concatenetion files in order by perl?

[semna]

hello everyone,
I have some fasta files like this:
>ARP3_HUMAN
----------------------------------------------MAGRLPACVVDCGT
GYTKLGYAGNTEPQFIIPSCIAIKESAKVGDQAQRRVMKGVDDLDFFIGDEAIEKP-TYA
TKWPIRHGIVEDWDLMERFMEQVIFKYLRAEPEDHYFLLTEPPLNTPENREYTAEIMFES
FNVPGLYIAVQAVLALAASWTSRQVGERTLTGTVIDSGDGVTHVIPVAEGYVIGSCIKHI
PIAGRDITYFIQQLLRDREVGIPPEQSLETAKAVKERYSYVCPDLVKEFNKYDTDGSKWI
KQYTGINAISKKEFSIDVGYERFLGPEIFFHPEFANPDFTQPISEVVDEVIQNCPIDVRR
PLYKNIVLSGGSTMFRDFGRRLQRDLKRTVDARLKLSEELSGGRLKPKPIDVQVITHHMQ
RYAVWFGGSMLASTPEFYQVCHTKKDYEEIGPSICRHNPVFGVMS
>ARP3_BOVIN
----------------------------------------------MAGRLPACVVDCGT
GYTKLGYAGNTEPQFIIPSCIAIKESAKVGDQAQRRVMKGVDDLDFFIGDEAIEKP-TYA
TKWPIRHGIVEDWDLMERFMEQVIFKYLRAEPEDHYFLLTEPPLNTPENREYTAEIMFES
FNVPGLYIAVQAVLALAASWTSRQVGERTLTGTVIDSGDGVTHVIPVAEGYVIGSCIKHI
PIAGRDITYFIQQLLRDREVGIPPEQSLETAKAVKERYSYVCPDLVKEFNKYDTDGSKWI
KQYTGINAISKKEFSIDVGYERFLGPEIFFHPEFANPDFTQPISEVVDEVIQNCPIDVRR
PLYKNIVLSGGSTMFRDFGRRLQRDLKRTVDARLKLSEELSGGRLKPKPIDVQVITHHMQ
RYAVWFGGSMLASTPEFYQVCHTKKDYEEIGPSICRHNPVFGVMS

I want to concatenate these files by consideration that each specious should concatenate with same specious in other files that might be in different order relate to this example file that I pasted. Any suggestion to concatenate theses file with perl script?thanks in advance

[zee]

Try this:

#!/bin/bash
#species_splitter.sh

perl -e '$count=0; $len=0; while(<>) {s/\r?\n//; s/\t/ /g; if (s/^>//) { if ($. != 1) {print "\n"} s/ |$/\t/; $count++; $_ .= "\t";} else {s/ //g; $len += length($_)};print }'  $1 | perl -lane '$species=$1 if $F[0] =~ /_(\S+)/;open(OUT,"+>>$species.fa"); print OUT ">$F[0]\n$F[1]"  '

and run it as

bash species_splitter.sh  input.fasta

Your output will be "HUMAN.fa" and "BOVIN.fa".

[semna]

thanks zee
because I am not familiar with programming when I run your script I saw:
species_splitter.sh: species_splitter.sh: No such file or directory
What can I do next?
thanks

[zee]

Oh, I left out the following I thought it was obvious:

Save all the code in the first listing to a file called "species_splitter.sh" using text editor.

Then run "bash species_splitter.sh <your input fasta file>"

[semna]

thanks zee,
it works but still empty.lets assume if we have just one file like that and I want to concatenate just the same specious and get again the 1 file result what the script would be?
thanks

[zee]

I dont understand the question. In the example you pasted two files will be created by the script

1. BOVIN.fa
2. HUMAN.fa

So which file are you saying is empty? Can you describe to me whether you got the files with same species in each one?

[Thorondor]

the script works, you have just ONE file as input, just one huge multifasta, like:

