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Add a MAF to Interval converter that produces a set of intervals with sequence data.

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This commit is contained in:
Daniel Blankenberg
2009-09-17 11:47:37 -04:00
parent 936742c3c8
commit 7cd1c6dfd0
5 changed files with 198 additions and 1 deletions
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tool_conf.xml.main
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<tool file="fasta_tools/fasta_to_tabular.xml" />
<tool file="filters/gff2bed.xml" />
<tool file="maf/maf_to_bed.xml" />
<tool file="maf/maf_to_interval.xml" />
<tool file="maf/maf_to_fasta.xml" />
<tool file="fasta_tools/tabular_to_fasta.xml" />
</section>
tool_conf.xml.sample
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<tool file="filters/gff2bed.xml" />
<tool file="filters/lav_to_bed.xml" />
<tool file="maf/maf_to_bed.xml" />
<tool file="maf/maf_to_interval.xml" />
<tool file="maf/maf_to_fasta.xml" />
<tool file="fasta_tools/tabular_to_fasta.xml" />
<tool file="next_gen_conversion/solid_to_fastq.xml" />
tools/maf/maf_reverse_complement.xml
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<tool id="MAF_Reverse_Complement_1" name="Reverse Compliment" version="1.0.1">
<tool id="MAF_Reverse_Complement_1" name="Reverse Complement" version="1.0.1">
<description>a MAF file</description>
<command interpreter="python">maf_reverse_complement.py $input1 $out_file1 $species</command>
<inputs>
tools/maf/maf_to_interval.py
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#!/usr/bin/env python
"""
Read a maf and output intervals for specified list of species.
"""
import sys, os
from galaxy import eggs
import pkg_resources; pkg_resources.require( "bx-python" )
from bx.align import maf
from galaxy.tools.util import maf_utilities
assert sys.version_info[:2] >= ( 2, 4 )
def __main__():
input_filename = sys.argv[1]
output_filename = sys.argv[2]
output_id = sys.argv[3]
#where to store files that become additional output
database_tmp_dir = sys.argv[4]
primary_spec = sys.argv[5]
species = sys.argv[6].split( ',' )
all_species = sys.argv[7].split( ',' )
partial = sys.argv[8]
keep_gaps = sys.argv[9]
out_files = {}
if "None" in species:
species = []
if primary_spec not in species:
species.append( primary_spec )
if primary_spec not in all_species:
all_species.append( primary_spec )
all_species.sort()
for spec in species:
if spec == primary_spec:
out_files[ spec ] = open( output_filename, 'wb+' )
else:
out_files[ spec ] = open( os.path.join( database_tmp_dir, 'primary_%s_%s_visible_interval_%s' % ( output_id, spec, spec ) ), 'wb+' )
out_files[ spec ].write( '#chrom\tstart\tend\tstrand\tscore\tname\t%s\n' % ( '\t'.join( all_species ) ) )
num_species = len( all_species )
file_in = open( input_filename, 'r' )
maf_reader = maf.Reader( file_in )
for i, m in enumerate( maf_reader ):
for j, block in enumerate( maf_utilities.iter_blocks_split_by_species( m ) ):
if len( block.components ) < num_species and partial == "partial_disallowed": continue
sequences = {}
for c in block.components:
spec, chrom = maf_utilities.src_split( c.src )
if keep_gaps == 'remove_gaps':
sequences[ spec ] = c.text.replace( '-', '' )
else:
sequences[ spec ] = c.text
sequences = '\t'.join( [ sequences.get( spec, '' ) for spec in all_species ] )
for spec in species:
c = block.get_component_by_src_start( spec )
if c is not None:
spec2, chrom = maf_utilities.src_split( c.src )
assert spec2 == spec, Exception( 'Species name inconsistancy found in component: %s != %s' % ( spec, spec2 ) )
out_files[ spec ].write( "%s\t%s\t%s\t%s\t%s\t%s\t%s\n" % ( chrom, c.forward_strand_start, c.forward_strand_end, c.strand, m.score, "%s_%s_%s" % (spec, i, j), sequences ) )
file_in.close()
for file_out in out_files.values():
file_out.close()
if __name__ == "__main__": __main__()
tools/maf/maf_to_interval.xml
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<tool id="MAF_To_Interval1" name="MAF to Interval" force_history_refresh="True">
<description>Converts a MAF formated file to the Interval format</description>
<command interpreter="python">maf_to_interval.py $input1 $out_file1 $out_file1.id $__new_file_path__ $input1.dbkey $species $input1.metadata.species $complete_blocks $remove_gaps</command>
<inputs>
<param format="maf" name="input1" type="data" label="MAF file to convert"/>
<param name="species" type="select" label="Select additional species" display="checkboxes" multiple="true" help="The species matching the dbkey of the alignment is always included. A separate history item will be created for each species.">
<options>
<filter type="data_meta" ref="input1" key="species" />
<filter type="remove_value" meta_ref="input1" key="dbkey" />
</options>
</param>
<param name="complete_blocks" type="select" label="Exclude blocks which have a species missing">
<option value="partial_allowed">include blocks with missing species</option>
<option value="partial_disallowed">exclude blocks with missing species</option>
</param>
<param name="remove_gaps" type="select" label="Remove Gap characters from sequences">
<option value="keep_gaps">keep gaps</option>
<option value="remove_gaps">remove gaps</option>
</param>
</inputs>
<outputs>
<data format="interval" name="out_file1" />
</outputs>
<tests>
<test>
<param name="input1" value="4.maf" dbkey="hg17"/>
<param name="complete_blocks" value="partial_disallowed"/>
<param name="remove_gaps" value="keep_gaps"/>
<param name="species" value="panTro1" />
<!-- <output name="out_file1" file="maf_to_interval_out_hg17.interval"/> cannot test primary species, because we cannot leave species blank and we can only test the last item added to a history-->
<output name="out_file1" file="maf_to_interval_out_panTro1.interval"/>
</test>
</tests>
<help>
**What it does**
This tool converts every MAF block to a set of genomic intervals describing the position of that alignment block within a corresponding genome. Sequences from aligning species are also included in the output.
