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How to count the length of fasta sequences?

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# 1  
Old 04-09-2019
How to count the length of fasta sequences?
I could calculate the length of entire fasta sequences by following command,
Code:
awk '/^>/{if (l!="") print l; print; l=0; next}{l+=length($0)}END{print l}' unique.fasta

But, I need to calculate the length of a particular fasta sequence specified/listed in another txt file. The results to to be printed in a csv file.
Therefore, please help me to do the same.
Thanks in advance.
# 2  
Old 04-09-2019
Quote:
Originally Posted by dineshkumarsrk
I could calculate the length of entire fasta sequences by following command,
Code:
awk '/^>/{if (l!="") print l; print; l=0; next}{l+=length($0)}END{print l}' unique.fasta

But, I need to calculate the length of a particular fasta sequence specified/listed in another txt file. The results to to be printed in a csv file.
Therefore, please help me to do the same.
Thanks in advance.
Sorry mate without seeing sample of Input and expected output it is NOT possible to tweak a solution. So kindly do add sample of your Input_file(fasta file) and show us expected output file(.csv one) in CODE TAGS and let us know then.

Thanks,
R. Singh
These 2 Users Gave Thanks to RavinderSingh13 For This Post:
drl jim mcnamara
# 3  
Old 04-09-2019
I have a multi fasta sequences in unique.fasta as given below,
Code:
>seq1
ATGCTA
>seq2
GCTAGTT
>seq3
TAGC

I need to count the length of following header's listed in id.txt as given below,
Code:
seq1
seq2

And the results(length) to be printed in csv file as shown below,
Code:
seq1   6
seq2   7

Moderator's Comments:
Mod Comment Changed QUOTE tags to CODE tags for sample Input_file.
Last edited by RavinderSingh13; 04-09-2019 at 10:16 AM..
# 4  
Old 04-09-2019
Quote:
NOTE: Following solutions will work only for a single Input_file, which OP later confirmed is not the case, so I am keeping these solutions here in case someone wants to get a string which starts with > and print length of lines following it.
Hello dineshkumarsrk,

Could you please try following.
Code:
awk 'BEGIN{FS="[> ]"} /^>/{val=$2;next}  {print val,length($0)}'   Input_file

Output will be as follows.
Code:
seq1 6
seq2 7
seq3 4

2nd Solution: Or let's say your Input_file may end with a line which starting with > in that case if you want to print that remaining whose length value will be NULL try following.
Code:
awk 'BEGIN{FS="[> ]"} /^>/{val=$2;next}  {print val,length($0);val=""} END{if(val!=""){print val}}'   Input_file


3rd Solution: In case your seq lines may have spaces in them in that case my previous solutions may NOT give their full value so to get their full line values(without >) use following.

Code:
awk '/^>/{sub(/^>/,"");val=$0;next}  {print val,length($0)}'   Input_file

OR to take care of scenario where your Input_file could be ending with > and seq string may have spaces in it try:
Code:
awk '/^>/{sub(/^>/,"");val=$0;next}  {print val,length($0);val=""} END{if(val!=""){print val}}'   Input_file

Thanks,
R. Singh
Last edited by RavinderSingh13; 04-09-2019 at 10:37 AM..
This User Gave Thanks to RavinderSingh13 For This Post:
000vikas
# 5  
Old 04-09-2019
Thank you singh,
Your command prints all the sequences. However, I need to print only few sequences length as listed in id.txt file. If I did not understand your commands properly, please let me know, where to include id.txt file in your command?
# 6  
Old 04-09-2019
Quote:
Originally Posted by dineshkumarsrk
Thank you singh,
Your command prints all the sequences. However, I need to print only few sequences length as listed in id.txt file. If I did not understand your commands properly, please let me know, where to include id.txt file in your command?
Oh ok, I was in impression that you want to print all seq strings length in a single Input_file, could you please try following now.
Code:
awk 'FNR==NR{a[$0];next} /^>/ && sub(/^>/,""){;found=val="";if($0 in a){val=$0;found=1};next} found{print val,length($0)} ' ids.txt  Input_file

Output will be as follows.
Code:
seq1 6
seq2 7

Thanks,
R. Singh
This User Gave Thanks to RavinderSingh13 For This Post:
dineshkumarsrk
# 7  
Old 04-09-2019
Thanks singh for your time and help. It works.
Sorry, earlier i did a mistake, that's why i did not get output.
Last edited by dineshkumarsrk; 04-09-2019 at 10:34 AM..
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