03-27-2013
Based on column in file1, find match in file2 and print matching lines
file1:
Quote:
comp54049_c1_seq33
comp51795_c0_seq4
comp46214_c0_seq1
comp51509_c0_seq2
comp1000362_c0_seq1
file2:
Quote:
>m.149837_g.149837__ORF_g.149837_m.149837_type:internal_len:169_(-)_comp100001_c0_seq1:3-509(-)
FHPPVSDSCKRCDMYKNQIKIAPENEKIQLNADHELHLRKAESARNGMNNDVELCKTDPN
>m.180533_g.180533__ORF_g.180533_m.180533_type:internal_len:99_(-)_comp1000362_c0_seq1:3-299(-)
QSLPFPPNYISLSHAGTLSVNPCTAYRLLKDFVSLSTGDFIIQNGANSGVGRVVIQLCKA
I need to find matches for any lines in file1 that appear in file2. Desired output is '>' plus the file1 term, followed by the line
after the match in file2 (so the title is a little misleading):
Quote:
>comp1000362_c0_seq1
QSLPFPPNYISLSHAGTLSVNPCTAYRLLKDFVSLSTGDFIIQNGANSGVGRVVIQLCKA
This is honestly beyond what I can do without spending the whole night on it, so I'm hoping someone out there is feeling altruistic.
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DIFF(1) General Commands Manual DIFF(1)
NAME
diff - print differences between two files
SYNOPSIS
diff [-c | -e | -C n] [-br]file1 file2
OPTIONS
-C n Produce output that contains n lines of context
-b Ignore white space when comparing
-c Produce output that contains three lines of context
-e Produce an ed-script to convert file1 into file2
-r Apply diff recursively to files and directories of
EXAMPLES
diff file1 file2 # Print differences between 2 files
diff -C 0 file1 file2
# Same as above
diff -C 3 file1 file2
# Output three lines of context with every
diff -c file1 file2 # Same
diff /etc /dev # Compares recursively the directories /etc and /dev
diff passwd /etc # Compares ./passwd to /etc/passwd
DESCRIPTION
the same name, when file1 and file2 are both directories" difference encountered"
Diff compares two files and generates a list of lines telling how the two files differ. Lines may not be longer than 128 characters. If
the two arguments on the command line are both directories, diff recursively steps through all subdirectories comparing files of the same
name. If a file name is found only in one directory, a diagnostic message is written to stdout. A file that is of either block special,
character special or FIFO special type, cannot be compared to any other file. On the other hand, if there is one directory and one file
given on the command line, diff tries to compare the file with the same name as file in the directory directory.
SEE ALSO
cdiff(1), cmp(1), comm(1), patch(1).
DIFF(1)