how to compare the columns in two files using awk

Question

I want to compare two files using awk command, with the File 1 and 2 containing the following information. The File 1 is the nucleotide positions as can be seen in the column 2 of File 2.

Now I need an awk command to compare the column (only one cloumn is present) in File 1 to the column 2 of File 2 and if a match is found, print the whole line in File 2 to File 3

File 1

7113528
8680847

File 2

chromosome01    6765006 .   C   T   22.8    .   DP=3;RPB=-8.745357e-01;AF1=1;AC1=2;DP4=1,1,1,0;MQ=35;FQ=-27;PV4=1,1,1,1;EFF=DOWNSTREAM(MODIFIER||1505||492|OS01G0223600|protein_coding|CODING|OS01T0223600-01||1|WARNING_TRANSCRIPT_NO_START_CODON),DOWNSTREAM(MODIFIER||262||174|OS01G0223500|protein_coding|CODING|OS01T0223500-00||1),INTERGENIC(MODIFIER||||||||||1)    PL  51,0,0
chromosome01    6765043 .   C   T   22.8    .   DP=3;RPB=-8.745357e-01;AF1=1;AC1=2;DP4=1,1,1,0;MQ=35;FQ=-27;PV4=1,1,1,1;EFF=DOWNSTREAM(MODIFIER||1468||492|OS01G0223600|protein_coding|CODING|OS01T0223600-01||1|WARNING_TRANSCRIPT_NO_START_CODON),DOWNSTREAM(MODIFIER||225||174|OS01G0223500|protein_coding|CODING|OS01T0223500-00||1),INTERGENIC(MODIFIER||||||||||1)    PL  51,0,0
chromosome01    7113528 .   GACAC   GAC 7.98    .   INDEL;IS=1,0.333333;DP=3;VDB=6.186179e-02;AF1=1;AC1=2;DP4=1,1,0,1;MQ=35;FQ=-34.5;PV4=1,1,1,1;EFF=DOWNSTREAM(MODIFIER||2254||107|OS01G0228901|protein_coding|CODING|OS01T0228901-01||1),DOWNSTREAM(MODIFIER||3930|||NCRNA_20319|ncRNA|NON_CODING|NCRNA_20319||1),INTERGENIC(MODIFIER||||||||||1),UPSTREAM(MODIFIER||3930|||NCRNA_21253|ncRNA|NON_CODING|NCRNA_21253||1),UPSTREAM(MODIFIER||4436||687|OS01G0228800|protein_coding|CODING|OS01T0228800-01||1)  PL  43,0,0
chromosome01    7113583 .   C   T   22.8    .   DP=3;RPB=-8.745357e-01;AF1=1;AC1=2;DP4=1,1,0,1;MQ=35;FQ=-27;PV4=1,1,1,1;EFF=DOWNSTREAM(MODIFIER||2202||107|OS01G0228901|protein_coding|CODING|OS01T0228901-01||1),DOWNSTREAM(MODIFIER||3982|||NCRNA_20319|ncRNA|NON_CODING|NCRNA_20319||1),INTERGENIC(MODIFIER||||||||||1),UPSTREAM(MODIFIER||3982|||NCRNA_21253|ncRNA|NON_CODING|NCRNA_21253||1),UPSTREAM(MODIFIER||4488||687|OS01G0228800|protein_coding|CODING|OS01T0228800-01||1)   PL  51,0,0
chromosome01    7427540 .   C   T   22.8    .   DP=3;RPB=8.745357e-01;AF1=1;AC1=2;DP4=0,2,0,1;MQ=35;FQ=-27;PV4=1,1,1,1;EFF=DOWNSTREAM(MODIFIER||1091|||NCRNA_19787|ncRNA|NON_CODING|NCRNA_19787||1),DOWNSTREAM(MODIFIER||1113|||NCRNA_7056|ncRNA|NON_CODING|NCRNA_7056||1),DOWNSTREAM(MODIFIER||2841||256|OS01G0234433|protein_coding|CODING|OS01T0234433-00||1|WARNING_TRANSCRIPT_NO_START_CODON),DOWNSTREAM(MODIFIER||4859|||NCRNA_25306|ncRNA|NON_CODING|NCRNA_25306||1),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Cca/Aca|P35T|421|OS01G0234200|protein_coding|CODING|OS01T0234200-00|1|1|WARNING_REF_DOES_NOT_MATCH_GENOME),UPSTREAM(MODIFIER||1091|||NCRNA_19719|ncRNA|NON_CODING|NCRNA_19719||1),UPSTREAM(MODIFIER||1113|||NCRNA_7253|ncRNA|NON_CODING|NCRNA_7253||1),UPSTREAM(MODIFIER||1844||386|OS01G0234300|protein_coding|CODING|OS01T0234300-00||1),UPSTREAM(MODIFIER||2862|||NCRNA_9648|ncRNA|NON_CODING|NCRNA_9648||1),UPSTREAM(MODIFIER||3028||255|OS01G0234499|protein_coding|CODING|OS01T0234499-00||1),UPSTREAM(MODIFIER||4863|||NCRNA_27966|ncRNA|NON_CODING|NCRNA_27966||1),UPSTREAM(MODIFIER||4872|||NCRNA_33984|ncRNA|NON_CODING|NCRNA_33984||1)   PL  51,0,0
chromosome01    7427583 .   T   C   26.1    .   DP=3;RPB=-9.668049e-01;AF1=1;AC1=2;DP4=0,1,0,1;MQ=42;FQ=-28;PV4=1,1,1,1;EFF=DOWNSTREAM(MODIFIER||1134|||NCRNA_19787|ncRNA|NON_CODING|NCRNA_19787||1),DOWNSTREAM(MODIFIER||1156|||NCRNA_7056|ncRNA|NON_CODING|NCRNA_7056||1),DOWNSTREAM(MODIFIER||2798||256|OS01G0234433|protein_coding|CODING|OS01T0234433-00||1|WARNING_TRANSCRIPT_NO_START_CODON),DOWNSTREAM(MODIFIER||4902|||NCRNA_25306|ncRNA|NON_CODING|NCRNA_25306||1),SYNONYMOUS_CODING(LOW|SILENT|ggC/ggG|G20|421|OS01G0234200|protein_coding|CODING|OS01T0234200-00|1|1|WARNING_REF_DOES_NOT_MATCH_GENOME),UPSTREAM(MODIFIER||1134|||NCRNA_19719|ncRNA|NON_CODING|NCRNA_19719||1),UPSTREAM(MODIFIER||1156|||NCRNA_7253|ncRNA|NON_CODING|NCRNA_7253||1),UPSTREAM(MODIFIER||1801||386|OS01G0234300|protein_coding|CODING|OS01T0234300-00||1),UPSTREAM(MODIFIER||2905|||NCRNA_9648|ncRNA|NON_CODING|NCRNA_9648||1),UPSTREAM(MODIFIER||2985||255|OS01G0234499|protein_coding|CODING|OS01T0234499-00||1),UPSTREAM(MODIFIER||4906|||NCRNA_27966|ncRNA|NON_CODING|NCRNA_27966||1),UPSTREAM(MODIFIER||4915|||NCRNA_33984|ncRNA|NON_CODING|NCRNA_33984||1)  PL  55,1,0