The interface for this tool contains several options:
* **MAF file to convert**. Choose multiple alignments from history to be converted to BED format.
* **Choose species**. Choose additional species from the alignment to be included in the output
* **Exclude blocks which have a species missing**. if an alignment block does not contain any one of the species found in the alignment set and this option is set to **exclude blocks with missing species**, then coordinates of such a block **will not** be included in the output (see **Example 2** below).
* **Remove Gap characters from sequences**. Gaps can be removed from sequences before they are output.
-----
**Example 1**: **Include only reference genome** (hg18 in this case) and **include blocks with missing species**:
For the following alignment::
##maf version=1
a score=68686.000000
s hg18.chr20 56827368 75 + 62435964 GACAGGGTGCATCTGGGAGGG---CCTGCCGGGCCTTTA-TTCAACACTAGATACGCCCCATCTCCAATTCTAATGGAC-
s panTro2.chr20 56528685 75 + 62293572 GACAGGGTGCATCTGAGAGGG---CCTGCCAGGCCTTTA-TTCAACACTAGATACGCCCCATCTCCAATTCTAATGGAC-
s rheMac2.chr10 89144112 69 - 94855758 GACAGGGTGCATCTGAGAGGG---CCTGCTGGGCCTTTG-TTCAAAACTAGATATGCCCCAACTCCAATTCTA-------
s mm8.chr2 173910832 61 + 181976762 AGAAGGATCCACCT------------TGCTGGGCCTCTGCTCCAGCAAGACCCACCTCCCAACTCAAATGCCC-------
s canFam2.chr24 46551822 67 + 50763139 CG------GCGTCTGTAAGGGGCCACCGCCCGGCCTGTG-CTCAAAGCTACAAATGACTCAACTCCCAACCGA------C
a score=10289.000000
s hg18.chr20 56827443 37 + 62435964 ATGTGCAGAAAATGTGATACAGAAACCTGCAGAGCAG
s panTro2.chr20 56528760 37 + 62293572 ATGTGCAGAAAATGTGATACAGAAACCTGCAGAGCAG
s rheMac2.chr10 89144181 37 - 94855758 ATGTGCGGAAAATGTGATACAGAAACCTGCAGAGCAG
the tool will create **a single** history item containing the following (**note** the name field is numbered iteratively: hg18_0_0, hg18_1_0 etc. where the first number is the block number and the second number is the iteration through the block (if a species appears twice in a block, that interval will be repeated) and sequences for each species are included in the order specified in the header: the field is left empty when no sequence is available for that species)::
#chrom start end strand score name canFam2 hg18 mm8 panTro2 rheMac2
chr20 56827368 56827443 + 68686.0 hg18_0_0 CG------GCGTCTGTAAGGGGCCACCGCCCGGCCTGTG-CTCAAAGCTACAAATGACTCAACTCCCAACCGA------C GACAGGGTGCATCTGGGAGGG---CCTGCCGGGCCTTTA-TTCAACACTAGATACGCCCCATCTCCAATTCTAATGGAC- AGAAGGATCCACCT------------TGCTGGGCCTCTGCTCCAGCAAGACCCACCTCCCAACTCAAATGCCC------- GACAGGGTGCATCTGAGAGGG---CCTGCCAGGCCTTTA-TTCAACACTAGATACGCCCCATCTCCAATTCTAATGGAC- GACAGGGTGCATCTGAGAGGG---CCTGCTGGGCCTTTG-TTCAAAACTAGATATGCCCCAACTCCAATTCTA-------
chr20 56827443 56827480 + 10289.0 hg18_1_0 ATGTGCAGAAAATGTGATACAGAAACCTGCAGAGCAG ATGTGCAGAAAATGTGATACAGAAACCTGCAGAGCAG ATGTGCGGAAAATGTGATACAGAAACCTGCAGAGCAG
-----
**Example 2**: **Include hg18 and mm8** and **exclude blocks with missing species**:
For the following alignment::
##maf version=1
a score=68686.000000
