Merge Fasta According The Beginning Of The Name

Question

[PoGibas]

I have thousands of .fa files in a directory. Names are:

ch14.fa_20452_206652_15-84.fa
ch14.fa_20452_206652_786-14.fa
ch14.fa_20452_206652_77-85.fa
ch14.fa_20452_206652_81-78.fa
ch2.fa_16903_17204-41-44.fa
ch2.fa_16903_17204-2-46.fa
ch2.fa_16903_17204-61-47.fa
ch2.fa_16903_17204-73-52.fa

I want to merge files with the similar beginning (ch14.ta_20452_206652 or ch2.ta_16903_17204) into one fasta.

Tried to do it manually with:

cat *ch14.fa_20452_206652* > ch14.fa_20452_206652.fa

But it's impossible and driving me crazy. Hope that someone could help me

Answer 1

[Michael]

try this:

for f in prefix*.fa ; do
  cat $f >> out.fa
done

Answer 2

[Damian Kao]

I am assuming the question is about how you can concatenate all the same prefix file names at once instead of typing a cat command one by one?

Try this extremely dirty python script:

import os,popen2,sys

prefices = dict([(x.split('-')[0],'') for x in popen2.popen3('ls')[0].read().strip().split('\n') if x != sys.argv[0]]).keys()

for prefix in prefices:
    cmd = 'cat ' + prefix + "* > " + prefix + ".fa"
    os.system(cmd)

Put it in the directory with the fasta files and run it. I would maybe test it out first on a smaller set of fastas. The script defines prefix by anything before the '-' character.

Answer 3

[Malcolm.Cook]

The following uses a perl 1-liner to distribute its standard input into files named systematically after the names of the input files.

# let's put the results in a new subdir.
mkdir merged
perl -wspe 'if ($. eq 1){($o=$ARGV); eval(q{$o=~}.${new}); open(STDOUT,q{>>},$o)}; close ARGV if eof' -- -new='s/(ch\d+.fa_\d+_\d+)_.*/merged\/$1.fa/' *.fa

should put your results in files named, in this case

ch14.fa_20452_206652.fa
ch2.fa_16903_17204.fa