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Grep Problem

 
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# 1  
Old 01-20-2015
Grep Problem
Dear all,
my question is about grep.

i have two files.

the first one is a list with ids (line number 188) like this:
Code:
comp10045_c0_seq1
comp10118_c0_seq1
comp10221_c0_seq2
comp10503_c0_seq1
comp10504_c0_seq1
comp10504_c0_seq2
comp10631_c0_seq1
comp10631_c0_seq2
comp10646_c0_seq1
comp10804_c0_seq1

the second file is a tab seperated table (line number 329) , like this:
Code:
comp10045_c0_seq1    tr|Q6PBS3|Q6PBS3_DANRE    79.31    464    93    1    2024    633    2    462    0.0     776
comp10118_c0_seq1    tr|Q6P0C4|Q6P0C4_DANRE    44.19    43    23    1    1066    1194    177    218    0.29    35.4
comp10221_c0_seq2    tr|Q7T340|Q7T340_DANRE    95.05    303    15    0    175    1083    1    303    0.0     543
comp10503_c0_seq1    tr|F1Q9U6|F1Q9U6_DANRE    69.07    472    142    2    2330    915    1    468    0.0     687
comp10504_c0_seq1    tr|F8W2T4|F8W2T4_DANRE    98.01    151    3    0    787    1239    6    156    2e-99     307
comp10504_c0_seq2    tr|F8W2T4|F8W2T4_DANRE    98.01    151    3    0    1095    1547    6    156    2e-98     307
comp10631_c0_seq1    tr|B0S5C5|B0S5C5_DANRE    90.61    394    37    0    145    1326    1    394    0.0     687
comp10631_c0_seq2    tr|B0S5C5|B0S5C5_DANRE    90.61    394    37    0    145    1326    1    394    0.0     687
comp10646_c0_seq1    tr|F1QDS2|F1QDS2_DANRE    84.82    850    110    7    173    2695    1    840    0.0    1333
comp10804_c0_seq1    tr|Q7ZUP6|Q7ZUP6_DANRE    93.58    452    26    2    156    1511    1    449    0.0     851
comp10991_c1_seq1    tr|E7F8T6|E7F8T6_DANRE    94.21    484    28    0    1974    523    9    492    0.0     943

i want to grep the lines of the second file which have the same ids of the first file using the following code:
Code:
 grep -f file1 file2 > output

but it does not work cause i have 329 lines instead of 188.

Can anybody explain what i am doing wrong?

Regards
# 2  
Old 01-20-2015
Hello kleinstadt,

Welcome to forums, thank you for using code tags in your posts for commands.
Following may help you in same.
Code:
awk 'FNR==NR{X[$1]=$1;next} ($1 in X){print $0}' file1 file2

Output will be as follows.
Code:
comp10045_c0_seq1    tr|Q6PBS3|Q6PBS3_DANRE    79.31    464    93    1    2024    633    2    462    0.0     776
comp10118_c0_seq1    tr|Q6P0C4|Q6P0C4_DANRE    44.19    43    23    1    1066    1194    177    218    0.29    35.4
comp10221_c0_seq2    tr|Q7T340|Q7T340_DANRE    95.05    303    15    0    175    1083    1    303    0.0     543
comp10503_c0_seq1    tr|F1Q9U6|F1Q9U6_DANRE    69.07    472    142    2    2330    915    1    468    0.0     687
comp10504_c0_seq1    tr|F8W2T4|F8W2T4_DANRE    98.01    151    3    0    787    1239    6    156    2e-99     307
comp10504_c0_seq2    tr|F8W2T4|F8W2T4_DANRE    98.01    151    3    0    1095    1547    6    156    2e-98     307
comp10631_c0_seq1    tr|B0S5C5|B0S5C5_DANRE    90.61    394    37    0    145    1326    1    394    0.0     687
comp10631_c0_seq2    tr|B0S5C5|B0S5C5_DANRE    90.61    394    37    0    145    1326    1    394    0.0     687
comp10646_c0_seq1    tr|F1QDS2|F1QDS2_DANRE    84.82    850    110    7    173    2695    1    840    0.0    1333
comp10804_c0_seq1    tr|Q7ZUP6|Q7ZUP6_DANRE    93.58    452    26    2    156    1511    1    449    0.0     851

Thanks,
R. Singh
This User Gave Thanks to RavinderSingh13 For This Post:
kleinstadt
# 3  
Old 01-20-2015
Hi Singh,
thanks for your solution and fast reply. the code you postet works.
But why does grep not work with my files? i know it should work...
# 4  
Old 01-20-2015
Hello kleinstadt,

You can check here about carriage charaters if they are there, by cat -v Input_file if they are present then you need to remove them. I tested the same command in my GNU grep and it worked fine for me, you can also check your grep version by grep --version too.


Thanks,
R. Singh
Last edited by RavinderSingh13; 01-20-2015 at 11:23 AM..
# 5  
Old 01-20-2015
My first guess would be DOS <CR> line terminators. How were those files produced? If I add <CR> chars, the grep -f fails, without it works. RavinderSingh13's proposal will also fail with <CR>s present (sub (/\r$/,"") could help in some awks).
Remove them with e.g. tr -d '\r' <file1 or dos2unix file1.
Last edited by RudiC; 01-20-2015 at 11:48 AM..
# 6  
Old 01-20-2015
Quote:
Originally Posted by kleinstadt
But why does grep not work with my files? i know it should work...
As suggested, your BLAST table and/or your sequence list may contain carriage returns, which can be removed by any of the above methods or

Code:
sed 's/\r//g' file

Also your grep would work, I suggest using Ravinders script or
Code:
grep -w

to avoid erroneous calls.
# 7  
Old 01-21-2015
Could it be that grep has a problem if there are more lines with the same id in file 2?
Also i could not find any carriage characters...
Last edited by kleinstadt; 01-21-2015 at 11:42 AM..
 
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