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Fixed a bug in the new joiner tool

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This commit is contained in:
Kelly Vincent
2010-04-12 19:11:36 -04:00
parent 75510d142b
commit 1e4a83ac22
2 changed files with 68 additions and 37 deletions
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tools/new_operations/column_join.py
+64 -33
View File
@@ -19,6 +19,32 @@ def stop_err( msg ):
sys.stderr.write( msg )
sys.exit()
def hinge_compare( hinge1, hinge2 ):
"""
Compares items like 'chr10' and 'chrM' or 'scaffold2' and scaffold10' so that
first part handled as text but last part as number
"""
pat = re.compile( '(?P<text>\D*)(?P<number>\d+)?' )
split_hinge1 = hinge1.split( '\t' )
split_hinge2 = hinge2.split( '\t' )
for i in range( len( split_hinge1 ) ):
if split_hinge1[ i ] == split_hinge2[ i ]:
continue
try:
if int( split_hinge1[ i ] ) > int( split_hinge2[ i ] ):
return 1
else:
return -1
except ValueError:
try:
if float( split_hinge1[ i ] ) > float( split_hinge2[ i ] ):
return 1
else:
return -1
except ValueError:
return ref_compare( split_hinge1[ i ], split_hinge2[ i ])
return 0
def ref_compare( ref1, ref2 ):
"""
Compares items like 'chr10' and 'chrM' or 'scaffold2' and scaffold10' so that
@@ -52,35 +78,31 @@ def ref_compare( ref1, ref2 ):
elif text1 < text2:
return -1
def ref_pos_sort( infile, outfile ):
def hinge_sort( infile, outfile, hinge ):
"""Given input file name, sorts logically (text vs. numeric) into provided output file name."""
ref_locs = {}
hinge_locs = {}
bad_lines = []
fin = open( infile, 'rb' )
line = fin.readline()
while line.strip():
if True:
try:
hinge_parts = line.split( '\t' )[ :hinge ]
try:
ref_seq, ref_loc = line.split( '\t' )[:2]
try:
ref_locs[ ref_seq ][ long( ref_loc ) ] = fin.tell() - len( line.strip() ) - 1
except KeyError:
ref_locs[ ref_seq ] = { long( ref_loc ): fin.tell() - len( line.strip() ) - 1 }
except ValueError:
bad_lines.append( line )
except ValueError:
bad_line.append( line )
hinge_locs[ '\t'.join( hinge_parts ) ].append( fin.tell() - len( line.strip() ) - 1 )
except KeyError:
hinge_locs[ '\t'.join( hinge_parts ) ] = [ fin.tell() - len( line.strip() ) - 1 ]
except ValueError:
bad_line.append( line )
line = fin.readline()
fin.close()
refs = ref_locs.keys()
refs.sort( ref_compare )
fin = open( infile, 'rb' )
fout = open( outfile, 'wb' )
for ref in refs:
locs = ref_locs[ ref ].keys()
locs.sort()
hinge_locs_sorted = hinge_locs.keys()
hinge_locs_sorted.sort( hinge_compare )
for hinge_loc in hinge_locs_sorted:
locs = hinge_locs[ hinge_loc ]
for loc in locs:
fin.seek( ref_locs[ ref ][ loc ] )
fin.seek( loc )
fout.write( fin.readline() )
fout.close()
fin.close()
@@ -90,14 +112,17 @@ def min_chr_pos( chr_pos ):
if len( chr_pos ) == 0 and ''.join( chr_pos ):
return ''
min_loc = len( chr_pos )
min_ref_pos = []
min_hinge = []
loc = 0
for c_pos in chr_pos:
if c_pos.strip():
split_c = c_pos.split( '\t' )
ref, pos = c_pos.split( '\t' )[:2]
pos = int( pos )
if not min_ref_pos:
min_ref_pos = [ ref, pos ]
if not min_hinge:
min_hinge = split_c
min_loc = loc
else:
ref_comp = ref_compare( ref, min_ref_pos[0] )
@@ -126,25 +151,33 @@ def __main__():
tmp_file = tempfile.NamedTemporaryFile()
tmp_file_name = tmp_file.name
tmp_file.close()
ref_pos_sort( in_file, tmp_file_name )
hinge_sort( in_file, tmp_file_name, hinge )
tmp_file = open( tmp_file_name, 'rb' )
tmp_input_files.append( tmp_file )
# cycle through files, getting smallest line of all files one at a time
# also have to keep track of vertical position of extra columns
fout = file( output, 'w' )
