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Remove FASTA filter script from BLAST+ tools (I want to generalise it)

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This commit is contained in:
Peter Cock
2010-10-25 10:28:39 +01:00
parent 54408aae53
commit 7ce54fe460
3 changed files with 0 additions and 76 deletions
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tool_conf.xml.sample
-1
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@@ -269,7 +269,6 @@
<tool file="ncbi_blast_plus/ncbi_tblastn_wrapper.xml" />
<tool file="ncbi_blast_plus/ncbi_tblastx_wrapper.xml" />
<tool file="ncbi_blast_plus/blastxml_to_tabular.xml" />
<tool file="ncbi_blast_plus/blast_filter_fasta.xml" />
</section>
<section name="NGS: Mapping" id="solexa_tools">
<tool file="sr_mapping/lastz_wrapper.xml" />
tools/ncbi_blast_plus/blast_filter_fasta.py
-38
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@@ -1,38 +0,0 @@
#!/usr/bin/env python
"""Filter a FASTA file using tabular output, e.g. from BLAST.
Takes five command line options, tabular BLAST filename, ID column number
(using one based counting), input FASTA filename, and two output FASTA
filenames (for records with and without any BLAST hits).
In the default NCBI BLAST+ tabular output, the query sequence ID is in column
one, and the ID of the match from the database is in column two.
"""
import sys
from galaxy_utils.sequence.fasta import fastaReader, fastaWriter
#Parse Command Line
blast_file, blast_col, in_file, out_positive_file, out_negative_file = sys.argv[1:]
blast_col = int(blast_col)-1
assert blast_col >= 0
#Read tabular BLAST file and record all queries with hit(s)
ids = set()
blast_handle = open(blast_file, "rU")
for line in blast_handle:
ids.add(line.split("\t")[blast_col])
blast_handle.close()
#Write filtered FASTA file based on IDs from BLAST file
reader = fastaReader(open(in_file, "rU"))
positive_writer = fastaWriter(open(out_positive_file, "w"))
negative_writer = fastaWriter(open(out_negative_file, "w"))
for record in reader:
#The [1:] is because the fastaReader leaves the > on the identifer.
if record.identifier and record.identifier.split()[0][1:] in ids:
positive_writer.write(record)
else:
negative_writer.write(record)
positive_writer.close()
negative_writer.close()
reader.close()
tools/ncbi_blast_plus/blast_filter_fasta.xml
-37
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@@ -1,37 +0,0 @@
<tool id="blast_filter_fasta" name="Filter FASTA using BLAST output" version="0.0.1">
<description>Divide a FASTA file based on BLAST hits</description>
<command interpreter="python">
blast_filter_fasta.py $blast_file $blast_col $in_file $out_positive_file $out_negative_file
</command>
<inputs>
<param name="in_file" type="data" format="fasta" label="FASTA file to filter"/>
<param name="blast_file" type="data" format="tabular" label="Tabular BLAST output"/>
<param name="blast_col" type="select" label="Column containing FASTA identifiers">
<option value="1">Column 1 - BLAST query ID</option>
<option value="2">Column 2 - BLAST match ID</option>
</param>
</inputs>
<outputs>
<data name="out_positive_file" format="fasta" label="Sequences with BLAST hits" />
<data name="out_negative_file" format="fasta" label="Sequences without BLAST hits" />
</outputs>
<requirements>
</requirements>
<tests>
</tests>
<help>
**What it does**
Typical use would be to take a multi-sequence FASTA and the tabular output of
running BLAST on it, and divide the FASTA file in two: those sequence with a
BLAST hit, and those without.
In the default NCBI BLAST+ tabular output, the query sequence ID is in column
one, and the ID of the match from the database is in column two.
This allows you to filter the FASTA file for the subjects in the BLAST search,
rather than filtering the FASTA file for the queries in the BLAST search.
</help>
</tool>