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I have following two lists. List1

m64041_200717_231916/100664277/0_42364 id=2440
m64041_200717_231916/100008029/0_42112 id=244006
m64041_200717_231916/100665802/0_46854 id=2440067
m64041_200717_231916/100008044/0_60161 id=24400
m64041_200717_231916/100928073/0_11804 id=2440152
m64041_200717_231916/10094492/0_44157 id=2440199
m64041_200717_231916/100008373/4102_50601 id=2440234

List2

m64041_200717_231916/100664277/0_42364
m64041_200717_231916/100665802/0_46854
m64041_200717_231916/100928073/0_11804
m64041_200717_231916/10094492/0_44157

These are sequence read ids from a genome file. List1 contains all the ids from the List2 but with some id numbers (id=2440). So the sequence ids are only similar to some extent. I want to compare these two files and I need to filter out List2 sequence ids from List one (with id numbers) as below. Output.

m64041_200717_231916/100664277/0_42364 id=2440
m64041_200717_231916/100665802/0_46854 id=2440067
m64041_200717_231916/100928073/0_11804 id=2440152
m64041_200717_231916/10094492/0_44157 id=2440199

I will be grateful if someone can help me with this issue.

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  • $\begingroup$ It sounds easy but I don't really understand exactly what you want to compare. Can U expand? $\endgroup$
    – Liam McIntyre
    Feb 4, 2021 at 7:08
  • $\begingroup$ For another example imagine there are two lists. List1. UnitedStates id=12, UnitedKingdom id=15, Spain id=20, France id=25, List2 UnitedStates, Spain I want to filter out UnitedStates id=12 and Spain id=20 using the List2. List1 and List2 are two files. Output should be, UnitedStates id=12, Spain id=20 $\endgroup$
    – MudithMMBc
    Feb 4, 2021 at 7:15
  • $\begingroup$ ah, so only keep whats in list 2? $\endgroup$
    – Liam McIntyre
    Feb 4, 2021 at 7:25
  • $\begingroup$ Yeah. list2 will be the query. $\endgroup$
    – MudithMMBc
    Feb 4, 2021 at 7:29

3 Answers 3

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3
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You really need to learn some python :)

with open('/path/list2.txt', 'r') as fin:
    to_keep = set([])
    for line in fin:
        to_keep.add(line.strip())
        
with open('/path/list1.txt', 'r') as fin:
    with open('/path/list3.txt', 'w') as fout:
        for line in fin:
            if line.strip().split(' ')[0] in to_keep:
                fout.write(line)
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5
  • $\begingroup$ Thank you very much. It worked. Yes, I need to learn python. $\endgroup$
    – MudithMMBc
    Feb 4, 2021 at 17:59
  • $\begingroup$ And another question. Do you know a way to filter out/remove those sequences from the original fasta file using the id list created from the above code? I have a piece of code I used earlier to remove sequences using a list. But since these ids contains a space, It's not working now. I tried to change it, but it didn't work. It'll be an easy thing for you,but I couldn't figure it out. Can you please help? $\endgroup$
    – MudithMMBc
    Feb 4, 2021 at 18:09
  • $\begingroup$ Sure. Post a new question with an example plz $\endgroup$
    – Liam McIntyre
    Feb 4, 2021 at 20:16
  • 2
    $\begingroup$ Why would you hardcode two file names instead of just reading argv for the input file and printing to stdout so you can then redirect? $\endgroup$
    – terdon
    Feb 5, 2021 at 15:34
  • $\begingroup$ He asked for files $\endgroup$
    – Liam McIntyre
    Feb 5, 2021 at 19:16
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There is no need for a highlevel language in such a simple case, an awk oneliner does just fine:

$ awk -F " " 'FNR==NR {a[$1]; next} $1 in a' List2 List1
m64041_200717_231916/100664277/0_42364 id=2440
m64041_200717_231916/100665802/0_46854 id=2440067
m64041_200717_231916/100928073/0_11804 id=2440152
m64041_200717_231916/10094492/0_44157 id=2440199
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0
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This can be done in python easily. If you have different text files then you can load them into a python list and follow from step 2

# Step 1
list1 = ["m64041_200717_231916/100664277/0_42364 id=2440",
"m64041_200717_231916/100008029/0_42112 id=244006",
"m64041_200717_231916/100665802/0_46854 id=2440067",
"m64041_200717_231916/100008044/0_60161 id=24400",
"m64041_200717_231916/100928073/0_11804 id=2440152",
"m64041_200717_231916/10094492/0_44157 id=2440199",
"m64041_200717_231916/100008373/4102_50601 id=2440234"]

list2 = ["m64041_200717_231916/100664277/0_42364",
"m64041_200717_231916/100665802/0_46854",
"m64041_200717_231916/100928073/0_11804",
"m64041_200717_231916/10094492/0_44157"]

# Step 2
split_list1 = [ele.split(" ")[0] for ele in list1 ]
mapdict = {split_list1[i]:list1[i] for i in range(len(list1))}
common = [value for value in split_list1 if value in list2] 
required = [mapdict[x] for x in common]
print(required)
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