mirror of
https://github.com/galaxyproject/galaxy.git
synced 2026-09-24 16:30:27 +08:00
119 lines
4.4 KiB
Python
119 lines
4.4 KiB
Python
#!/usr/bin/env python
|
|
# This tool takes a tab-delimited textfile as input and creates another column in the file which is the result of
|
|
# a computation performed on every row in the original file. The tool will skip over invalid lines within the file,
|
|
# informing the user about the number of lines skipped.
|
|
import sys, re, os.path
|
|
from galaxy import eggs
|
|
from galaxy.tools import validation
|
|
from galaxy.datatypes import metadata
|
|
from math import log,exp,sqrt,ceil,floor
|
|
|
|
assert sys.version_info[:2] >= ( 2, 4 )
|
|
|
|
def stop_err( msg ):
|
|
sys.stderr.write( msg )
|
|
sys.exit()
|
|
|
|
inp_file = sys.argv[1]
|
|
out_file = sys.argv[2]
|
|
expr = sys.argv[3]
|
|
round_result = sys.argv[4]
|
|
try:
|
|
in_columns = int( sys.argv[5] )
|
|
except:
|
|
stop_err( "Missing or invalid 'columns' metadata value, click the pencil icon in the history item and select the Auto-detect option to correct it. This tool can only be used with tab-delimited data." )
|
|
if in_columns < 2:
|
|
# To be considered tabular, data must fulfill requirements of the sniff.is_column_based() method.
|
|
stop_err( "Missing or invalid 'columns' metadata value, click the pencil icon in the history item and select the Auto-detect option to correct it. This tool can only be used with tab-delimited data." )
|
|
try:
|
|
in_column_types = sys.argv[6].split( ',' )
|
|
except:
|
|
stop_err( "Missing or invalid 'column_types' metadata value, click the pencil icon in the history item and select the Auto-detect option to correct it. This tool can only be used with tab-delimited data." )
|
|
if len( in_column_types ) != in_columns:
|
|
stop_err( "The 'columns' metadata setting does not conform to the 'column_types' metadata setting, click the pencil icon in the history item and select the Auto-detect option to correct it. This tool can only be used with tab-delimited data." )
|
|
|
|
# Unescape if input has been escaped
|
|
mapped_str = {
|
|
'__lt__': '<',
|
|
'__le__': '<=',
|
|
'__eq__': '==',
|
|
'__ne__': '!=',
|
|
'__gt__': '>',
|
|
'__ge__': '>=',
|
|
'__sq__': '\'',
|
|
'__dq__': '"',
|
|
}
|
|
for key, value in mapped_str.items():
|
|
expr = expr.replace( key, value )
|
|
|
|
# Prepare the column variable names and wrappers for column data types
|
|
cols, type_casts = [], []
|
|
for col in range( 1, in_columns + 1 ):
|
|
col_name = "c%d" % col
|
|
cols.append( col_name )
|
|
col_type = in_column_types[ col - 1 ].strip()
|
|
if round_result == 'no' and col_type == 'int':
|
|
col_type = 'float'
|
|
type_cast = "%s(%s)" % ( col_type, col_name )
|
|
type_casts.append( type_cast )
|
|
|
|
col_str = ', '.join( cols ) # 'c1, c2, c3, c4'
|
|
type_cast_str = ', '.join( type_casts ) # 'str(c1), int(c2), int(c3), str(c4)'
|
|
assign = "%s = line.split( '\\t' )" % col_str
|
|
wrap = "%s = %s" % ( col_str, type_cast_str )
|
|
skipped_lines = 0
|
|
first_invalid_line = 0
|
|
invalid_line = None
|
|
lines_kept = 0
|
|
total_lines = 0
|
|
out = open( out_file, 'wt' )
|
|
|
|
# Read input file, skipping invalid lines, and perform computation that will result in a new column
|
|
code = '''
|
|
for i, line in enumerate( file( inp_file ) ):
|
|
total_lines += 1
|
|
line = line.rstrip( '\\r\\n' )
|
|
if not line or line.startswith( '#' ):
|
|
skipped_lines += 1
|
|
if not invalid_line:
|
|
first_invalid_line = i + 1
|
|
invalid_line = line
|
|
continue
|
|
try:
|
|
%s
|
|
%s
|
|
new_val = %s
|
|
if round_result == "yes":
|
|
new_val = int( round( new_val ) )
|
|
new_line = line + '\\t' + str( new_val )
|
|
print >> out, new_line
|
|
lines_kept += 1
|
|
except:
|
|
skipped_lines += 1
|
|
if not invalid_line:
|
|
first_invalid_line = i + 1
|
|
invalid_line = line
|
|
''' % ( assign, wrap, expr )
|
|
|
|
valid_expr = True
|
|
try:
|
|
exec code
|
|
except Exception, e:
|
|
out.close()
|
|
if str( e ).startswith( 'invalid syntax' ):
|
|
valid_expr = False
|
|
stop_err( 'Expression "%s" likely invalid. See tool tips, syntax and examples.' % expr )
|
|
else:
|
|
stop_err( str( e ) )
|
|
|
|
if valid_expr:
|
|
out.close()
|
|
valid_lines = total_lines - skipped_lines
|
|
print 'Creating column %d with expression %s' % ( in_columns + 1, expr )
|
|
if valid_lines > 0:
|
|
print 'kept %4.2f%% of %d lines.' % ( 100.0*lines_kept/valid_lines, total_lines )
|
|
else:
|
|
print 'Possible invalid expression "%s" or non-existent column referenced. See tool tips, syntax and examples.' % expr
|
|
if skipped_lines > 0:
|
|
print 'Skipped %d invalid lines starting at line #%d: "%s"' % ( skipped_lines, first_invalid_line, invalid_line )
|