Extract Common Line Out Of Multiple Files

Question

[macmath]

Need to extract common list of Organisms from different files based on the second tab separated column

Example :

Below is the Query: File A:

• YP_001173296 Pseudomonas stutzeri A1501
• ZP_10847128 Pseudomonas fragi A22
• YP_006325640 Pseudomonas fluorescens A506
• ZP_08518919 Aeromonas caviae Ae398
• ZP_10474222 Rickettsiella grylli
• EKB21198 Aeromonas veronii AMC34

File B:

• P_02062827 Rickettsiella grylli
• YP_004473601 Pseudomonas fulva 12-X
• ZP_10438680 Pseudomonas extremaustralis 14-3 substr. 14-3b
• YP_528004 Aeromonas caviae Ae398
• ZP_11138829 Gallaecimonas xiamenensis 3-C-1
• YP_52800475 Pseudomonas stutzeri A1501

File C:

• P_02062827 Pseudomonas extremaustralis
• YP_004473601 Pseudomonas fulva 12-X
• ZP_10438680 Pseudomonas extremaustralis 14-3 substr. 14-3b
• YP_528004 Aeromonas caviae Ae398
• ZP_11138829 Rickettsiella grylli
• YP_52800475 Pseudomonas stutzeri A1501

Expected Result file : Common organism

• Aeromonas caviae Ae398
• Pseudomonas stutzeri A1501
• Rickettsiella grylli

Answer 1

[Pierre Lindenbaum]

cut the 2nd column, sort and get the lines having a count=3.

   cut -d '  ' -f 2 file*.tsv | sort | uniq -c |  grep -E '^      3 ' | cut -c 9-

[macmath]

actual i have 1000 files and i want to get common set of organisms using tab separated 2nd column I checked this command. Could you explain if I am wrong, the 3 stands for three files? In each file duplicates are present of the same organism

[Pierre Lindenbaum]

yes, "3" is for "3" files. Try : (for F in *.tsv; do cut -d ' ' -f2 $F | sort | uniq: done )| sort | uniq -c | grep -E '^ 1000 ' | cut -c 9-

[macmath]

I received syntax error near unexpected token `)'

[Pierre Lindenbaum]

I let you solve that syntax error as an exercise. :-)

[macmath]

hehe :) thanks dude