From 42adeabbc9630e81ca565c053632d579beadd2e1 Mon Sep 17 00:00:00 2001 From: Anton Nekrutenko Date: Wed, 21 Jan 2009 09:51:06 -0500 Subject: [PATCH] Lca commit. The tool itself is written by guru with minor modification made by me. --- tool_conf.xml.sample | 1 + tools/taxonomy/lca.py | 19 ++++++++++----- tools/taxonomy/lca.xml | 55 ++++++++++++++++++++++++++++++++++++------ 3 files changed, 62 insertions(+), 13 deletions(-) diff --git a/tool_conf.xml.sample b/tool_conf.xml.sample index f46c9cef558..bb1dcbab138 100644 --- a/tool_conf.xml.sample +++ b/tool_conf.xml.sample @@ -156,6 +156,7 @@ +
diff --git a/tools/taxonomy/lca.py b/tools/taxonomy/lca.py index ca6a320af24..d70425db366 100644 --- a/tools/taxonomy/lca.py +++ b/tools/taxonomy/lca.py @@ -99,7 +99,10 @@ def main(): out_list[0] = str(prev_item) out_list[1] = str(prev_vals[0][0]) out_list[2] = str(prev_vals[1][0]) - out_list[24] = str(prev_vals[23][0]) + try: + out_list[24] = str(prev_vals[23][0]) + except: + pass for k, col in enumerate(cols): if col >= 3 and col < 24: if len(set(prev_vals[k])) == 1: @@ -111,12 +114,12 @@ def main(): k += 1 if rank_bound == 0: - print >>fout, '\t'.join(out_list) + print >>fout, '\t'.join(out_list).strip() #print 'n'*( 24 - rank_bound ) else: #print '\t'.join(out_list[rank_bound:24]) if ''.join(out_list[rank_bound:24]) != 'n'*( 24 - rank_bound ): - print >>fout, '\t'.join(out_list) + print >>fout, '\t'.join(out_list).strip() block_valid = True prev_item = item @@ -145,7 +148,11 @@ def main(): out_list[0] = str(prev_item) out_list[1] = str(prev_vals[0][0]) out_list[2] = str(prev_vals[1][0]) - out_list[24] = str(prev_vals[23][0]) + try: + out_list[24] = str(prev_vals[23][0]) + except: + pass + for k, col in enumerate(cols): if col >= 3 and col < 24: if len(set(prev_vals[k])) == 1: @@ -157,12 +164,12 @@ def main(): k += 1 if rank_bound == 0: - print >>fout, '\t'.join(out_list) + print >>fout, '\t'.join(out_list).strip() else: #print ''.join(out_list[rank_bound:24]) #print 'n'*( 24 - rank_bound ) if ''.join(out_list[rank_bound:24]) != 'n'*( 24 - rank_bound ): - print >>fout, '\t'.join(out_list) + print >>fout, '\t'.join(out_list).strip() if skipped_lines > 0: print "Skipped %d invalid lines." % ( skipped_lines ) diff --git a/tools/taxonomy/lca.xml b/tools/taxonomy/lca.xml index f608a16cfc3..ca5e246d41a 100644 --- a/tools/taxonomy/lca.xml +++ b/tools/taxonomy/lca.xml @@ -1,12 +1,12 @@ - + lca.py $input1 $out_file1 $rank_bound - - - + + + @@ -32,13 +32,54 @@ - + + + + + + + + - + **What it does** -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. +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. + +------- + +**Example** + +Suppose you have two reads, **read_1** and **read_2**, with the following taxonomic profiles (scroll sideways to see the entire dataset):: + + 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 + 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 + 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 + 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 + +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:: + + 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 + 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 + +where, **n** means *EMPTY*. + +-------- + +**What's up with the drop down?** + +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:: + + 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 + +.. class:: infomark + +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. + + + + \ No newline at end of file