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https://github.com/galaxyproject/galaxy.git
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Merged
This commit is contained in:
Ian Schenck
@@ -155,6 +155,7 @@
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<tool file="taxonomy/t2t_report.xml" />
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<tool file="taxonomy/t2ps_wrapper.xml" />
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<tool file="taxonomy/find_diag_hits.xml" />
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<tool file="taxonomy/lca.xml" />
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<tool file="taxonomy/poisson2test.xml" />
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</section>
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<section name="Solexa tools" id="solexa_tools">
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+22
-30
@@ -1,10 +1,9 @@
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#!/usr/bin/env python
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#Guruprasad Ananda
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"""
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This tool provides the SQL "group by" functionality.
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Least Common Ancestor tool.
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"""
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import sys, string, re, commands, tempfile, random
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#from rpy import *
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def stop_err(msg):
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sys.stderr.write(msg)
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@@ -42,8 +41,8 @@ def main():
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"""
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except:
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stop_err("Syntax error: Use correct syntax: program infile outfile")
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group_col = 0
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tmpfile = tempfile.NamedTemporaryFile()
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try:
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@@ -68,10 +67,6 @@ def main():
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prev_vals = []
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remaining_vals = []
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skipped_lines = 0
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first_invalid_line = 0
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invalid_line = ''
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invalid_value = ''
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invalid_column = 0
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fout = open(outfile, "w")
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cols = range(1,25)
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block_valid = False
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@@ -104,9 +99,10 @@ def main():
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out_list[0] = str(prev_item)
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out_list[1] = str(prev_vals[0][0])
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out_list[2] = str(prev_vals[1][0])
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out_list[24] = str(prev_vals[23][0])
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#print >> fout, prev_vals
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#sys.exit()
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try:
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out_list[24] = str(prev_vals[23][0])
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except:
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pass
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for k, col in enumerate(cols):
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if col >= 3 and col < 24:
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if len(set(prev_vals[k])) == 1:
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@@ -116,17 +112,14 @@ def main():
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while k < 23:
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out_list[k+1] = 'n'
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k += 1
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# print >>fout, '\t'.join(out_list)
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if rank_bound == 0:
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print >>fout, ''.join(out_list)
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print 'n'*( 24 - rank_bound )
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print >>fout, '\t'.join(out_list).strip()
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#print 'n'*( 24 - rank_bound )
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else:
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print '\t'.join(out_list[rank_bound:24])
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#print '\t'.join(out_list[rank_bound:24])
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if ''.join(out_list[rank_bound:24]) != 'n'*( 24 - rank_bound ):
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print >>fout, '\t'.join(out_list)
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print >>fout, '\t'.join(out_list).strip()
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block_valid = True
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prev_item = item
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@@ -145,21 +138,21 @@ def main():
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val_list.append(fields[col].strip())
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prev_vals.append(val_list)
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except Exception, exc:
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except:
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skipped_lines += 1
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if not first_invalid_line:
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first_invalid_line = ii+1
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else:
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skipped_lines += 1
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if not first_invalid_line:
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first_invalid_line = ii+1
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# Handle the last grouped value
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out_list = ['']*25
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out_list[0] = str(prev_item)
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out_list[1] = str(prev_vals[0][0])
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out_list[2] = str(prev_vals[1][0])
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out_list[24] = str(prev_vals[23][0])
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try:
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out_list[24] = str(prev_vals[23][0])
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except:
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pass
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for k, col in enumerate(cols):
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if col >= 3 and col < 24:
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if len(set(prev_vals[k])) == 1:
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@@ -171,16 +164,15 @@ def main():
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k += 1
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if rank_bound == 0:
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print >>fout, '\t'.join(out_list)
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print >>fout, '\t'.join(out_list).strip()
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else:
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print ''.join(out_list[rank_bound:24])
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print 'n'*( 24 - rank_bound )
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#print ''.join(out_list[rank_bound:24])
