mirror of
https://github.com/galaxyproject/galaxy.git
synced 2026-09-24 16:30:27 +08:00
Tool to find the least common ancestor added under Taxonomy section.
This commit is contained in:
Guruprasad Anada
@@ -0,0 +1,145 @@
|
||||
#!/usr/bin/env python
|
||||
#Guruprasad Ananda
|
||||
"""
|
||||
This tool provides the SQL "group by" functionality.
|
||||
"""
|
||||
import sys, string, re, commands, tempfile, random
|
||||
#from rpy import *
|
||||
|
||||
def stop_err(msg):
|
||||
sys.stderr.write(msg)
|
||||
sys.exit()
|
||||
|
||||
def main():
|
||||
try:
|
||||
inputfile = sys.argv[1]
|
||||
outfile = sys.argv[2]
|
||||
except:
|
||||
stop_err("Syntax error: Use correct syntax: program infile outfile")
|
||||
group_col = 0
|
||||
|
||||
tmpfile = tempfile.NamedTemporaryFile()
|
||||
|
||||
try:
|
||||
"""
|
||||
The -k option for the Posix sort command is as follows:
|
||||
-k, --key=POS1[,POS2]
|
||||
start a key at POS1, end it at POS2 (origin 1)
|
||||
In other words, column positions start at 1 rather than 0, so
|
||||
we need to add 1 to group_col.
|
||||
if POS2 is not specified, the newer versions of sort will consider the entire line for sorting. To prevent this, we set POS2=POS1.
|
||||
"""
|
||||
command_line = "sort -f -k " + str(group_col+1) +"," + str(group_col+1) + " -o " + tmpfile.name + " " + inputfile
|
||||
except Exception, exc:
|
||||
stop_err( 'Initialization error -> %s' %str(exc) )
|
||||
|
||||
error_code, stdout = commands.getstatusoutput(command_line)
|
||||
|
||||
if error_code != 0:
|
||||
stop_err( "Sorting input dataset resulted in error: %s: %s" %( error_code, stdout ))
|
||||
|
||||
prev_item = ""
|
||||
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
|
||||
|
||||
for ii, line in enumerate( file( tmpfile.name )):
|
||||
if line and not line.startswith( '#' ):
|
||||
line = line.rstrip( '\r\n' )
|
||||
try:
|
||||
fields = line.split("\t")
|
||||
item = fields[group_col]
|
||||
if prev_item != "":
|
||||
# At this level, we're grouping on values (item and prev_item) in group_col
|
||||
if item == prev_item:
|
||||
# Keep iterating and storing values until a new value is encountered.
|
||||
if block_valid:
|
||||
for i, col in enumerate(cols):
|
||||
if col >= 3:
|
||||
prev_vals[i].append(fields[col].strip())
|
||||
if len(set(prev_vals[i])) > 1:
|
||||
block_valid = False
|
||||
break
|
||||
|
||||
else:
|
||||
"""
|
||||
When a new value is encountered, write the previous value and the
|
||||
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[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])
|
||||
#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:
|
||||
out_list[col] = prev_vals[k][0]
|
||||
else:
|
||||
break
|
||||
while k < 23:
|
||||
out_list[k+1] = 'n'
|
||||
k += 1
|
||||
|
||||
print >>fout, '\t'.join(out_list)
|
||||
|
||||
block_valid = True
|
||||
prev_item = item
|
||||
prev_vals = []
|
||||
for col in cols:
|
||||
val_list = []
|
||||
val_list.append(fields[col].strip())
|
||||
prev_vals.append(val_list)
|
||||
|
||||
else:
|
||||
# This only occurs once, right at the start of the iteration.
|
||||
block_valid = True
|
||||
prev_item = item #groupby item
|
||||
for col in cols: #everyting else
|
||||
val_list = []
|
||||
val_list.append(fields[col].strip())
|
||||
prev_vals.append(val_list)
|
||||
|
||||
except Exception, exc:
|
||||
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)
|
||||
out_list[1] = str(prev_vals[0][0])
|
||||
out_list[2] = str(prev_vals[1][0])
|
||||
out_list[24] = str(prev_vals[23][0])
|
||||
for k, col in enumerate(cols):
|
||||
if col >= 3 and col < 24:
|
||||
if len(set(prev_vals[k])) == 1:
|
||||
out_list[col] = prev_vals[k][0]
|
||||
else:
|
||||
break
|
||||
while k < 23:
|
||||
out_list[k+1] = 'n'
|
||||
k += 1
|
||||
|
||||
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
|
||||
|
||||
if __name__ == "__main__":
|
||||
main()
|
||||
@@ -0,0 +1,12 @@
|
||||
<tool id="lca1" name="Least Common Ancestor" version="1.0.0">
|
||||
<description></description>
|
||||
<command interpreter="python">
|
||||
lca.py $input1 $out_file1
|
||||
</command>
|
||||
<inputs>
|
||||
<param format="taxonomy" name="input1" type="data" label="Select taxonomy dataset"/>
|
||||
</inputs>
|
||||
<outputs>
|
||||
<data format="taxonomy" name="out_file1" metadata_source="input1" />
|
||||
</outputs>
|
||||
</tool>
|
||||
Reference in New Issue
Block a user