mirror of
https://github.com/galaxyproject/galaxy.git
synced 2026-10-29 17:42:12 +08:00
peterjc
aafd2d0a51
When using this tool to produce a tally table, often want to have the most common entries listed first - rather than the sort order coming from the values being counted.
139 lines
4.2 KiB
Python
139 lines
4.2 KiB
Python
# Filename: uniq.py
|
|
# Author: Ian N. Schenck
|
|
# Version: 19/12/2005
|
|
#
|
|
# This script accepts an input file, an output file, a column
|
|
# delimiter, and a list of columns. The script then grabs unique
|
|
# lines based on the columns, and returns those records with a count
|
|
# of occurences of each unique column (ignoring trailing spaces),
|
|
# inserted before the columns.
|
|
#
|
|
# This executes the command pipeline:
|
|
# cut -f $fields | sort | uniq -C
|
|
#
|
|
# -i Input file
|
|
# -o Output file
|
|
# -d Delimiter
|
|
# -c Column list (Comma Seperated)
|
|
|
|
import sys
|
|
import re
|
|
import string
|
|
import commands
|
|
|
|
# This function is exceedingly useful, perhaps package for reuse?
|
|
def getopts(argv):
|
|
opts = {}
|
|
while argv:
|
|
if argv[0][0] == '-':
|
|
opts[argv[0]] = argv[1]
|
|
argv = argv[2:]
|
|
else:
|
|
argv = argv[1:]
|
|
return opts
|
|
|
|
def main():
|
|
args = sys.argv[1:]
|
|
|
|
try:
|
|
opts = getopts(args)
|
|
except IndexError:
|
|
print "Usage:"
|
|
print " -i Input file"
|
|
print " -o Output file"
|
|
print " -c Column list (comma seperated)"
|
|
print " -d Delimiter:"
|
|
print " T Tab"
|
|
print " C Comma"
|
|
print " D Dash"
|
|
print " U Underscore"
|
|
print " P Pipe"
|
|
print " Dt Dot"
|
|
print " Sp Space"
|
|
print " -s Sorting: value (default), largest, or smallest"
|
|
return 0
|
|
|
|
outputfile = opts.get("-o")
|
|
if outputfile == None:
|
|
print "No output file specified."
|
|
return -1
|
|
|
|
inputfile = opts.get("-i")
|
|
if inputfile == None:
|
|
print "No input file specified."
|
|
return -2
|
|
|
|
delim = opts.get("-d")
|
|
if delim == None:
|
|
print "Field delimiter not specified."
|
|
return -3
|
|
|
|
columns = opts.get("-c")
|
|
if columns == None or columns == 'None':
|
|
print "Columns not specified."
|
|
return -4
|
|
|
|
sorting = opts.get("-s")
|
|
if sorting is None:
|
|
sorting = "value"
|
|
if sorting not in ["value", "largest", "smallest"]:
|
|
print "Unknown sorting option %r" % sorting
|
|
return -5
|
|
|
|
# All inputs have been specified at this point, now validate.
|
|
fileRegEx = re.compile("^[A-Za-z0-9./\-_]+$")
|
|
columnRegEx = re.compile("([0-9]{1,},?)+")
|
|
|
|
if not columnRegEx.match(columns):
|
|
print "Illegal column specification."
|
|
return -4
|
|
if not fileRegEx.match(outputfile):
|
|
print "Illegal output filename."
|
|
return -5
|
|
if not fileRegEx.match(inputfile):
|
|
print "Illegal input filename."
|
|
return -6
|
|
|
|
column_list = re.split(",",columns)
|
|
columns_for_display = "c" + ", c".join(column_list)
|
|
|
|
commandline = "cut "
|
|
# Set delimiter
|
|
if delim=='C':
|
|
commandline += "-d \",\" "
|
|
if delim=='D':
|
|
commandline += "-d \"-\" "
|
|
if delim=='U':
|
|
commandline += "-d \"_\" "
|
|
if delim=='P':
|
|
commandline += "-d \"|\" "
|
|
if delim=='Dt':
|
|
commandline += "-d \".\" "
|
|
if delim=='Sp':
|
|
commandline += "-d \" \" "
|
|
|
|
# set columns
|
|
commandline += "-f " + columns
|
|
# we want to remove *trailing* spaces from each field,
|
|
# so look for spaces then tab (for first and middle selected columns)
|
|
# and replacw with just tab, and remove any spaces at end of the line
|
|
# (for the final selected column):
|
|
commandline += " " + inputfile + " | sed 's/\ *\t/\t/' | sed 's/\ *$//'"
|
|
commandline += " | sort | uniq -c"
|
|
# uniq -C puts counts at the start, so we can sort lines by numerical value
|
|
if sorting == "largest":
|
|
commandline += " | sort -n -r"
|
|
elif sorting == "smallest":
|
|
commandline += " | sort -n"
|
|
# uniq -C produces lines with leading spaces, use sed to remove that
|
|
# uniq -C puts a space between the count and the field, want a tab.
|
|
# To replace just first tab, use sed again with 1 as the index
|
|
commandline += " | sed 's/^\ *//' | sed 's/ /\t/1' > " + outputfile
|
|
errorcode, stdout = commands.getstatusoutput(commandline)
|
|
|
|
print "Count of unique values in " + columns_for_display
|
|
return errorcode
|
|
|
|
if __name__ == "__main__":
|
|
main()
|