Counting the characters in a row using python

Question

I am using python 3 and biopython 1.72. I have been using a protein sequence file in clustal format.

CLUSTAL 2.1 multiple sequence alignment


Human           ------------------------------------------------------------
Chimpanzee      ------------------------------------------------------------
Dog             ------------------------------------------------------------
Mouse           ------------------------------------------------------------
Xenopus         ------------------------------------------------------------
Amphioxus       MQWTGFRVSMTTLMMIMGVVAVLIALLPAKAQQPHDKSLRTTSTLTDTGASADEADMGSA


Human           ------------------------------------------------------------
Chimpanzee      ------------------------------------------------------------
Dog             ------------------------------------------------------------
Mouse           ------------------------------------------------------------
Xenopus         ------------------------------------------------------------
Amphioxus       HVELLDGDDDVGNGSDQMMVTLHLQSIFQCIRRPCEKVDRAIDPVTQRWRTANTRNDYQK


Human           ------------------MRLRVRLLKRTWPLEVPETEPTLGHLRSHLRQSLLCTWGYSS
Chimpanzee      ------------------MRLRVRLLKRTWPLEVPETEPTLGHLRSRLRQSLLCTWGYSS
Dog             ------------------MKLRVRLQKRTWPLDLPDAEPTLGQLRAHLSQALLPSWGFGS
Mouse           ------------------MKLRVRLQKRTQPLEVPESEPTLGQLRAHLSQVLLPTLGFSS
Xenopus         ------------------MKLRVRVRKQTNRLELEAESPTLGDLRSKLSSVTLPALGYST
Amphioxus       INVCVVPAYDVSLSTGVRMKLRVKISGQKTRVDVGQDCHTLGTLRTLLAPVLGEQYGLGD
                                  *:***::  :.  :::     *** **: *        * . 

Human           NTRFTITLNYKDPLTGDEETLASYGIVSGDLICLILQDDIPA---------------PNI
Chimpanzee      NTRFTITLNYKDPLTGDEETLASYGIVSGDLICLILQDDIPA---------------PNI
Dog             DTRFAITLNNKDALTGDEETLASYGIVSGDLICLILEDAIPA---------------PNL
Mouse           DTRFAITLNNKDALTGDEETLASYGIVSGDLICLVLEDDMPA---------------PNL
Xenopus         EANFTITLNGKDALTGDQNTLESAGIISGDLIVVVLPDSQLP---------------PPQ
Amphioxus       DMPFEISLNGRDALLGDDKPLSDLGIVSGDLIHILLASVDQPSTNHNTQQQGQHPSSPEH
                :  * *:** :*.* **::.* . **:***** ::* .   .               *  

I need to iterate over the rows of my file so that I could count the occurrence of characters in each row. I tried using the code:

file_var = input("File: ")
count = 0
with open (file_var , 'r') as fo:
    for i in fo:
        count += 1
        print (i)
    print (count)

But this results just counting the total number of rows in a file(count variable). If I iterate over the file using biopython, it does'nt work also.

for seq_record in SeqIO.parse("sample.aln","clustal"):
    print (seq_record.id)
    print (repr(seq_record.seq))

seq_record.id results the names of the sequences used in the file. repr(seq_record.seq) results the sequences of each specie alongwith description.

While I need to

1. get the rows only with amino acids (exclusing the symbols '*,.,:' line) and nothing else from the row and for each row I need to count the number of characters (exclusing '-' dashes)
2. the number of characters of that row be placed at the end of each of the row.

for example: for above example file, the counter should work like;

------------------------------------------------------------ 0
MQWTGFRVSMTTLMMIMGVVAVLIALLPAKAQQPHDKSLRTTSTLTDTGASADEADMGSA 60
------------------MRLRVRLLKRTWPLEVPETEPTLGHLRSHLRQSLLCTWGYSS 42

Answer 1

Here's one way with pure Python:

#!/usr/bin/env python3
import sys
import re

with open (sys.argv[1] , 'r') as fo:
    for line in fo:
        fields = line.split()
        if len(fields)==2:
            print(fields[1],len(fields[1].replace('-','')))

Running this on your file gives:

$ foo.py file.aln 
------------------------------------------------------------ 0
------------------------------------------------------------ 0
------------------------------------------------------------ 0
------------------------------------------------------------ 0
------------------------------------------------------------ 0
MQWTGFRVSMTTLMMIMGVVAVLIALLPAKAQQPHDKSLRTTSTLTDTGASADEADMGSA 60
------------------------------------------------------------ 0
------------------------------------------------------------ 0
------------------------------------------------------------ 0
------------------------------------------------------------ 0
------------------------------------------------------------ 0
HVELLDGDDDVGNGSDQMMVTLHLQSIFQCIRRPCEKVDRAIDPVTQRWRTANTRNDYQK 60
------------------MRLRVRLLKRTWPLEVPETEPTLGHLRSHLRQSLLCTWGYSS 42
------------------MRLRVRLLKRTWPLEVPETEPTLGHLRSRLRQSLLCTWGYSS 42
------------------MKLRVRLQKRTWPLDLPDAEPTLGQLRAHLSQALLPSWGFGS 42
------------------MKLRVRLQKRTQPLEVPESEPTLGQLRAHLSQVLLPTLGFSS 42
------------------MKLRVRVRKQTNRLELEAESPTLGDLRSKLSSVTLPALGYST 42
INVCVVPAYDVSLSTGVRMKLRVKISGQKTRVDVGQDCHTLGTLRTLLAPVLGEQYGLGD 60
NTRFTITLNYKDPLTGDEETLASYGIVSGDLICLILQDDIPA---------------PNI 45
NTRFTITLNYKDPLTGDEETLASYGIVSGDLICLILQDDIPA---------------PNI 45
DTRFAITLNNKDALTGDEETLASYGIVSGDLICLILEDAIPA---------------PNL 45
DTRFAITLNNKDALTGDEETLASYGIVSGDLICLVLEDDMPA---------------PNL 45
EANFTITLNGKDALTGDQNTLESAGIISGDLIVVVLPDSQLP---------------PPQ 45
DMPFEISLNGRDALLGDDKPLSDLGIVSGDLIHILLASVDQPSTNHNTQQQGQHPSSPEH 60