>ARP3_HUMAN
----------------------------------------------MAGRLPACVVDCGT
GYTKLGYAGNTEPQFIIPSCIAIKESAKVGDQAQRRVMKGVDDLDFFIGDEAIEKP-TYA
TKWPIRHGIVEDWDLMERFMEQVIFKYLRAEPEDHYFLLTEPPLNTPENREYTAEIMFES
FNVPGLYIAVQAVLALAASWTSRQVGERTLTGTVIDSGDGVTHVIPVAEGYVIGSCIKHI
PIAGRDITYFIQQLLRDREVGIPPEQSLETAKAVKERYSYVCPDLVKEFNKYDTDGSKWI
KQYTGINAISKKEFSIDVGYERFLGPEIFFHPEFANPDFTQPISEVVDEVIQNCPIDVRR
PLYKNIVLSGGSTMFRDFGRRLQRDLKRTVDARLKLSEELSGGRLKPKPIDVQVITHHMQ
RYAVWFGGSMLASTPEFYQVCHTKKDYEEIGPSICRHNPVFGVMS
>ARP3_BOVIN
----------------------------------------------MAGRLPACVVDCGT
GYTKLGYAGNTEPQFIIPSCIAIKESAKVGDQAQRRVMKGVDDLDFFIGDEAIEKP-TYA
TKWPIRHGIVEDWDLMERFMEQVIFKYLRAEPEDHYFLLTEPPLNTPENREYTAEIMFES
FNVPGLYIAVQAVLALAASWTSRQVGERTLTGTVIDSGDGVTHVIPVAEGYVIGSCIKHI
PIAGRDITYFIQQLLRDREVGIPPEQSLETAKAVKERYSYVCPDLVKEFNKYDTDGSKWI
KQYTGINAISKKEFSIDVGYERFLGPEIFFHPEFANPDFTQPISEVVDEVIQNCPIDVRR
PLYKNIVLSGGSTMFRDFGRRLQRDLKRTVDARLKLSEELSGGRLKPKPIDVQVITHHMQ
RYAVWFGGSMLASTPEFYQVCHTKKDYEEIGPSICRHNPVFGVMS
>ARP3_BOVIN
----------------------------------------------MAGRLPACVVDCGT
GYTKLGYAGNTEPQFIIPSCIAIKESAKVGDQAQRRVMKGVDDLDFFIGDEAIEKP-TYA
TKWPIRHGIVEDWDLMERFMEQVIFKYLRAEPEDHYFLLTEPPLNTPENREYTAEIMFES
FNVPGLYIAVQAVLALAASWTSRQVGERTLTGTVIDSGDGVTHVIPVAEGYVIGSCIKHI
~

by calling species_splitter.sh test_file.fa

you get 2 fasta files, HUMAN.fa looks like:

>ARP3_HUMAN
----------------------------------------------MAGRLPACVVDCGTGYTKLGYAGNTEPQFIIPSCIAIKESAKVGDQAQRRVMKGVDDLDFFIGDEAIEKP-TYATKWPIRHGIVEDWDLMERFMEQVIFKYLRAEPEDHYFLLTEPPLNTPENREYTAEIMFESFNVPGLYIAVQAVLALAASWTSRQVGERTLTGTVIDSGDGVTHVIPVAEGYVIGSCIKHIPIAGRDITYFIQQLLRDREVGIPPEQSLETAKAVKERYSYVCPDLVKEFNKYDTDGSKWIKQYTGINAISKKEFSIDVGYERFLGPEIFFHPEFANPDFTQPISEVVDEVIQNCPIDVRRPLYKNIVLSGGSTMFRDFGRRLQRDLKRTVDARLKLSEELSGGRLKPKPIDVQVITHHMQRYAVWFGGSMLASTPEFYQVCHTKKDYEEIGPSICRHNPVFGVMS

and the BOVIN.fa :

>ARP3_BOVIN
----------------------------------------------MAGRLPACVVDCGTGYTKLGYAGNTEPQFIIPSCIAIKESAKVGDQAQRRVMKGVDDLDFFIGDEAIEKP-TYATKWPIRHGIVEDWDLMERFMEQVIFKYLRAEPEDHYFLLTEPPLNTPENREYTAEIMFESFNVPGLYIAVQAVLALAASWTSRQVGERTLTGTVIDSGDGVTHVIPVAEGYVIGSCIKHIPIAGRDITYFIQQLLRDREVGIPPEQSLETAKAVKERYSYVCPDLVKEFNKYDTDGSKWIKQYTGINAISKKEFSIDVGYERFLGPEIFFHPEFANPDFTQPISEVVDEVIQNCPIDVRRPLYKNIVLSGGSTMFRDFGRRLQRDLKRTVDARLKLSEELSGGRLKPKPIDVQVITHHMQRYAVWFGGSMLASTPEFYQVCHTKKDYEEIGPSICRHNPVFGVMS
>ARP3_BOVIN
----------------------------------------------MAGRLPACVVDCGTGYTKLGYAGNTEPQFIIPSCIAIKESAKVGDQAQRRVMKGVDDLDFFIGDEAIEKP-TYATKWPIRHGIVEDWDLMERFMEQVIFKYLRAEPEDHYFLLTEPPLNTPENREYTAEIMFESFNVPGLYIAVQAVLALAASWTSRQVGERTLTGTVIDSGDGVTHVIPVAEGYVIGSCIKHI

probably this is not exactly what you want, or is it?

[zee]

I think I misunderstood your question. You would like to separate the sequences not by species names but by GENE names. Is that correct?

[Thorondor]

well i guess it's still the "old" problem:

http://seqanswers.com/forums/showthread.php?t=9660

but for me it's also not that clear.

