How to break protein sequence into equal size of 20 in python

extract sequence from fasta file python
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I want to break the structure of protein into the chunks of 20 equal size the structure of the protein is something like this

MASTEGANNMPKQVEVRMHDSHLGSEEPKHRHLGLRLCDKLGKNLLLTLTVFGVILGAVCGGLLRLASPI
HPDVVMLIAFPGDILMRMLKMLILPLIISSLITGLSGLDAKASGRLGTRAMVYYMSTTIIAAVLGVILVL
AIHPGNPKLKKQLGPGKKNDEVSSLDAFLDLIRNLFPENLVQACFQQIQTVTKKVLVAPPPDEEANATSA
VVSLLNETVTEVPEETKMVIKKGLEFKDGMNVLGLIGFFIAFGIAMGKMGDQAKLMVDFFNILNEIVMKL
VIMIMWYSPLGIACLICGKIIAIKDLEVVARQLGMYMVTVIIGLIIHGGIFLPLIYFVVTRKNPFSFFAG
IFQAWITALGTASSAGTLPVTFRCLEENLGIDKRVTRFVLPVGATINMDGTALYEAVAAIFIAQMNGVVL
DGGQIVTVSLTATLASVGAASIPSAGLVTMLLILTAVGLPTEDISLLVAVDWLLDRMRTSVNVVGDSFGA
GIVYHLSKSELDTIDSQHRVHEDIEMTKTQSIYDDMKNHRESNSNQCVYAAHNSVIVDECKVTLAANGKS
ADCSVEEEPWKREK

I have tried the by iterating loop

    x="abfgjjhuyuryitfvbkjuhhgyuumnabcdfrfhghhoiutgfctrdgfvijnk"
    length=len(x)
    values= [length/20+1]

    a=1
    for i in length(a,x)
    print(i)

but this is not working

Try this by importing the textwrap

import textwrap
myArray="MASTEGANNMPKQVEVRMHDSHLGSEEPKHRHLGLRLCDKLGKNLLLTLTVFGVILGAVCGGLLRLASPIHPDVVMLIAFPGDILMRMLKMLILPLIISSLITGLSGLDAKASGRLGTRAMVYYMSTTIIAAVLGVILVLAIHPGNPKLKKQLGPGKKNDEVSSLDAFLDLIRNLFPENLVQACFQQIQTVTKKVLVAPPPDEEANATSAVVSLLNETVTEVPEETKMVIKKGLEFKDGMNVLGLIGFFIAFGIAMGKMGDQAKLMVDFFNILNEIVMKLVIMIMWYSPLGIACLICGKIIAIKDLEVVARQLGMYMVTVIIGLIIHGGIFLPLIYFVVTRKNPFSFFAGIFQAWITALGTASSAGTLPVTFRCLEENLGIDKRVTRFVLPVGATINMDGTALYEAVAAIFIAQMNGVVLDGGQIVTVSLTATLASVGAASIPSAGLVTMLLILTAVGLPTEDISLLVAVDWLLDRMRTSVNVVGDSFGAGIVYHLSKSELDTIDSQHRVHEDIEMTKTQSIYDDMKNHRESNSNQCVYAAHNSVIVDECKVTLAANGKSADCSVEEEPWKREK"
list_string = str(myArray)
textwrap.wrap(list_string, 20)

the output is something like this!

['MASTEGANNMPKQVEVRMHD',
 'SHLGSEEPKHRHLGLRLCDK',
 'LGKNLLLTLTVFGVILGAVC',
 'GGLLRLASPIHPDVVMLIAF',
 'PGDILMRMLKMLILPLIISS',
 'LITGLSGLDAKASGRLGTRA',
 'MVYYMSTTIIAAVLGVILVL',
 'AIHPGNPKLKKQLGPGKKND',
 'EVSSLDAFLDLIRNLFPENL',
 'VQACFQQIQTVTKKVLVAPP',
 'PDEEANATSAVVSLLNETVT',
 'EVPEETKMVIKKGLEFKDGM',
 'NVLGLIGFFIAFGIAMGKMG',
 'DQAKLMVDFFNILNEIVMKL',
 'VIMIMWYSPLGIACLICGKI',
 'IAIKDLEVVARQLGMYMVTV',
 'IIGLIIHGGIFLPLIYFVVT',
 'RKNPFSFFAGIFQAWITALG',
 'TASSAGTLPVTFRCLEENLG',
 'IDKRVTRFVLPVGATINMDG',
 'TALYEAVAAIFIAQMNGVVL',
 'DGGQIVTVSLTATLASVGAA',
 'SIPSAGLVTMLLILTAVGLP',
 'TEDISLLVAVDWLLDRMRTS',
 'VNVVGDSFGAGIVYHLSKSE',
 'LDTIDSQHRVHEDIEMTKTQ',
 'SIYDDMKNHRESNSNQCVYA',
 'AHNSVIVDECKVTLAANGKS',
 'ADCSVEEEPWKREK']

Split a FASTA file into several equal pieces, I used this piece of biopython codes written by Eric Normandeau to parse several sequences from a no accepted_hits.bam generated. Hi, I am using tophat to do​  Chunks of equal size. To partition a sequence into chunks of equal size, To break a sequence into chunks on some separators, size File type Python version

Something like this would do the trick:

values = [x[i:i+20] for i in range(0, len(x), 20)]

Just as a reference:

x[a:b] takes a slice of the string x from the index a up to (but not including) index b, therefore x[i:i+20] takes a slice of size twenty starting from index i.

range(a, b, step) would generate a sequence of numbers from a up to (but not including) b with increments of step.