---

Some other options:

1. awk

   $ awk 'NF==2{l=$2;gsub(/-/,"",$2); print l,length($2)}' file.aln 
   ------------------------------------------------------------ 0
   ------------------------------------------------------------ 0
   ------------------------------------------------------------ 0
   ------------------------------------------------------------ 0
   ------------------------------------------------------------ 0
   MQWTGFRVSMTTLMMIMGVVAVLIALLPAKAQQPHDKSLRTTSTLTDTGASADEADMGSA 60
   ------------------------------------------------------------ 0
   ------------------------------------------------------------ 0
   ------------------------------------------------------------ 0
   ------------------------------------------------------------ 0
   ------------------------------------------------------------ 0
   HVELLDGDDDVGNGSDQMMVTLHLQSIFQCIRRPCEKVDRAIDPVTQRWRTANTRNDYQK 60
   ------------------MRLRVRLLKRTWPLEVPETEPTLGHLRSHLRQSLLCTWGYSS 42
   ------------------MRLRVRLLKRTWPLEVPETEPTLGHLRSRLRQSLLCTWGYSS 42
   ------------------MKLRVRLQKRTWPLDLPDAEPTLGQLRAHLSQALLPSWGFGS 42
   ------------------MKLRVRLQKRTQPLEVPESEPTLGQLRAHLSQVLLPTLGFSS 42
   ------------------MKLRVRVRKQTNRLELEAESPTLGDLRSKLSSVTLPALGYST 42
   INVCVVPAYDVSLSTGVRMKLRVKISGQKTRVDVGQDCHTLGTLRTLLAPVLGEQYGLGD 60
   NTRFTITLNYKDPLTGDEETLASYGIVSGDLICLILQDDIPA---------------PNI 45
   NTRFTITLNYKDPLTGDEETLASYGIVSGDLICLILQDDIPA---------------PNI 45
   DTRFAITLNNKDALTGDEETLASYGIVSGDLICLILEDAIPA---------------PNL 45
   DTRFAITLNNKDALTGDEETLASYGIVSGDLICLVLEDDMPA---------------PNL 45
   EANFTITLNGKDALTGDQNTLESAGIISGDLIVVVLPDSQLP---------------PPQ 45
   DMPFEISLNGRDALLGDDKPLSDLGIVSGDLIHILLASVDQPSTNHNTQQQGQHPSSPEH 60
   

2. Perl

   $ perl -lane '$l=$F[1];$l=~s/-//g; $#F==1 && print "$F[1] ", length($l)' file.aln 
   ------------------------------------------------------------ 0
   ------------------------------------------------------------ 0
   ------------------------------------------------------------ 0
   ------------------------------------------------------------ 0
   ------------------------------------------------------------ 0
   MQWTGFRVSMTTLMMIMGVVAVLIALLPAKAQQPHDKSLRTTSTLTDTGASADEADMGSA 60
   ------------------------------------------------------------ 0
   ------------------------------------------------------------ 0
   ------------------------------------------------------------ 0
   ------------------------------------------------------------ 0
   ------------------------------------------------------------ 0
   HVELLDGDDDVGNGSDQMMVTLHLQSIFQCIRRPCEKVDRAIDPVTQRWRTANTRNDYQK 60
   ------------------MRLRVRLLKRTWPLEVPETEPTLGHLRSHLRQSLLCTWGYSS 42
   ------------------MRLRVRLLKRTWPLEVPETEPTLGHLRSRLRQSLLCTWGYSS 42
   ------------------MKLRVRLQKRTWPLDLPDAEPTLGQLRAHLSQALLPSWGFGS 42
   ------------------MKLRVRLQKRTQPLEVPESEPTLGQLRAHLSQVLLPTLGFSS 42
   ------------------MKLRVRVRKQTNRLELEAESPTLGDLRSKLSSVTLPALGYST 42
   INVCVVPAYDVSLSTGVRMKLRVKISGQKTRVDVGQDCHTLGTLRTLLAPVLGEQYGLGD 60
   NTRFTITLNYKDPLTGDEETLASYGIVSGDLICLILQDDIPA---------------PNI 45
   NTRFTITLNYKDPLTGDEETLASYGIVSGDLICLILQDDIPA---------------PNI 45
   DTRFAITLNNKDALTGDEETLASYGIVSGDLICLILEDAIPA---------------PNL 45
   DTRFAITLNNKDALTGDEETLASYGIVSGDLICLVLEDDMPA---------------PNL 45
   EANFTITLNGKDALTGDQNTLESAGIISGDLIVVVLPDSQLP---------------PPQ 45
   DMPFEISLNGRDALLGDDKPLSDLGIVSGDLIHILLASVDQPSTNHNTQQQGQHPSSPEH 60