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