Merging list problem

Question

Sorry about the bad heading, but the question was not easy to compress into one sentence...

I have two lists of contigs (list1 and list2). They contain mostly unique contigs, but with some overlap. I want to compare list1 and list2 and then create a list3 that contains all contigs in list1 minus those also present in list2. Is this possible with a simple cat/paste/grep/sort/uniq kind of batch command?

Thanks!

Answer 1

Take a look at the Iesi.Collections library , please also refer to the article at Codeproject http://www.codeproject.com/KB/recipes/sets.aspx#xx703510xx

Answer 2

you can do it with sort and uniq :

sort list1 list2 list2 | uniq -u 

any lines in list2 will appear at least twice in the sorted output and so will be filtered by the uniq filter

Answer 3

try comm -23

example (first list: numbers 1-10, second list contains numbers 5-8)

comm -23 <(seq 1 10) <(seq 5 8)

the assumption is that your list1 and list2 are sorted

Answer 4

you did not show any sample data about your lists, so i made it up. assume

$ cat file1
11
12
5
13
7
14
15

$ cat file2
6
7
8
5
4
1

$ awk 'FNR==NR { a[$0]; next } (! ($0 in a) ) ' file2 file1
11
12
13
14
15

if its not what you want, describe more clearly with examples of your lists and your desired output

Answer 5

I also work in Bioinformatics and Genomics.

You'd better use python or perl to make this problem with a overlap/mismacth threadhold if you really want to get the uniq contig sequence!

BY GentleYang from BGI Shenzhen in China :)