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Merge multiple lines in one line

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# 1  
Old 01-31-2013
Merge multiple lines in one line
Hi guys,

So i have a input file with several sequences aligned (fasta)

Code:
>NC_005930 241 bp
MNMINIFIINNIFDQFIPVKLSIFSLTSVGSIIA
LSWVWINTKTHWAISRSNTP-SLLLNSL
WTLLITNL-NEKTNPWAPWLFSLFLLCFSFNIMSLI-PYTF-SQ
TSHLSFTFGLSLPIWIMVNIAGFKNNWKKKISHLLPQGTPIYLVPVMII
IETISLFIQPLTLGFRLGANLLAGHLLIFLCSCTIWE
AINYNIYL-GTISFSLILVLLILEIAVAFIQATVFLILSKNYLEENIN-
>NC_000425 241 bp
MNMINIFIINNIFDQFIPVKLSIFSLTSVGSIIA
LSWVWINTKTHWAISRSNTP-SLLLNSL
WTLLITNL-NEKTNPWAPWLFSLFLLCFSFNIMSLI-PYTF-SQ
TSHLSFTFGLSLPIWIMVNIAGFKNNWKKKISHLLPQGTPIYLVPVMII
IETISLFIQPLTLGFRLGANLLAGHLLIFLCSCTIWE
AINYNIYL-GTISFSLILVLLILEIAVAFIQATVFLILSKNYLEENIN-
.
.
.

and i want get on output:

Code:
>NC_005930 241 bp
MNMINIFIINNIFDQFIPVKLSIFSLTSVGSIIALSWVWINTKTHWAISRSNTPSLLLNSLWTLLITNLNEKTNPWAPWLFSLFLLCFSFNIMSLIPYTFSQTSHLSFTFGLSLPIWIMVNIAGFKNNWKKKISHLLPQGTPIYLVPVMIIIETISLFIQPLTLGFRLGANLLAGHLLIFLCSCTIWEAINYNIYLGTISFSLILVLLILEIAVAFIQATVFLILSKNYLEENIN-
>NC_000425 241 bp
MNMINIFIINNIFDQFIPVKLSIFSLTSVGSIIALSWVWINTKTHWAISRSNTPSLLLNSLWTLLITNLNEKTNPWAPWLFSLFLLCFSFNIMSLIPYTFSQTSHLSFTFGLSLPIWIMVNIAGFKNNWKKKISHLLPQGTPIYLVPVMIIIETISLFIQPLTLGFRLGANLLAGHLLIFLCSCTIWEAINYNIYLGTISFSLILVLLILEIAVAFIQATVFLILSKNYLEENIN-
.
.
.

I have tried perl and shell script with s/\n//; only for the sequence but i dont get the correct output!

Thanks for the help Smilie

Andreia
Moderator's Comments:
Mod Comment
Please use code tags when posting data and code samples!
Last edited by vgersh99; 01-31-2013 at 06:52 PM.. Reason: code tags, please!
# 2  
Old 01-31-2013
try:
Code:
awk '/^>/;!/^>/ {printf}' infile

# 3  
Old 01-31-2013
Code:
awk '/^>/ { print ((FNR==1)?"":ORS) $0;next} {printf $0}' myFile

Last edited by vgersh99; 01-31-2013 at 07:06 PM.. Reason: ooops...
# 4  
Old 01-31-2013
Code:
awk '/^>/&&NR==1{print;next}/^>/&&NR!=1{printf "\n%s\n",$0;}!/^>/{printf "%s",$0}END{printf "\n"}' filename

# 5  
Old 01-31-2013
You implied that you just want to merge lines, but most (but not all) minus signs in your input file were removed.

Please explain what determines whether a minus sign found on an input line is supposed to be copied to an output line.
# 6  
Old 01-31-2013
Thanks for the answers ...

yes, the minus sign (on sequence) needs to include on search like if was an similar letter A-Z ... its a fasta sequence aligned so its normal when protein/nucleotide sequence gets minus sign ...
# 7  
Old 01-31-2013
Quote:
Originally Posted by andreia
Thanks for the answers ...

yes, the minus sign (on sequence) needs to include on search like if was an similar letter A-Z ... its a fasta sequence aligned so its normal when protein/nucleotide sequence gets minus sign ...
I'm sorry, but biology was not my major. Please explain how a program reading your input file is supposed to know which minus signs should be removed when merging input lines. (None of the provided scripts produce the output you said you wanted because the output you said you want to get drops five out of six minus signs in the second line of each output pair.)
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