[semna]

sorry might be because of my fault.that I pasted just some part of file.now I want to concatenate within file.so assume have 1 file with some human fasta file, bovin fasta file and so on.so the file result be again one file.
thanks

[zee]

to cat a file do:

cat file1.fa file2.fa > bigfile.fa

[semna]

but there is a problem .I want all protein specious for certain protein under one hedaer line. for example if we have :
>APA human
AAAAAAAAAAAA
>TSA human
BBBBBBBBBBBBB
I need this:
>human
AAAAAAAAAAAA
BBBBBBBBBBBBB

thanks for your help

[Thorondor]

ok to make it clear, in one file you have something like

>ARP3_BOVIN
----------------------------------------------MAGRLPACVVDCGT
GYTKLGYAGNTEPQFIIPSCIAIKESAKVGDQAQRRVMKGVDDLDFFIGDEAIEKP-TYA
TKWPIRHGIVEDWDLMERFMEQVIFKYLRAEPEDHYFLLTEPPLNTPENREYTAEIMFES
FNVPGLYIAVQAVLALAASWTSRQVGERTLTGTVIDSGDGVTHVIPVAEGYVIGSCIKHI
PIAGRDITYFIQQLLRDREVGIPPEQSLETAKAVKERYSYVCPDLVKEFNKYDTDGSKWI
KQYTGINAISKKEFSIDVGYERFLGPEIFFHPEFANPDFTQPISEVVDEVIQNCPIDVRR
PLYKNIVLSGGSTMFRDFGRRLQRDLKRTVDARLKLSEELSGGRLKPKPIDVQVITHHMQ
RYAVWFGGSMLASTPEFYQVCHTKKDYEEIGPSICRHNPVFGVMS
>HUMAN
PIAGRDITYFIQQLLRDREVGIPPEQSLETAKAVKERYSYVCPDLVKEFNKYDTDGSKWI
KQYTGINAISKKEFSIDVGYERFLGPEIFFHPEFANPDFTQPISEVVDEVIQNCPIDVR
>HUMAN
-----PLYKNIVLSGGSTMFRDFGRRLQRDLKRTVDARLKLSEELSGGRLKPKPIDVQVITHHMQ
RYAVWFGGSMLASTPEFYQVCHTKKDYEEIGPSICRHNPVFGVMS
>ARP3_BOVIN
----------------------------------------------MAGRLPACVVDCGT
GYTKLGYAGNTEPQFIIPSCIAIKESAKVGDQAQRRVMKGVDDLDFFIGDEAIEKP-TYA
TKWPIRHGIVEDWDLMERFMEQVIFKYLRAEPEDHYFLLTEPPLNTPENREYTAEIMFES
FNVPGLYIAVQAVLALAASWTSRQVGERTLTGTVIDSGDGVTHVIPVAEGYVIGSCIKHI

and the output should be:

>HUMAN
PIAGRDITYFIQQLLRDREVGIPPEQSLETAKAVKERYSYVCPDLVKEFNKYDTDGSKWI
KQYTGINAISKKEFSIDVGYERFLGPEIFFHPEFANPDFTQPISEVVDEVIQNCPIDVR-----PLYKNIVLSGGSTMFRDFGRRLQRDLKRTVDARLKLSEELSGGRLKPKPIDVQVITHHMQ
RYAVWFGGSMLASTPEFYQVCHTKKDYEEIGPSICRHNPVFGVMS
>ARP3_BOVIN
----------------------------------------------MAGRLPACVVDCGT
GYTKLGYAGNTEPQFIIPSCIAIKESAKVGDQAQRRVMKGVDDLDFFIGDEAIEKP-TYA
TKWPIRHGIVEDWDLMERFMEQVIFKYLRAEPEDHYFLLTEPPLNTPENREYTAEIMFES
FNVPGLYIAVQAVLALAASWTSRQVGERTLTGTVIDSGDGVTHVIPVAEGYVIGSCIKHI
PIAGRDITYFIQQLLRDREVGIPPEQSLETAKAVKERYSYVCPDLVKEFNKYDTDGSKWI
KQYTGINAISKKEFSIDVGYERFLGPEIFFHPEFANPDFTQPISEVVDEVIQNCPIDVRR
PLYKNIVLSGGSTMFRDFGRRLQRDLKRTVDARLKLSEELSGGRLKPKPIDVQVITHHMQ
RYAVWFGGSMLASTPEFYQVCHTKKDYEEIGPSICRHNPVFGVMS----------------------------------------------MAGRLPACVVDCGT
GYTKLGYAGNTEPQFIIPSCIAIKESAKVGDQAQRRVMKGVDDLDFFIGDEAIEKP-TYA
TKWPIRHGIVEDWDLMERFMEQVIFKYLRAEPEDHYFLLTEPPLNTPENREYTAEIMFES
FNVPGLYIAVQAVLALAASWTSRQVGERTLTGTVIDSGDGVTHVIPVAEGYVIGSCIKHI

correct?

edit: saw your comment to late, so you have even different headers like >xxx human and >yyy human which should be all under >human?

it's getting complicated. :-/

[zee]

OK, how large is your input file? Could you attach the whole file to this thread?

[semna]

yes I want to concatenate all sequence of certain specious under one header of that specious. and it doest not matter that might be the first of the header is different because of different protein but it blongs to certain specious
like: APT_human
BTC_human
thanks