Extract Common Line Out Of Multiple Files
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
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GouthamAtla
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macmath
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macmath
3 answers
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-
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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-
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Pierre Lindenbaum
fileA = open("A.txt",'r')
fileB = open("B.txt",'r')
fileC = open("C.txt",'r')
listA1 = []
for line1 in fileA:
listA = line1.split('\t')
listA1.append(listA)
listB1 = []
for line1 in fileB:
listB = line1.split('\t')
listB1.append(listB)
listC1 = []
for line1 in fileC:
listC = line1.split('\t')
listC1.append(listC)
for key1 in listA1:
for key2 in listB1:
for key3 in listC1:
if key1[1] == key2[1] and key2[1] == key3[1] and key3[1] == key1[1]:
print key1[1]
This code also helps you. The three files should be in same format i.e the ID separated by organism name by 'tab' and no empty lines at the end of the file.
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GouthamAtla
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