seq = ''
tmp_seq_count = 0
seq_hash = {}
if keep_first == 0:
keep_first = None
for i, line in enumerate( file( input_filename ) ):
line = line.rstrip( '\r\n' )
if not line or line.startswith( '#' ):
@@ -38,7 +42,7 @@ def __main__():
output_handle = open( output_filename, 'w' )
for i, fasta_title in title_keys:
tmp_seq = seq_hash[ ( i, fasta_title ) ]
output_handle.write( "%s\t%d\n" % ( fasta_title[ 1: ], len( tmp_seq ) ) )
output_handle.write( "%s\t%d\n" % ( fasta_title[ 1:keep_first ], len( tmp_seq ) ) )
output_handle.close()
if __name__ == "__main__" : __main__()
tools/fasta_tools/fasta_compute_length.xml
+14 -17
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@@ -1,8 +1,9 @@
<tool id="fasta_compute_length" name="Count FASTA Length">
<description> </description>
<command interpreter="python">fasta_compute_length.py $input $output </command>
<tool id="fasta_compute_length" name="Compute">
<description>sequence length</description>
<command interpreter="python">fasta_compute_length.py $input $output $keep_first</command>
<inputs>
<param name="input" type="data" format="fasta" label="Fasta file"/>
<param name="input" type="data" format="fasta" label="Compute length for these sequences"/>
<param name="keep_first" type="integer" size="5" value="0" label="How many title characters to keep?" help="'0' = keep the whole thing"/>
</inputs>
<outputs>
<data name="output" format="tabular"/>
@@ -10,10 +11,12 @@
<tests>
<test>
<param name="input" value="454.fasta" />
<param name="keep_first" value="0"/>
<output name="output" file="fasta_tool_compute_length_1.out" />
</test>
<test>
<param name="input" value="extract_genomic_dna_out1.fasta" />
<param name="keep_first" value="0"/>
<output name="output" file="fasta_tool_compute_length_2.out" />
</test>
</tests>
@@ -21,27 +24,21 @@
**What it does**
This tool counts the length of each fasta sequence in the file. The output file has two columns per line (separated by tab): fasta titles and lengths of the sequences.
This tool counts the length of each fasta sequence in the file. The output file has two columns per line (separated by tab): fasta titles and lengths of the sequences. The option *How many characters to keep?* allows to select a specified number of letters from the beginning of each FASTA entry.
-----
**Example**
- assume the input file contains fasta sequences::
Suppose you have the following FASTA formatted sequences from a Roche (454) FLX sequencing run::
&gt;seq1
TCATTTA
&gt;seq2
ATGGCGTCGGCC
&gt;seq3
TCACATGATG
&gt;EYKX4VC02EQLO5 length=108 xy=1826_0455 region=2 run=R_2007_11_07_16_15_57_␍ TCCGCGCCGAGCATGCCCATCTTGGATTCCGGCGCGATGACCATCGCCCGCTCCACCACG␍ TTCGGCCGGCCCTTCTCGTCGAGGAATGACACCAGCGCTTCGCCCACG␍ &gt;EYKX4VC02D4GS2 length=60 xy=1573_3972 region=2 run=R_2007_11_07_16_15_57_␍ AATAAAACTAAATCAGCAAAGACTGGCAAATACTCACAGGCTTATACAATACAAATGTAA
- the tool will return(first column is the titles, second column is the length of the sequences)::
&gt;seq1 7
&gt;seq2 12
&gt;seq3 10
Running this tool while setting **How many characters to keep?** to **14** will produce this::
EYKX4VC02EQLO5 108
EYKX4VC02D4GS2 60
</help>
</tool>
tools/fasta_tools/fasta_concatenate_by_species.xml
+8 -3
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@@ -1,5 +1,5 @@
<tool id="fasta_concatenate0" name="Concatenate FASTA" version="0.0.0">
<description>alignment by species</description>
<tool id="fasta_concatenate0" name="Concatenate" version="0.0.0">
<description>FASTA alignment by species</description>
<command interpreter="python">fasta_concatenate_by_species.py $input1 $out_file1</command>
<inputs>
<param name="input1" type="data" format="fasta" label="FASTA alignment"/>
@@ -14,9 +14,14 @@
</test>
</tests>
<help>
**What it does**
This tools attempts to parse FASTA headers to determine the species for each sequence in a multiple FASTA alignment.
