Matching the entries and printing data

Shell Programming and Scripting
1

Hi all,

I have a file with Id which I want to compare it with other file to get the sequence of a particular id.

File 1 with ID

Q7L8J4
Q676U5
Q8NAA4
Q5TYW2
Q5SQ80
Q5VUR7
Q4UJ75
Q96IX9
Q7Z4T9
Q6NTF7
Q8IZP0
Q9NYB9
Q9P2A4
O14639
Q9ULW3
Q969K4
Q15057
Q5T8D3
Q8N7X0
Q9Y2D8
Q8TED9
Q8N4X5

File 2 with sequence information

>sp|Q7L8J4|3BP5L_HUMAN SH3 domain-binding protein 5-like OS=Homo sapiens GN=SH3BP5L PE=1 SV=1
MAELRQVPGGRETPQGELRPEVVEDEVPRSPVAEEPGGGGSSSSEAKLSPREEEELDPRI
QEELEHLNQASEEINQVELQLDEARTTYRRILQESARKLNTQGSHLGSCIEKARPYYEAR
RLAKEAQQETQKAALRYERAVSMHNAAREMVFVAEQGVMADKNRLDPTWQEMLNHATCKV
NEAEEERLRGEREHQRVTRLCQQAEARVQALQKTLRRAIGKSRPYFELKAQFSQILEEHK
AKVTELEQQVAQAKTRYSVALRNLEQISEQIHARRRGGLPPHPLGPRRSSPVGAEAGPED
MEDGDSGIEGAEGAGLEEGSSLGPGPAPDTDTLSLLSLRTVASDLQKCDSVEHLRGLSDH
VSLDGQELGTRSGGRRGSDGGARGGRHQRSVSL
>sp|Q676U5|A16L1_HUMAN Autophagy-related protein 16-1 OS=Homo sapiens GN=ATG16L1 PE=1 SV=2
MSSGLRAADFPRWKRHISEQLRRRDRLQRQAFEEIILQYNKLLEKSDLHSVLAQKLQAEK
HDVPNRHEISPGHDGTWNDNQLQEMAQLRIKHQEELTELHKKRGELAQLVIDLNNQMQRK
DREMQMNEAKIAECLQTISDLETECLDLRTKLCDLERANQTLKDEYDALQITFTALEGKL
RKTTEENQELVTRWMAEKAQEANRLNAENEKDSRRRQARLQKELAEAAKEPLPVEQDDDI
EVIVDETSDHTEETSPVRAISRAATKRLSQPAGGLLDSITNIFGRRSVSSFPVPQDNVDT
HPGSGKEVRVPATALCVFDAHDGEVNAVQFSPGSRLLATGGMDRRVKLWEVFGEKCEFKG
SLSGSNAGITSIEFDSAGSYLLAASNDFASRIWTVDDYRLRHTLTGHSGKVLSAKFLLDN
ARIVSGSHDRTLKLWDLRSKVCIKTVFAGSSCNDIVCTEQCVMSGHFDKKIRFWDIRSES
IVREMELLGKITALDLNPERTELLSCSRDDLLKVIDLRTNAIKQTFSAPGFKCGSDWTRV
VFSPDGSYVAAGSAEGSLYIWSVLTGKVEKVLSKQHSSSINAVAWSPSGSHVVSVDKGCK
AVLWAQY
>sp|Q8NAA4|A16L2_HUMAN Autophagy-related protein 16-2 OS=Homo sapiens GN=ATG16L2 PE=2 SV=2
MAGPGVPGAPAARWKRHIVRQLRLRDRTQKALFLELVPAYNHLLEKAELLDKFSKKLQPE
PNSVTPTTHQGPWEESELDSDQVPSLVALRVKWQEEEEGLRLVCGEMAYQVVEKGAALGT
LESELQQRQSRLAALEARVAQLREARAQQAQQVEEWRAQNAVQRAAYEALRAHVGLREAA
LRRLQEEARDLLERLVQRKARAAAERNLRNERRERAKQARVSQELKKAAKRTVSISEGPD
TLGDGMRERRETLALAPEPEPLEKEACEKWKRPFRSASATSLTLSHCVDVVKGLLDFKKR
RGHSIGGAPEQRYQIIPVCVAARLPTRAQDVLDAHLSEVNAVRFGPNSSLLATGGADRLI
HLWNVVGSRLEANQTLEGAGGSITSVDFDPSGYQVLAATYNQAAQLWKVGEAQSKETLSG
HKDKVTAAKFKLTRHQAVTGSRDRTVKEWDLGRAYCSRTINVLSYCNDVVCGDHIIISGH
NDQKIRFWDSRGPHCTQVIPVQGRVTSLSLSHDQLHLLSCSRDNTLKVIDLRVSNIRQVF
RADGFKCGSDWTKAVFSPDRSYALAGS

I want these two files to be compared by comapring ID in the first file with the ID encoded between the pipeline "||" in the second file. If it is same then print the complete sequence.

For example, Q676U5 is found in first file and in the second file. So in the output I should have something like this given below
Expected output

>sp|Q676U5|A16L1_HUMAN Autophagy-related protein 16-1 OS=Homo sapiens GN=ATG16L1 PE=1 SV=2
MSSGLRAADFPRWKRHISEQLRRRDRLQRQAFEEIILQYNKLLEKSDLHSVLAQKLQAEK
HDVPNRHEISPGHDGTWNDNQLQEMAQLRIKHQEELTELHKKRGELAQLVIDLNNQMQRK
DREMQMNEAKIAECLQTISDLETECLDLRTKLCDLERANQTLKDEYDALQITFTALEGKL
RKTTEENQELVTRWMAEKAQEANRLNAENEKDSRRRQARLQKELAEAAKEPLPVEQDDDI
EVIVDETSDHTEETSPVRAISRAATKRLSQPAGGLLDSITNIFGRRSVSSFPVPQDNVDT
HPGSGKEVRVPATALCVFDAHDGEVNAVQFSPGSRLLATGGMDRRVKLWEVFGEKCEFKG
SLSGSNAGITSIEFDSAGSYLLAASNDFASRIWTVDDYRLRHTLTGHSGKVLSAKFLLDN
ARIVSGSHDRTLKLWDLRSKVCIKTVFAGSSCNDIVCTEQCVMSGHFDKKIRFWDIRSES
IVREMELLGKITALDLNPERTELLSCSRDDLLKVIDLRTNAIKQTFSAPGFKCGSDWTRV
VFSPDGSYVAAGSAEGSLYIWSVLTGKVEKVLSKQHSSSINAVAWSPSGSHVVSVDKGCK
AVLWAQY

Thanks in advance

2

I assume you want any entry from the second file to print if it's ID is in the first. This might do it:

awk -F "|" '
    NR == FNR { idx[$1] = 1; next; }
    /^>sp/ { snarf = $2 in idx  }
    snarf
' file1 file2 >output-file
3

Hi,

It does work but it prints me other records which are not in the file 1 with IDs. These records which are not in file 1 are printed after the last entry in file 1. Why does this happen?

4

try the below code put it in some script like test.sh
give it the permissions to execute and then

run it

for i in `cat pathto file1`
do
grep $i file2 >> outputfile
done

thanks

5

Unsure. I tested my code with a file that contained entries that weren't matched in file 1 and never got anything but what was matched. Only thing I can think of is it's an awk version issue. Do you get the same results with this:

awk -F "|" '
    NR == FNR { idx[$1] = 1; next; }
    /^>sp/ {  snarf = idx[$2]+0; }
    snarf
' file1 file2 >output-file
6

Are the data lines split or have you wrapped the output in you demo file2?