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Bug fixes to LCA tool

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This commit is contained in:
Guruprasad Anada
2010-02-22 16:22:12 -05:00
parent 7e96a18c68
commit f47cd6a27f
2 changed files with 50 additions and 23 deletions
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tools/taxonomy/lca.py
+32 -17
View File
@@ -42,6 +42,16 @@ def main():
except:
stop_err("Syntax error: Use correct syntax: program infile outfile")
fin = open(sys.argv[1],'r')
for j, line in enumerate( fin ):
elems = line.strip().split('\t')
if len(elems) < 24:
stop_err("The format of the input dataset is incorrect. Taxonomy datatype should contain at least 24 columns.")
if j > 30:
break
cols = range(1,len(elems))
fin.close()
group_col = 0
tmpfile = tempfile.NamedTemporaryFile()
@@ -68,11 +78,11 @@ def main():
remaining_vals = []
skipped_lines = 0
fout = open(outfile, "w")
cols = range(1,25)
block_valid = False
for ii, line in enumerate( file( tmpfile.name )):
if line and not line.startswith( '#' ):
if line and not line.startswith( '#' ) and len(line.split('\t')) >= 24: #Taxonomy datatype should have at least 24 columns
line = line.rstrip( '\r\n' )
try:
fields = line.split("\t")
@@ -95,14 +105,11 @@ def main():
corresponding aggregate values into the output file. This works
due to the sort on group_col we've applied to the data above.
"""
out_list = ['']*25
out_list = ['']*24
out_list[0] = str(prev_item)
out_list[1] = str(prev_vals[0][0])
out_list[2] = str(prev_vals[1][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:
@@ -113,11 +120,17 @@ def main():
out_list[k+1] = 'n'
k += 1
j = 0
while True:
try:
out_list.append(str(prev_vals[23+j][0]))
j += 1
except:
break
if rank_bound == 0:
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).strip()
@@ -144,15 +157,11 @@ def main():
skipped_lines += 1
# Handle the last grouped value
out_list = ['']*25
out_list = ['']*24
out_list[0] = str(prev_item)
out_list[1] = str(prev_vals[0][0])
out_list[2] = str(prev_vals[1][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:
@@ -163,11 +172,17 @@ def main():
out_list[k+1] = 'n'
k += 1
j = 0
while True:
try:
out_list.append(str(prev_vals[23+j][0]))
j += 1
except:
break
if rank_bound == 0:
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).strip()
tools/taxonomy/lca.xml
+18 -6
View File
@@ -1,4 +1,4 @@
<tool id="lca1" name="Find lowest diagnostic rank" version="1.0.0">
<tool id="lca1" name="Find lowest diagnostic rank" version="1.0.1">
<description></description>
<command interpreter="python">
lca.py $input1 $out_file1 $rank_bound
@@ -34,11 +34,23 @@
<data format="taxonomy" name="out_file1" metadata_source="input1" />
</outputs>
<tests>
<test>
<param name="input1" value="lca_input.taxonomy" ftype="taxonomy"/>
<param name="rank_bound" value="0" />
<output name="out_file1" file="lca_output.taxonomy" ftype="taxonomy"/>
</test>
<test>
<param name="input1" value="lca_input.taxonomy" ftype="taxonomy"/>
<param name="rank_bound" value="0" />
<output name="out_file1" file="lca_output.taxonomy" ftype="taxonomy"/>
</test>
<test>
<param name="input1" value="lca_input2.taxonomy" ftype="taxonomy"/>
<param name="rank_bound" value="7" />
<output name="out_file1" file="lca_output2.taxonomy" ftype="taxonomy"/>
</test>
<!--Test case with invalid lines -->
<test>
<param name="input1" value="lca_input3.taxonomy" ftype="taxonomy"/>
<param name="rank_bound" value="10" />
<output name="out_file1" file="lca_output3.taxonomy" ftype="taxonomy"/>
</test>
</tests>
<help>