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Matching numbers of characters in two lines

 
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# 1  
Old 03-09-2011
Matching numbers of characters in two lines
Dear all,

I'm stuck on a certain problem regarding counting the number of characters in one line and then adjusting the number of characters of another line to this number.

This was my original input data:

Code:
@HWI-ST471_57:1:1:1231:2079/2
TTGGTTTATATGGTTTCGGTTGCCTTCTATTAGGCTGTGATTGGCTCATGTAATTGANNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
+
IFF;CGBAFFFFFDBBBD=EAA7DBDFDCDF?A.C:;:7:@4@,8,.787>+AAD>?###########################################
@HWI-ST471_57:1:1:1220:2195/2
TTGGATGGAGCAGAGCAGGNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
+
<;>?59,<99B@C@<CDDC#################################################################################
@HWI-ST471_57:1:1:1230:2241/2
GGCTGGGTGAGGTTTCCCGTGTTGAGTCAANNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
+
GDGG;D6+D=@A6@9BEEE>D=D@<5<?@C######################################################################

Now I'm using this comand to delete T's and A's at the beginning of every 4th line starting at line #2:

Code:
sed -e '2~4 s/T*//' -e '2~4 s/A*//'

This results in
Code:
@HWI-ST471_57:1:1:1231:2079/2
GGTTTATATGGTTTCGGTTGCCTTCTATTAGGCTGTGATTGGCTCATGTAATTGANNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
+
IFF;CGBAFFFFFDBBBD=EAA7DBDFDCDF?A.C:;:7:@4@,8,.787>+AAD>?###########################################
@HWI-ST471_57:1:1:1220:2195/2
GGATGGAGCAGAGCAGGNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
+
<;>?59,<99B@C@<CDDC#################################################################################
@HWI-ST471_57:1:1:1230:2241/2
GGCTGGGTGAGGTTTCCCGTGTTGAGTCAANNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
+
GDGG;D6+D=@A6@9BEEE>D=D@<5<?@C######################################################################

Now I want the number of characters of every 4th line starting at line 1 to match the characters of every 4th line starting at line 2. The desired output is:

Code:
@HWI-ST471_57:1:1:1231:2079/2
GGTTTATATGGTTTCGGTTGCCTTCTATTAGGCTGTGATTGGCTCATGTAATTGANNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
+
F;CGBAFFFFFDBBBD=EAA7DBDFDCDF?A.C:;:7:@4@,8,.787>+AAD>?###########################################
@HWI-ST471_57:1:1:1220:2195/2
GGATGGAGCAGAGCAGGNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
+
>?59,<99B@C@<CDDC#################################################################################
@HWI-ST471_57:1:1:1230:2241/2
GGCTGGGTGAGGTTTCCCGTGTTGAGTCAANNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
+
GDGG;D6+D=@A6@9BEEE>D=D@<5<?@C######################################################################

Do you have any idea how I can alter my approach or add another command using awk/sed to reach this result?

THx!
# 2  
Old 03-09-2011
Hope this could help you,

Code:
awk 'NR%4==2{sub("T*|A*","");l=length($0)}NR%4==0{$0=substr($0,length($0)-l+1)}1' file

This User Gave Thanks to yinyuemi For This Post:
DerSeb
# 3  
Old 03-09-2011
Quote:
Originally Posted by DerSeb
Dear all,
Code:
sed -e '2~4 s/T*//' -e '2~4 s/A*//'

What does "2~4" in the above code signifies? I am damn sure it is not selecting lines from 2 to 4 when I tested it. It just process the 2nd line only.
# 4  
Old 03-10-2011
Quote:
Originally Posted by royalibrahim
What does "2~4" in the above code signifies? I am damn sure it is not selecting lines from 2 to 4 when I tested it. It just process the 2nd line only.
No, it's not selecting lines 2 to 4.

It means start at line 2 (included) and from there select every fourth line. At least that's what I hope it does Smilie

Therefor it should process all lines that describe the ATGC sequence in my file.

---------- Post updated at 04:21 AM ---------- Previous update was at 04:15 AM ----------

Quote:
Originally Posted by yinyuemi
Hope this could help you,

Code:
awk 'NR%4==2{sub("T*|A*","");l=length($0)}NR%4==0{$0=substr($0,length($0)-l+1)}1' file

thanks, this works great!

Is it also possible to print only those sets of four lines where more that 15 Ts or As where deleted?
# 5  
Old 03-11-2011
Quote:
Originally Posted by DerSeb
No, it's not selecting lines 2 to 4.

It means start at line 2 (included) and from there select every fourth line. At least that's what I hope it does Smilie.
Yes, thanks for the clarification Smilie
 
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