It then linearly concatenates the sequences for each species in the file, creating one sequence per determined species.
-------
**Example**
Starting FASTA::
@@ -45,7 +50,7 @@ Starting FASTA::
Becomes::
becomes::
>hg18
GTGT
tools/fasta_tools/fasta_filter_by_length.xml
+8 -8
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@@ -1,10 +1,10 @@
<tool id="fasta_filter_by_length" name="Filter FASTA by Length">
<description> </description>
<tool id="fasta_filter_by_length" name="Filter">
<description>sequences by length</description>
<command interpreter="python">fasta_filter_by_length.py $input $min_length $max_length $output </command>
<inputs>
<param name="input" type="data" format="fasta" label="Fasta file"/>
<param name="min_length" type="integer" size="15" value="0" label="Minimal length of the return sequence" />
<param name="max_length" type="integer" size="15" value="0" label="Maximum length of the return sequence" help="no limitation if 0"/>
<param name="min_length" type="integer" size="15" value="0" label="Minimal length" />
<param name="max_length" type="integer" size="15" value="0" label="Maximum length" help="Setting to '0' will return all sequences longer than the 'Minimal length'"/>
</inputs>
<outputs>
<data name="output" format="fasta"/>
@@ -21,19 +21,19 @@
.. class:: infomark
**TIP**. If only want to show sequences longer than a threshold, set *minimal length* to the threshold and leave *maximum length* to zero.
**TIP**. To return sequences longer than a certain length, set *Minimal length* to desired value and leave *Maximum length* set to '0'.
-----
**What it does**
This tool accepts two parameters: *minimal length* and *maximum length*, and returns sequences of length within the two thresholds.
Outputs sequences between *Minimal length* and *Maximum length*.
-----
**Example**
- assume the input file contains fasta sequences::
Suppose you have the following FASTA formatted sequences::
&gt;seq1
TCATTTAATGAC
@@ -44,7 +44,7 @@
&gt;seq4
ATGGAAGC
- return sequences with length longer than 10bp (set the *minimal length* to 10, and the *maximum length* to 0 (no limitation))::
Setting the **Minimal length** to **10**, and the **Maximum length** to **0** will return all sequences longer than 10 bp::
&gt;seq1
TCATTTAATGAC
tools/fasta_tools/fasta_to_tabular.py
+6 -1
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@@ -13,9 +13,14 @@ seq_hash = {}
def __main__():
infile = sys.argv[1]
outfile = sys.argv[2]
keep_first = int( sys.argv[3] ) + 1
title = ''
sequence = ''
sequence_count = 0
if keep_first == 0:
keep_first = None
for i, line in enumerate( open( infile ) ):
line = line.rstrip( '\r\n' )
if not line or line.startswith( '#' ):
@@ -38,7 +43,7 @@ def __main__():
out = open( outfile, 'w' )
for i, fasta_title in title_keys:
sequence = seq_hash[( i, fasta_title )]
out.write( "%s\t%s\n" %( fasta_title, sequence ) )
out.write( "%s\t%s\n" %( fasta_title[ 1:keep_first ], sequence ) )
out.close()
if __name__ == "__main__" : __main__()
tools/fasta_tools/fasta_to_tabular.xml
+18 -11
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@@ -1,8 +1,9 @@
<tool id="fasta2tab" name="FASTA-to-Tabular" version="1.0.0">
<description>Converts a FASTA file to Tabular format</description>
<command interpreter="python">fasta_to_tabular.py $input $output</command>
<description>converts FASTA file to tabular format</description>
<command interpreter="python">fasta_to_tabular.py $input $output $keep_first</command>
<inputs>
<param name="input" type="data" format="fasta" label="Fasta file"/>
<param name="input" type="data" format="fasta" label="Convert these sequences"/>
<param name="keep_first" type="integer" size="5" value="0" label="How many title characters to keep?" help="'0' = keep the whole thing"/>
</inputs>
<outputs>
<data name="output" format="tabular"/>
@@ -10,28 +11,34 @@
<tests>
<test>
<param name="input" value="454.fasta" />
<param name="keep_first" value="0"/>
<output name="output" file="fasta_to_tabular_out1.tabular" />
</test>
<test>
<param name="input" value="4.fasta" />
<param name="keep_first" value="0"/>
<output name="output" file="fasta_to_tabular_out2.tabular" />
</test>
</tests>
<help>
**What it does**
This tool converts FASTA formatted sequences to TAB-delimited format. The option *How many characters to keep?* allows to select a specified number of letters from the beginning of each FASTA entry.