Answer 1

You can use grep:

grep -f file1 file2 > outputfile

The -f option tells grep to read the patterns from a file, one per line.

Note: Thanks to @fedorqui for pointing out that there can be problems if one of the patterns in file1 appears in another column in file2.

Answer 2

You can use this awk:

awk 'FNR==NR {a[$1]; next} $2 in a' f1 f2

To redirect to another file:

awk 'FNR==NR {a[$1]; next} $2 in a' f1 f2 > f3

Explanation

• FNR==NR {a[$1]; next} loop through the first file storing the values in the array a[].
• $2 in a if 2nd column of 2nd file is present in the array a[], then this is true and the full line is printed.

Test

$ awk 'FNR==NR {a[$1]; next} $2 in a' f1 f2
chromosome01    7113528 .   GACAC   GAC 7.98    .   INDEL;IS=1,0.333333;DP=3;VDB=6.186179e-02;AF1=1;AC1=2;DP4=1,1,0,1;MQ=35;FQ=-34.5;PV4=1,1,1,1;EFF=DOWNSTREAM(MODIFIER||2254||107|OS01G0228901|protein_coding|CODING|OS01T0228901-01||1),DOWNSTREAM(MODIFIER||3930|||NCRNA_20319|ncRNA|NON_CODING|NCRNA_20319||1),INTERGENIC(MODIFIER||||||||||1),UPSTREAM(MODIFIER||3930|||NCRNA_21253|ncRNA|NON_CODING|NCRNA_21253||1),UPSTREAM(MODIFIER||4436||687|OS01G0228800|protein_coding|CODING|OS01T0228800-01||1)  PL  43,0,0