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#print 'n'*( 24 - rank_bound )
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if ''.join(out_list[rank_bound:24]) != 'n'*( 24 - rank_bound ):
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print >>fout, '\t'.join(out_list)
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print >>fout, '\t'.join(out_list).strip()
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if skipped_lines > 0:
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msg= "Skipped %d invalid lines starting with line %d. Value '%s' in column %d is not numeric." % ( skipped_lines, first_invalid_line, invalid_value, invalid_column )
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print msg
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print "Skipped %d invalid lines." % ( skipped_lines )
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if __name__ == "__main__":
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main()
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+48
-7
@@ -1,12 +1,12 @@
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<tool id="lca1" name="Least Common Ancestor" version="1.0.0">
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<tool id="lca1" name="Find lowest diagnostic rank" version="1.0.0">
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<description></description>
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<command interpreter="python">
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lca.py $input1 $out_file1 $rank_bound
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</command>
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<inputs>
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<param format="taxonomy" name="input1" type="data" label="Select taxonomy dataset"/>
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<param name="rank_bound" label="rank bound" type="select" help="Choose smallest diagnostic level">
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<option value="0">Everything</option>
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<param format="taxonomy" name="input1" type="data" label="for taxonomy dataset"/>
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<param name="rank_bound" label="require the lowest rank to be at least" type="select">
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<option value="0">No restriction</option>
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<option value="3">Superkingdom</option>
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<option value="4">Kingdom</option>
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<option value="5">Subkingdom</option>
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@@ -32,13 +32,54 @@
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</inputs>
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<outputs>
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<data format="taxonomy" name="out_file1" metadata_source="input1" />
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</outputs>
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</outputs>
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<tests>
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<test>
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<param name="input1" value="lca_input.taxonomy" ftype="taxonomy"/>
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<param name="rank_bound" value="0" />
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<output name="out_file1" file="lca_output.taxonomy" ftype="taxonomy"/>
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</test>
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</tests>
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<help>
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<help>
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**What it does**
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When performing metagenomic analyses it is often necessary to identify sequence reads corresponding to a particular taxonomic group, or, in other words, diagnostic of a particular taxonomic rank. This utility performs this analysis. It takes data generated by *Taxonomy manipulation->Fetch Taxonomic Ranks* as input and outputs either a list of sequence reads unique to a particular taxonomic rank, or a list of taxonomic ranks and the count of unique reads corresponding to each rank.
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This tool identifies the lowest taxonomic rank for which a mategenomic sequencing read is diagnostic. It takes datasets produced by *Fetch Taxonomic Ranks* tool (aka Taxonomy format) as the input.
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-------
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**Example**
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Suppose you have two reads, **read_1** and **read_2**, with the following taxonomic profiles (scroll sideways to see the entire dataset)::
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read_1 1 root superkingdom1 kingdom1 subkingdom1 superphylum1 phylum1 subphylum1 superclass1 class1 subclass1 superorder1 order1 suborder1 superfamily1 family1 subfamily1 tribe1 subtribe1 genus1 subgenus1 species1 subspecies1
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read_1 2 root superkingdom1 kingdom1 subkingdom1 superphylum1 phylum1 subphylum1 superclass1 class1 subclass1 superorder1 order1 suborder1 superfamily1 family1 subfamily1 tribe1 subtribe1 genus2 subgenus2 species2 subspecies2
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read_2 3 root superkingdom1 kingdom1 subkingdom1 superphylum1 phylum3 subphylum3 superclass3 class3 subclass3 superorder3 order3 suborder3 superfamily3 family3 subfamily3 tribe3 subtribe3 genus3 subgenus3 species3 subspecies3
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read_2 4 root superkingdom1 kingdom1 subkingdom1 superphylum1 phylum4 subphylum4 superclass4 class4 subclass4 superorder4 order4 suborder4 superfamily4 family4 subfamily4 tribe4 subtribe4 genus4 subgenus4 species4 subspecies4
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For **read_1** taxonomic labels are consistent until the genus level, where the taxonomy splits into two branches, one ending with *subspecies1* and the other with *subspecies2*. This implies **that the lowest taxomomic rank read_1 can identify is SUBTRIBE**. Similarly, read_2 is diagnostic up until the **superphylum** level. As a results the output of this tool will be::
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read_1 2 root superkingdom1 kingdom1 subkingdom1 superphylum1 phylum1 subphylum1 superclass1 class1 subclass1 superorder1 order1 suborder1 superfamily1 family1 subfamily1 tribe1 subtribe1 n n n n
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read_2 3 root superkingdom1 kingdom1 subkingdom1 superphylum1 n n n n n n n n n n n n n n n n n
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where, **n** means *EMPTY*.
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--------
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**What's up with the drop down?**
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Why do we need the *require the lowest rank to be at least* dropdown? Let's look at the above example again. Suppose you need to find only those reads that are diagnostic on at least phylum level. To do this you need to set the *require the lowest rank to be at least* to **phylum**. As a result your output will look like this::
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read_1 2 root superkingdom1 kingdom1 subkingdom1 superphylum1 phylum1 subphylum1 superclass1 class1 subclass1 superorder1 order1 suborder1 superfamily1 family1 subfamily1 tribe1 subtribe1 n n n n
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.. class:: infomark
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Note, that **read_2** is now omitted as it matches two phyla (**phylum3** and **phylum4**) and therefore is not diagnostic (but rather cosmopolitan) on *phylum* level.
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</help>
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</tool>
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