-----
**Example**
A fasta file with two sequences::
Suppose you have the following FASTA formatted sequences from a Roche (454) FLX sequencing run::
&gt;seq1
CCGGTATCCG
&gt;seq2
CTTACC
&gt;EYKX4VC02EQLO5 length=108 xy=1826_0455 region=2 run=R_2007_11_07_16_15_57_␍ TCCGCGCCGAGCATGCCCATCTTGGATTCCGGCGCGATGACCATCGCCCGCTCCACCACG␍ TTCGGCCGGCCCTTCTCGTCGAGGAATGACACCAGCGCTTCGCCCACG␍ &gt;EYKX4VC02D4GS2 length=60 xy=1573_3972 region=2 run=R_2007_11_07_16_15_57_␍ AATAAAACTAAATCAGCAAAGACTGGCAAATACTCACAGGCTTATACAATACAAATGTAA
Returns::
Running this tool while setting **How many characters to keep?** to **14** will produce this::
EYKX4VC02EQLO5 TCCGCGCCGAGCATGCCCATCTTGGATTCCGGCGCGATGACCATCGCCCGCTCCACCACGTTCGGCCGGCCCTTCTCGTCGAGGAATGACACCAGCGCTTCGCCCACG
EYKX4VC02D4GS2 AATAAAACTAAATCAGCAAAGACTGGCAAATACTCACAGGCTTATACAATACAAATGTAA
&gt;seq1 CCGGTATCCG
&gt;seq2 CTTACC
</help>
</tool>
tools/fasta_tools/tabular_to_fasta.xml
+9 -3
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@@ -1,5 +1,5 @@
<tool id="tab2fasta" name="Tabular-to-FASTA" version="1.1.0">
<description>Converts a tabular file to FASTA format</description>
<description>converts tabular file to FASTA format</description>
<command interpreter="python">tabular_to_fasta.py $input $title_col $seq_col $output </command>
<inputs>
<param name="input" type="data" format="tabular" label="Tab-delimited file"/>
@@ -19,14 +19,20 @@
</tests>
<help>
**What it does**
Converts tab delimited data into FASTA formatted sequences.
-----------
**Example**
Solexa data::
Suppose this is a sequence file produced by Illumina (Solexa) sequencer::
5 300 902 419 GACTCATGATTTCTTACCTATTAGTGGTTGAACATC
5 300 880 431 GTGATATGTATGTTGACGGCCATAAGGCTGCTTCTT
Selecting **c3 and c4** as the Title Columns and **c5** as the Sequence Column will result in::
Selecting **c3** and **c4** as the **Title column(s)** and **c5** as the **Sequence column** will result in::
&gt;902_419
GACTCATGATTTCTTACCTATTAGTGGTTGAACATC