Hi, I have a text file containing sequence IDs and COG identifiers in following format:
ID=ANJKHBIP_00005;eC_number=6.3.4.2;Name=pyrG_1;dbxref=COG:COG0504;gene=pyrG_1;inference=ab initio prediction:Prodigal:2.6,similar to AA sequence:UniProtKB:P0A7E5;locus_tag=ANJKHBIP_00005;product=CTP synthase
ID=ANJKHBIP_00037;eC_number=1.2.1.5;Name=puuC_1;dbxref=COG:COG1012;gene=puuC_1;inference=ab initio prediction:Prodigal:2.6,similar to AA sequence:UniProtKB:P23883;locus_tag=ANJKHBIP_00037;product=NADP/NAD-dependent aldehyde dehydrogenase PuuC
ID=ANJKHBIP_00038;eC_number=3.6.3.34;Name=fhuC_1;dbxref=COG:COG1120;gene=fhuC_1;inference=ab initio prediction:Prodigal:2.6,similar to AA sequence:UniProtKB:P07821;locus_tag=ANJKHBIP_00038;product=Iron(3+)-hydroxamate import ATP-binding protein FhuC
ID=ANJKHBIP_00043;Name=rpsJ_1;dbxref=COG:COG0051;gene=rpsJ_1;inference=ab initio prediction:Prodigal:2.6,similar to AA sequence:UniProtKB:Q6N4T6;locus_tag=ANJKHBIP_00043;product=30S ribosomal protein S10
From this file I want to extract sequence IDs and COGs in tab separated format something like below:
ANJKHBIP_00005 COG0504
ANJKHBIP_00037 COG1012
and so on...........
I will highly appreciate if anyone can please suggest me a simple code to do this. I tried to use grep and cut options but could not get the things in proper format required above.
•
written
by
Anuj Tyagi •
tr ";" "\n" < input.txt | grep -E '^(ID|dbxref=COG:)' | cut -d '=' -f 2 | paste - -
I don't think OP wants to keep COG: information
tr ";" "\n" < input.txt | grep -E '^(ID|dbxref=COG:)' | cut -d '=' -f 2 | cut -d ':' -f 2 | paste - -
Thanks a lot. it was keeping COG: information earlier. Now it is in exactly my required format.
I think you can do this trick with a single Unix command line but as you are actually learning (I guess) how to parse a text file, it's more interesting to understand the step by step process to parse any file at your convinience.
This is a python script.
#Make your new file ready
new_file = open("your_new_file.csv", "a")
#Open txt file
with open("your_file.txt", 'r') as cog_file:
#For each line of this file
for line in cog_file:
#If the line start with ID
if line.startswith('ID'):
#Split the line on ; and put the result in an array
items = line.split(";")
#For each item in array
for i in items:
#You can get a key/value splitting on =
key = i.split("=")[0]
value = i.split("=")[1]
#If the key is ID
if key == "ID":
#Write it in your new file
new_file.write(value)
#If the key is dbxref
if key == "dbxref":
new_file.write("\t")
#Split the COG term on : to remove COG:
just_cog_code = value.split(":")[1]
#Write it in your new file
new_file.write(just_cog_code)
#Line back
new_file.write("\n")
Hi Bastien, thanks for this script. Yes, I have been learning python but still not very familiar with file parsing. Interesting!
Assuming that gene is always after cog id:
$ grep -Po -i '(?<=ID=).*(?=;gene)' ids.text | sed 's/;.*:/\t/g'
ANJKHBIP_00005 COG0504
ANJKHBIP_00037 COG1012
ANJKHBIP_00038 COG1120
ANJKHBIP_00043 COG0051
with sed:
$ sed 's/ID=\(\w\+\).*\(COG[0-9]\+\).*/\1\t\2/g' ids.text
ANJKHBIP_00005 COG0504
ANJKHBIP_00037 COG1012
ANJKHBIP_00038 COG1120
ANJKHBIP_00043 COG0051
Thanks. yes it does the job.
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Did you try something in Perl or Python ?