old_current_chr_pos = ''
old_current = ''
first_line = True
current_lines = [ f.readline() for f in tmp_input_files ]
last_lines = ''.join( current_lines ).strip()
last_loc = -1
i = 0
while last_lines:
# get the "minimum" hinge, which should come first, and the file location in list
current_chr_pos, loc = min_chr_pos( [ '\t'.join( line.split( '\t' )[ :hinge ] ) for line in current_lines ] )
hinges = [ '\t'.join( line.split( '\t' )[ :hinge ] ) for line in current_lines ]
hinge_dict = {}
for i in range( len( hinges ) ):
if not hinge_dict.has_key( hinges[ i ] ):
hinge_dict[ hinges[ i ] ] = i
hinges.sort( hinge_compare )
hinges = [ h for h in hinges if h ]
current, loc = hinges[0], hinge_dict[ hinges[0] ]
# first output empty columns for vertical alignment (account for "missing" files)
if current_chr_pos != old_current_chr_pos:
if current != old_current:
last_loc = -1
if loc - last_loc > 1:
current_data = [ '' for col in range( ( loc - last_loc - 1 ) * len( cols[ hinge: ] ) ) ]
current_data = [ '' for col in range( ( loc - last_loc - 1 ) * len( [ col for col in cols if col > hinge ] ) ) ]
else:
current_data = []
# now output actual data
@@ -154,22 +187,20 @@ def __main__():
if col > hinge:
current_data.append( split_line[ col - 1 ] )
current_lines[ loc ] = tmp_input_files[ loc ].readline()
if current_chr_pos == old_current_chr_pos:
fout.write( '\t%s' % '\t'.join( current_data ) )
if current == old_current:
if current_data:
fout.write( '\t%s' % '\t'.join( current_data ) )
else:
if not first_line:
fout.write( '\n' )
fout.write( '%s\t%s' % ( current_chr_pos, '\t'.join( current_data ) ) )
fout.write( '%s\t%s' % ( current, '\t'.join( current_data ) ) )
first_line = False
old_current_chr_pos = current_chr_pos
if last_lines == ''.join( current_lines ).strip():
break
old_current = current
last_lines = ''.join( current_lines ).strip()
last_loc = loc
fout.write( '\n' )
for f in tmp_input_files:
os.unlink( f.name )
fout.close()
# sys.stderr.write('******************\n'+file(fout.name, 'r').read()+'\n******************\n')
if __name__ == "__main__" : __main__()
tools/new_operations/column_join.xml
+4 -4
View File
@@ -21,7 +21,7 @@
</repeat>
</inputs>
<outputs>
<data name="output" format="pileup" />
<data name="output" format="tabular" />
</outputs>
<tests>
<test>
@@ -30,7 +30,7 @@
<param name="hinge" value="1,2" />
<param name="input2" value="column_join_in2.pileup" ftype="pileup" />
<param name="input" value="column_join_in3.pileup" ftype="pileup" />
<output name="output" file="column_join_out1.pileup" ftype="pileup" />
<output name="output" file="column_join_out1.pileup" ftype="tabular" />
</test>
<test>
<param name="input1" value="column_join_in4.pileup" ftype="pileup" />
@@ -38,7 +38,7 @@
<param name="hinge" value="1,2" />
<param name="input2" value="column_join_in5.pileup" ftype="pileup" />
<param name="input" value="column_join_in6.pileup" ftype="pileup" />
<output name="output" file="column_join_out2.pileup" ftype="pileup" />
<output name="output" file="column_join_out2.pileup" ftype="tabular" />
</test>
<test>
<param name="input1" value="column_join_in7.pileup" ftype="pileup" />
@@ -46,7 +46,7 @@
<param name="hinge" value="1,2" />
<param name="input2" value="column_join_in8.pileup" ftype="pileup" />
<param name="input" value="column_join_in9.pileup" ftype="pileup" />
<output name="output" file="column_join_out3.pileup" ftype="pileup" />
<output name="output" file="column_join_out3.pileup" ftype="tabular" />
</test>
</tests>
<help>