I was on Seqanswer forum and found someone asked a question:
http://seqanswers.com/forums/showthread.php?p=119263&posted=1#post119263
"Hi guys,
i hv got a GO file for my differentially expressed genes file, it goes like:
FBgn00001 GO:0016301 [Name:****(annotation)]
FBgn00002 GO:0016301 [Name:****(annotation)]
FBgn00003 GO:0016301 [Name:****(annotation)]
FBgn00004 GO:0003700 [Name:****(annotation)]
FBgn00004 GO:0009651 [Name:****(annotation)]
FBgn00004 GO:0006355 [Name:****(annotation)]
FBgn00005 GO:0009556 [Name:****(annotation)]
FBgn00005 GO:0005515 [Name:****(annotation)]
FBgn00005 GO:0080019 [Name:****(annotation)]
FBgn00005 GO:0016563 [Name:****(annotation)]
FBgn00005 GO:0016627 [Name:****(annotation)]
FBgn00006 GO:0003700 [Name:****(annotation)]
FBgn00006 GO:0010018 [Name:****(annotation)]
now i want to use WEGO ,so i need to convert it like:
FBgn00001 GO:0016301
FBgn00002 GO:0016301
FBgn00003 GO:0016301
FBgn00004 GO:0003700 GO:0009651 GO:0006355
FBgn00005 GO:0009556 GO:0005515 GO:0080019 GO:0016563 GO:0016627
FBgn00006 GO:0003700 GO:0010018
I think this could be solved using a perl script. I am not able to do this since i am a beginner. Can someone help me out? A simple perl script is good enough for me^^ "
The question is on very basic text manipulation, and I quickly wrote a python script for that:
import csv
reader = csv.reader(open("GO.txt","r"), delimiter="\t")
new={}
for row in reader:
if row[0] not in new.keys():
new[row[0]] = [row[1]]
else:
new[row[0]].append(row[1])
with open("wego.txt","w") as f:
for key, value in sorted(new.items()):
f.write(key+"\t"+"\t".join(value)+"\n")
update 10/19/13, I used the gist in github to display the code
basically, I store the ID as the key, and a list of GO terms as the value, and then write the dictionary
to a txt file.
I was thinking if there are any easier ways to do it, I mean by awk or sed.
A quick google search
http://stackoverflow.com/questions/10286522/group-by-sum-from-shell/10289422#10289422
the question is a little bit different from the one above:
"I have a large file containing data like this:
a 23
b 8
a 22
b 1
I want to be able to get this:
a 45
b 9
"
awk array is very handy for that purpose see a post here http://www.thegeekstuff.com/2010/03/awk-arrays-explained-with-5-practical-examples/:
let's first creat the file:
tommy@tommy-ThinkPad-T420:~$ cat > foo.txt
a 23
b 8
a 22
b 1
#control+D to indicate cat this is the end of the file.
tommy@tommy-ThinkPad-T420:~$ cat foo.txt | awk '{new[$1]+=$2}END{for (key in new) print key, new[key]}'
a 45
b 9
#or you can redirect the result to a new file
tommy@tommy-ThinkPad-T420:~$ cat foo.txt | awk '{new[$1]+=$2}END{for (key in new) print key, new[key]}' > new.txt
I do not know whether the array value can hold multiple strings like a list in python.
updated on 10/21/13, an awk one liner can solve this problem
tommy@tommy-ThinkPad-T420:~$ cat foo.txt | awk '{ if (new[$1]) new[$1]=new[$1]"\t"$2; else new[$1]=$2;} END { for (i in new) print i, new[i]}' OFS="\t"
a 23 22
b 8 1
Amazing awk!