s hg18.chr20 56827368 75 + 62435964 GACAGGGTGCATCTGGGAGGG---CCTGCCGGGCCTTTA-TTCAACACTAGATACGCCCCATCTCCAATTCTAATGGAC-
s panTro2.chr20 56528685 75 + 62293572 GACAGGGTGCATCTGAGAGGG---CCTGCCAGGCCTTTA-TTCAACACTAGATACGCCCCATCTCCAATTCTAATGGAC-
s rheMac2.chr10 89144112 69 - 94855758 GACAGGGTGCATCTGAGAGGG---CCTGCTGGGCCTTTG-TTCAAAACTAGATATGCCCCAACTCCAATTCTA-------
s mm8.chr2 173910832 61 + 181976762 AGAAGGATCCACCT------------TGCTGGGCCTCTGCTCCAGCAAGACCCACCTCCCAACTCAAATGCCC-------
s canFam2.chr24 46551822 67 + 50763139 CG------GCGTCTGTAAGGGGCCACCGCCCGGCCTGTG-CTCAAAGCTACAAATGACTCAACTCCCAACCGA------C
a score=10289.000000
s hg18.chr20 56827443 37 + 62435964 ATGTGCAGAAAATGTGATACAGAAACCTGCAGAGCAG
s panTro2.chr20 56528760 37 + 62293572 ATGTGCAGAAAATGTGATACAGAAACCTGCAGAGCAG
s rheMac2.chr10 89144181 37 - 94855758 ATGTGCGGAAAATGTGATACAGAAACCTGCAGAGCAG
the tool will create **two** history items (one for hg18 and one for mm8) containing the following (**note** that both history items contain only one line describing the first alignment block. The second MAF block is not included in the output because it does not contain mm8):
History item **1** (for hg18)::
#chrom start end strand score name canFam2 hg18 mm8 panTro2 rheMac2
chr20 56827368 56827443 + 68686.0 hg18_0_0 CG------GCGTCTGTAAGGGGCCACCGCCCGGCCTGTG-CTCAAAGCTACAAATGACTCAACTCCCAACCGA------C GACAGGGTGCATCTGGGAGGG---CCTGCCGGGCCTTTA-TTCAACACTAGATACGCCCCATCTCCAATTCTAATGGAC- AGAAGGATCCACCT------------TGCTGGGCCTCTGCTCCAGCAAGACCCACCTCCCAACTCAAATGCCC------- GACAGGGTGCATCTGAGAGGG---CCTGCCAGGCCTTTA-TTCAACACTAGATACGCCCCATCTCCAATTCTAATGGAC- GACAGGGTGCATCTGAGAGGG---CCTGCTGGGCCTTTG-TTCAAAACTAGATATGCCCCAACTCCAATTCTA-------
History item **2** (for mm8)::
#chrom start end strand score name canFam2 hg18 mm8 panTro2 rheMac2
chr2 173910832 173910893 + 68686.0 mm8_0_0 CG------GCGTCTGTAAGGGGCCACCGCCCGGCCTGTG-CTCAAAGCTACAAATGACTCAACTCCCAACCGA------C GACAGGGTGCATCTGGGAGGG---CCTGCCGGGCCTTTA-TTCAACACTAGATACGCCCCATCTCCAATTCTAATGGAC- AGAAGGATCCACCT------------TGCTGGGCCTCTGCTCCAGCAAGACCCACCTCCCAACTCAAATGCCC------- GACAGGGTGCATCTGAGAGGG---CCTGCCAGGCCTTTA-TTCAACACTAGATACGCCCCATCTCCAATTCTAATGGAC- GACAGGGTGCATCTGAGAGGG---CCTGCTGGGCCTTTG-TTCAAAACTAGATATGCCCCAACTCCAATTCTA-------
-------
.. class:: infomark
**About formats**
**MAF format** multiple alignment format file. This format stores multiple alignments at the DNA level between entire genomes.
- The .maf format is line-oriented. Each multiple alignment ends with a blank line.
- Each sequence in an alignment is on a single line.
- Lines starting with # are considered to be comments.
- Each multiple alignment is in a separate paragraph that begins with an "a" line and contains an "s" line for each sequence in the multiple alignment.
- Some MAF files may contain two optional line types:
- An "i" line containing information about what is in the aligned species DNA before and after the immediately preceding "s" line;
- An "e" line containing information about the size of the gap between the alignments that span the current block.
</help>
</tool>