8th International Conference on Bioinformatics and Biomedical , in table I, where positive is equal to basic_polar and negative is equal to acidic_polar. All features extracted from protein sequence are shown in table II. Types of feature Dimension of feature Feature Amino acid composition 20 A,C,D,​E, METHODS A program compiled by Python was used to divide the dataset into 10  The sequence of amino acids is unique for each type of protein and all proteins are built from the same set of just 20 amino acids for all living things. Instructions in the DNA are first transcribed into RNA and the RNA is then translated into proteins. We can think of DNA, when read as sequences of three letters, as a dictionary of life.

You could use re.findall, after first removing all whitespace, e.g.:

inp = """MASTEGANNMPKQVEVRMHDSHLGSEEPKHRHLGLRLCDKLGKNLLLTLTVFGVILGAVCGGLLRLASPI
HPDVVMLIAFPGDILMRMLKMLILPLIISSLITGLSGLDAKASGRLGTRAMVYYMSTTIIAAVLGVILVL
AIHPGNPKLKKQLGPGKKNDEVSSLDAFLDLIRNLFPENLVQACFQQIQTVTKKVLVAPPPDEEANATSA"""
inp = re.sub(r'\s+', '', inp)
chunks = re.findall(r'.{1,20}', inp)

This prints:

['MASTEGANNMPKQVEVRMHD',
 'SHLGSEEPKHRHLGLRLCDK',
 'LGKNLLLTLTVFGVILGAVC',
 'GGLLRLASPIHPDVVMLIAF',
 'PGDILMRMLKMLILPLIISS',
 'LITGLSGLDAKASGRLGTRA',
 'MVYYMSTTIIAAVLGVILVL',
 'AIHPGNPKLKKQLGPGKKND',
 'EVSSLDAFLDLIRNLFPENL',
 'VQACFQQIQTVTKKVLVAPP',
 'PDEEANATSA']

How to split a very large .fasta file into roughly equally sized files , I would like to break these up into smaller more manageable files. RotatingFileHandler("verylarge.fasta", maxBytes=2**20*100, backupCount=100) log. /tools/protein_analysis/seq_analysis_utils.py#L102 if found to write the description information and sequence data to another file using Biopython. It happened to me several times to have alignments with sequences of different lengths. These can arise in several situations when you do more sophisticated things, e.g. manual edits, combining several alignments into one using some sequence alignment editors etc.

You could use something like this :

## With protein your string containing the data
size_of_split = 20
splited_protein = list(map(''.join, zip(*[iter(protein)]*size_of_split)))

It uses zip() in a way that is described in its documentation.

To quote it :

[...] clustering a data series into n-length groups using zip(*[iter(s)]*n). This repeats the same iterator n times so that each output tuple has the result of n calls to the iterator. This has the effect of dividing the input into n-length chunks.

Biopython Tutorial and Cookbook, The ability to parse bioinformatics files into Python utilizable data a DNA or protein sequence (okay, a protein with a lot of Alanines, Glycines, do cool things with them is in the Cookbook (Chapter 20 of this Tutorial). Then, logically​, Seq("ACGT", IUPAC.protein) and Seq("ACGT") should also be equal. Don’t forget the newline character if you’d like to actually be able to read the text. Be careful out there scientists, making the sequence length longer than 6 will start to enter gigabyte file size territory (increasing 20-fold each time) and runtimes will become ~20-fold longer for each additional peptide added.

Illustrating Python via Bioinformatics Examples, However, the leading Python software for bioinformatics applications is In fact, all built-in objects in Python that contain a set of elements in a particular sequence allow a for Note that all the DNA strings must have the same length. Basically, the algorithm divides [0,1] into intervals of lengths equal to  Starting with a GlimmerHMM output file in GFF3 format, produce a FASTA file of predicted protein sequences. Solution. Setting this up, we import the required modules and parse our input FASTA file into a standard python dictionary, using SeqIO. SeqIO is also used for writing the output file.

COVID-19 Coronavirus spike protein analysis for synthetic vaccines , This paper continues a recent study of the spike protein sequence of the Most common cold strains fall into one of two coronavirus serotypes: It is an epitope that typically means a patch of some 5 to 20 amino acid residues. Its large size and numerous epitopes generate a substantial immune  Write a program to determine if a patient has a mutation in their DNA sequence which results in a change of amino acid sequence. Your program should work like this: Enter original DNA: AAT Enter patient DNA: AAC The patient's amino acid sequence is not mutated.

[PDF] Pfeature Manual, To calculate Amino acid composition by splitting peptide into The compositions of all 20 natural amino acids were calculated have developed number of python function (brief description is given below). In web number of tripeptides of type ​i and length of a protein sequence. residues corresponding to every split. In the event that the line read is longer than 16 characters I want to break it down into sections of 16 character long strings and push each section out after a certain delay (e.g. 10 seconds), once complete the code should move onto the next line of the input file and continue.

Comments
  • I think a closing square bracket is missing at the end. ']'
  • I think you should increase i by len(x)/20 instead of 20. Cause the question said "20 equal size" not 20 characters.
  • I think the OP (@sania-kareem) should weigh in here, because the question is a bit vague. You might be right, or not!