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Changes to exception handling in LCA.

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This commit is contained in:
Guruprasad Anada
2009-01-20 13:24:12 -05:00
parent ba3fd2175d
commit 84535eb6e8
1 changed files with 10 additions and 25 deletions
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tools/taxonomy/lca.py
+10 -25
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@@ -1,10 +1,9 @@
#!/usr/bin/env python
#Guruprasad Ananda
"""
This tool provides the SQL "group by" functionality.
Least Common Ancestor tool.
"""
import sys, string, re, commands, tempfile, random
#from rpy import *
def stop_err(msg):
sys.stderr.write(msg)
@@ -42,8 +41,8 @@ def main():
"""
except:
stop_err("Syntax error: Use correct syntax: program infile outfile")
group_col = 0
tmpfile = tempfile.NamedTemporaryFile()
try:
@@ -68,10 +67,6 @@ def main():
prev_vals = []
remaining_vals = []
skipped_lines = 0
first_invalid_line = 0
invalid_line = ''
invalid_value = ''
invalid_column = 0
fout = open(outfile, "w")
cols = range(1,25)
block_valid = False
@@ -105,8 +100,6 @@ def main():
out_list[1] = str(prev_vals[0][0])
out_list[2] = str(prev_vals[1][0])
out_list[24] = str(prev_vals[23][0])
#print >> fout, prev_vals
#sys.exit()
for k, col in enumerate(cols):
if col >= 3 and col < 24:
if len(set(prev_vals[k])) == 1:
@@ -116,17 +109,14 @@ def main():
while k < 23:
out_list[k+1] = 'n'
k += 1
# print >>fout, '\t'.join(out_list)
if rank_bound == 0:
print >>fout, ''.join(out_list)
print 'n'*( 24 - rank_bound )
print >>fout, '\t'.join(out_list)
#print 'n'*( 24 - rank_bound )
else:
print '\t'.join(out_list[rank_bound:24])
#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)
block_valid = True
prev_item = item
@@ -145,15 +135,11 @@ def main():
val_list.append(fields[col].strip())
prev_vals.append(val_list)
except Exception, exc:
except:
skipped_lines += 1
if not first_invalid_line:
first_invalid_line = ii+1
else:
skipped_lines += 1
if not first_invalid_line:
first_invalid_line = ii+1
# Handle the last grouped value
out_list = ['']*25
out_list[0] = str(prev_item)
@@ -173,14 +159,13 @@ def main():
if rank_bound == 0:
print >>fout, '\t'.join(out_list)
else:
print ''.join(out_list[rank_bound:24])
print 'n'*( 24 - rank_bound )
#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)
if skipped_lines > 0:
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 )
print msg
print "Skipped %d invalid lines." % ( skipped_lines )
if __name__ == "__main__":
main()