08-05-2009
Help parsing and replacing text with file name
Hi everyone,
I'm having trouble figuring this one out. I have ~100 *.fa files with multiple lines of fasta sequences like this: file1.fa
>xyzsequence
atcatgcacac......
ataccgagagg.....
atataccagag.....
>abcsequence
atgagatatat.....
acacacggd.....
atcgaacac....
agttccagat....
The name of each sequence is delimited by a ">" and followed by a newline. I'm trying to figure out how iterate through all of my files with a ".fa" extension and create a single tab-delimited table with the name of the sequence (tab) and the name of the file it came from. Like so:
xyzsequence file1
abcsequence file1
somsequence file2
etc...
Can anyone point me in the right direction?
Many thanks,
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PASTE(1) General Commands Manual PASTE(1)
NAME
paste - paste multiple files together
SYNOPSIS
paste [-s] [-d list] file...
OPTIONS
-d Set delimiter used to separate columns to list.
-s Print files sequentially, file k on line k.
EXAMPLES
paste file1 file2 # Print file1 in col 1, file2 in col 2
paste -s f1 f2 # Print f1 on line 1 and f2 on line 2
paste -d : file1 file2
# Print the lines separated by a colon
DESCRIPTION
Paste concatenates corresponding lines of the given input files and writes them to standard output. The lines of the different files are
separated by the delimiters given with the option -s. If no list is given, a tab is substituted for every linefeed, except the last one.
If end-of-file is hit on an input file, subsequent lines are empty. Suppose a set of k files each has one word per line. Then the paste
output will have k columns, with the contents of file j in column j. If the -s flag is given, then the first file is on line 1, the second
file on line 2, etc. In effect, -s turns the output sideways.
If a list of delimiters is given, they are used in turn. The C escape sequences
, , \, and are used for linefeed, tab, backslash,
and the null string, respectively.
PASTE(1)