there's a mistake here, it takes the lowest
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lessismore
How to remove duplicate rows and keep highest values only for a gene list with scores
Dear all,
i have a two columns table of 20k lines.
1st column: list of gene IDs (there can be duplicated IDs)
2nd column: a value
What i want is to rank my list leaving with only unique gene IDs. For the duplicated gene IDs i want to leave only the ones with the highest score.
here an example, Thanks in advance
TMCS09g1008699 6.4
TMCS09g1008671 6.4
TMCS09g1008672 6.5
TMCS09g1008673 6
TMCS09g1008674 5.4
TMCS09g1008675 5.4
TMCS09g1008676 4.9
TMCS09g1008677 4.6
TMCS09g1008677 4.4
TMCS09g1008679 4.3
TMCS09g1008680 3.9
TMCS09g1008681 3.8
TMCS09g1008682 3.6
TMCS09g1008683 3.5
TMCS09g1008684 3.5
TMCS09g1008685 3.4
TMCS09g1008686 3.4
TMCS09g1008687 3.4
TMCS09g1008688 3
TMCS09g1008689 2.6
TMCS09g1008690 2
TMCS09g1008699 5.9
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arta
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lessismore
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lessismore
2 answers
when i put it into a script in this way:
test = commandArgs(trailingOnly=TRUE)
read.delim(test, header = FALSE, sep ="\t")
test[order(test$V1, -abs(test$V2) ), ] ### sort first
test[ !duplicated(test$V1), ] ### Keep highest
i get a partial output and then this error:
Error in test$V1 : $ operator is invalid for atomic vectors
Calls: order
Execution halted
do you know what that means?
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lessismore
i did, now i get this:
Error in abs(test["V2"]) : non-numeric argument to mathematical function
Calls: order
Execution halted
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lessismore
Very useful code. Any idea how to make this working for a list of data frames???
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thanos_docp •
Can definitely be done in bash/awk, but it'd probably take me longer to figure out when it's easy enough with python.
import sys
in_file = sys.argv[1]
out_file = sys.argv[2]
genes = {}
with open(in_file) as f:
for line in f:
line = line.strip().split()
gene_id = line[0]
val = float(line[1])
# Find and replace dups if necessary.
if gene_id in genes:
if val > genes[gene_id]:
genes[gene_id] = val
else:
genes[gene_id] = val
out = open(out_file, "w")
# Actually print to output.
for x in genes:
output = "\t".join(x, str(genes[x]))
print(output, file = out)
out.close()
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jared.andrews07
Sorry im not proficient in python, assuming i want to put your script in a bash for loop for a list of files, could you tell me how to complete your script?
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lessismore
If you want a single output file for each input file (rather than one for many input files), you can just run the script several times from the command line for your files - which is particularly easy if you segregate them and they have a common file extension:
for x in *.txt; do
python my_python_script.py "$x" "$x".out
done
I've edited my answer slightly to set up the input and output files.
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jared.andrews07
i get this error
File "filter_unique_best_score.py", line 25
print(output, file = out)
^
SyntaxError: invalid syntax
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lessismore
Are you using python 3? If you're using python 2, try adding this as the first line in the script:
from __future__ import print_function.
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jared.andrews07
unfortunately yes.
i did and i get this
Traceback (most recent call last):
File "filter_unique_best_score.py", line 26, in <module>
output = "\t".join(x, string(genes[x]))
NameError: name 'string' is not defined
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lessismore
Oh, that's my mistake. Mixing languages too frequently, python uses str for string conversions, not string. I've updated the code.
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jared.andrews07
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