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Grep Problem

 
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# 8  
Old 01-21-2015
Pls attach the original files so we can look into them.
# 9  
Old 01-21-2015
The grep utility does not care if there are duplicates.

Show us the output from the command:
Code:
head file1 | od -bc

where file1 is the file containing the list of ids you mentioned in the 1st post in this thread.
# 10  
Old 01-22-2015
Dear all,
thanks again for your kindly help!
Attached you can find the files which i am using at the moment.
The lociid file (=file1) was generated with the following steps:
Code:
cut -f1 table > loci
sort loci > loci_sorted
uniq loci_sorted > lociids

For uploading the files i had to "rename" them:
Code:
mv lociids lociids.txt
mv table table.txt

Here is the output of the
Code:
 head lociids.txt | od -bc

requested by Don Cragun
Code:
0000000 143 157 155 160 061 060 060 064 065 137 143 060 137 163 145 161
          c   o   m   p   1   0   0   4   5   _   c   0   _   s   e   q
0000020 061 012 143 157 155 160 061 060 060 071 061 137 143 060 137 163
          1  \n   c   o   m   p   1   0   0   9   1   _   c   0   _   s
0000040 145 161 061 012 143 157 155 160 061 060 061 061 070 137 143 060
          e   q   1  \n   c   o   m   p   1   0   1   1   8   _   c   0
0000060 137 163 145 161 061 012 143 157 155 160 061 060 061 065 061 137
          _   s   e   q   1  \n   c   o   m   p   1   0   1   5   1   _
0000100 143 060 137 163 145 161 061 012 143 157 155 160 061 060 061 065
          c   0   _   s   e   q   1  \n   c   o   m   p   1   0   1   5
0000120 061 137 143 060 137 163 145 161 062 012 143 157 155 160 061 060
          1   _   c   0   _   s   e   q   2  \n   c   o   m   p   1   0
0000140 061 065 071 137 143 060 137 163 145 161 061 012 143 157 155 160
          1   5   9   _   c   0   _   s   e   q   1  \n   c   o   m   p
0000160 061 060 061 071 070 137 143 060 137 163 145 161 061 012 143 157
          1   0   1   9   8   _   c   0   _   s   e   q   1  \n   c   o
0000200 155 160 061 060 062 060 064 137 143 060 137 163 145 161 061 012
          m   p   1   0   2   0   4   _   c   0   _   s   e   q   1  \n
0000220 143 157 155 160 061 060 062 060 064 137 143 060 137 163 145 161
          c   o   m   p   1   0   2   0   4   _   c   0   _   s   e   q
0000240 062 012 143 157 155 160 061 060 062 062 061 137 143 060 137 163
          2  \n   c   o   m   p   1   0   2   2   1   _   c   0   _   s
0000260 145 161 062 012
          e   q   2  \n
0000264

lociids.txt (76.8 KB) 
table.txt (447.5 KB) 
# 11  
Old 01-22-2015
Code:
grep -f lociids.txt table.txt

works as intended on two different systems, although extremely slowly on one of them. To speed it up, try
Code:
grep -Ff lociids.txt table.txt

# 12  
Old 01-22-2015
When i try it there are again as many lines as in the table file...
# 13  
Old 01-22-2015
You have 1955 duplicates in table.txt. Well possible that all are found in lociids.txt. Convince yourself - reduce lociids.tst to, say, 10 lines and try again...
# 14  
Old 01-22-2015
i tried it with 10 lines but got 11 in my outputfile
 
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