compare IDs and extract corresponding similar sequences with IDs
Hi,
I am stuck in same kind of problem, as a newbie in bioinformatics, I am trying to extract the fasta sequences from a file_2 with similar ids from another list file_1
File_1.fasta
>comp148_c0_seq1
>comp169_c0_seq1
>comp258_c0_seq1
>comp285_c0_seq1
>comp350_c0_seq1
>comp424_c0_seq1
>comp783_c0_seq1
>comp1089_c0_seq1
File_2.fasta
>comp6_c1_seq1 -1 22 237
MAILRFMDSWVVGVNVCGKRPRRFVDPINMIRETIIRVHVRPFGVWISIICLIISLTSQCWKEWRRLLIRRF
>comp11_c0_seq1 -2 35 358
MKEDDKVIEDDEKAEGSKGDIQKEEPGADDETEESNKLIGDNQGKDEANADEDDPQNEETIDKSEENKQREEQQQITLLHFIGRSFASLLKNLLKKTCPSAAEGNNYY
>comp42_c0_seq1 +3 114 305
MPSTLKFLLIYESHWYDKNSEKLVNEFLSLLAHCTQLRYMPILLEDYDLLKLIEEKNTRQFDKI
>comp43_c0_seq1 -2 38 298
MSSSNWAFYIGVSNGHVHDNLLVCKAPNCYCFPTRMDHCYIGGTQHHFEWPTDAISRPQWNGIGDTLGCGILLNPKNELAIFFTANG
>comp48_c0_seq1 +3 18 242
MLYKSLINSKSLRGKTPAEVVNMFANDGQRIFDAVTFAPLVLIGPLVLVGGLIYLLRVIGPVSLLAVSVFLIFDF
>comp53_c0_seq1 -1 55 312
MIGNRLRVKRDKVTLKMEISHCLHSQIIGRGGRNTQKIMRDTGCHIHFPDSNKCLTNPVTMPQQAKNDQVSISGCAKDVEKAREML
>comp56_c0_seq1 -2 110 379
MNNARLNAEINELHAAIHANVHYGRPFKPSHISMNKSQATDRSDNNVCGQLATIDNKNENDHDNDNDDNEANDETRERRRFTVADYMPGG
>comp56_c1_seq1 -1 52 408
MWIWSGPIFSTTILFGHISPFLKPGWRRRAYFCPNFPRRLRVYWATTALLSLLIITFLLGRHFFLGVPSQLTTSPEAIFPSTLGLDCGNVTLSFTAAANDEKVPSNQTLAADKVVASFA
>comp72_c0_seq1 +2 14 271
MYALTWNGLMELKLGADTCPDVNVNWEVFGERGLKSISLFAVADKVFIFSTPNELLVYDRGSATISQFPIASPPLKTLLAVSQSSQ
>comp74_c0_seq1 +3 96 305
MVIPFIFLKAQTIQLEAKDESNFCQNRVDLLAHEVEVRVRIGKRQKRALASSAGCCSCGRGPMGERGAPG
>comp79_c0_seq1 -1 31 213
MASAMFCCQVCMLLSSAYHIFGCHSPNRRKRWLRADLFGVSAGLIGLYLSGLYTSFYHFPV
I used awk:
diff <(cat file_1 | grep ">" | sort) <(cat file_2 | grep ">" | sort) | grep "^<" | awk -F\> '{print $2}'
I'm just getting ids only, I need sequences to corresponding ID also.
Can anyone suggest "awk" or perl code for the same?
Thanks
RV
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Hello ruchi1st2002!
We believe that this post does not fit the main topic of this site.
Please search the forum, There are dozens of questions addressing every variant, and you have the simplest challenge of all.
For this reason we have closed your question. This allows us to keep the site focused on the topics that the community can help with.
If you disagree please tell us why in a reply below, we'll be happy to talk about it.
Cheers!
Ok, no problem. I followed this post "find similar sequences between different sources" but I was unable to get answer using this post and few others, I added this question in other people's comment too, but if someone asks to put this as a unique question, That's y I put this as a separate question.
Thanks
RV
The keywords you are looking for are "FASTA", "id", "extract". Use those and you will see at least 10 posts along the lines of your query.
Ok thanks! I will dig in deep.
RV
Ok, no problem. I followed this post find similar sequences between different sources but I was unable to get answer using this post and few others, I added this question in other people's comment too, but if someone asks to put this as a unique question. That's why I put this as a separate question.
Thanks
RV