concatenation by perl

[semna]

Hi everyone,
I have some files like this:
E.coli ---MGKALVIVESPAKAKTINKYLGSD-----------YVVKSSVGHIRDLPTSGSAAKK
A.aeolicus -----MELFIVESPTKAKTIQKFLGKG-----------FLVKATLGHVKDLPEK------
B.subtillis ---MSDYLVIVESPAKAKTIERYLGKK-----------YKVKASMGHVRDLPKS------
helicobacter ----MKHLIIVESPAKAKTIKNFLDKN-----------YEVIASKGHVRDLSKFALG---
Thermotoga MSKKVKKYIVVESPAKAKTIKSILGNE-----------YEVFASMGHIIDLPKS------
mycoplasma ---MSKNLVVIESPNKVKTLQKYLPND-----------FEIVSTIGHIREMVHKNFG---
B.fragil -----MIALIAEKPSVAKDIARIIGATGRNDGYLSGNGYMVTWAFGHLIQLAMPEAYG--
.: *.* .* : : : : : **: ::

E.coli SADSTSTKTAKKPKKDERGALVNRMGVDPWHNWEAHYEVLPGKEKVVSELKQLAEKADHI
A.aeolicus -----------------------ELGVD-LRTLKAKYVYKRGKKKLVEQLKKLSRRSSIV
B.subtillis -----------------------QMGVDIEQNFEPKYITIRGKGPVLKELKTAAKKAKKV
helicobacter -------------------------IKIDETGFTPNYVVDKDHKELVKQIIELSKKASIT
Thermotoga -----------------------KFGVDLEKDFEPEFAVIKGKEKVVEKLKDLAKKG-EL
mycoplasma ------FNEADYSPVWEDWTKSKKKFSSLSFKGNLKGKKLLSKYDIIKSIKEKASKATNI
B.fragil --------VANFRRESLPILPPDFQLIPRQVKAEKGYKADPGVLKQLKVIKEVFDQCDRI

and I want to concatenate each lines for certain species within file and then concatenate of the result of each file with another file and get output.I know that there are some easier way to do that but I like to know how can do that with perl script?
Thanks for your help

[Thomas Doktor]

Can you give an example of the intended output?

I'm thinking you would like this:
File 1:
E.coli ---MGKALVIVESPAKAKTINKYLGSD-----------YVVKSSVGHIRDLPTSGSAAKK
E.coli ---ALISLILIASLILILAISLA

File 2:
E.coli SADSTSTKTAKKPKKDERGALVNRMGVDPWHNWEAHYEVLPGKEKVVSELKQLAEKADHI

Output:
E.coli ---MGKALVIVESPAKAKTINKYLGSD-----------YVVKSSVGHIRDLPTSGSAAKK---ALISLILIASLILILAISLASADSTSTKTAKKPKKDERGALVNRMGVDPWHNWEAHYEVLPGKEKVVSELKQLAEKADHI

Is that correct?

EDIT
Ignore the whitespace in the sequences.

[semna]

Hi Thomas,
yes you are almost right.but this is tht I show just 1 file. And I want to do the same thing for other file and finally concatenate for each species and genereate just one final uotput.
for eample for E.coli we have:
AAAAAAAAAAAA

and again within this file for E.coli
BBBBB----BBB
for this file so we will have
AAAAAAAAAAAABBBBBBBB
and this for other species and so on.
Thanks

[Thorondor]

well i won't write the script for you, but it is quite easy. ;-)

get the files you want ( @files = <*.txt>)

go over all these files (foreach (@files)){ while <$_> { chomp;....
user pattern matching $_ ~= /((w+)|(w+\.w+))\s+(*.)/
remove the --- in $2
...
store it in a hash sequences($1) = "sequences($1)"."$2"

and in the end print the hash like you want it in the output file.

something like that, of course there will be some problems, but try it on your own first, then show what you got.

[JohnK]

in a file prog_name.pl:

#!/usr/bin/perl

$in=$ARGV[0]; #input file name
$out=$ARGV[1];

open(FH, "< $in") || die "here1";
open(OUT, "> $out") || die "here2";

while(<FH>){
if($_=~/E. coli/){
$hash{"e_coli"}.=$_;
}elsif($_=~/A. aeolicus/){
$hash{"a_aeol"}.=$_;
}elsif( keep listing it out for as many lines){

}

}
foreach $key (keys %hash){
print OUT $hash{$key}, "\n";
}
close FH;
close OUT;