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README

Build Status

C Project: FASTA sequences manipulation

This project is about working on protein and nucleic sequences, stored in FASTA formatted files, in order to make specific searches (by gene name, sequence, position in the genome and sub-string), translations and later calculate distances or make sequencing simulations.

Authors

Sophie LEMATRE

Gabriel CRETIN

Install and execute

Compilation:

make

Clean *.o files:

make clean

Clean *.o and executable file:

make wipeout

Execute project:

./fasta_project

Implemented functions

Search by:

  • Gene name
  • Sequence
  • Position in the genome
  • Sub sequence (e.g. search for sequences having this kind of regex patern: [ATCG].*[ATCG].*[ATCG] etc)

Search in the dictionary-tree:

  • Full sequences
  • Number of sequences starting by a given prefix

Translation:

Nucleic sequences are translated into their proteic sequences. Output is in data/translation.txt

Assembly:

Give the header (or a particular element of the header that is a unique identificator of that sequence) to the program and it will simulate a sequencing followed by an assembly de novo. The goal is to align and merge fragments (randomly generated) of this sequence in order to reconstruct the original sequence. You can set different parameters to change the assembly precision and number of reads: NB_NUCL : average time of apparition of each base. READ_LENGTH : size of each read created de novo. READ_OVERLAP_LENGTH: length of the accepted overlap between two reads.

Debug

Valgrind command line example to test with S_pombe.fasta file only:

valgrind --track-origins=yes --leak-check=full --show-leak-kinds=all --max-stackframe=3000000 ./projet_fasta -n data/S_pombe.fasta

--max-stackframe=3000000 is set because we initialize a huge array of structure at the begining of the program. That means a large range of adresses to allocate, and valgrind warns for that.

Valgrind command line example to test with S_pombe_genome.fasta file only:

valgrind --track-origins=yes --leak-check=full --show-leak-kinds=all ./projet_fasta -a data/S_pombe_complet.fasta -c "MT dna:chromosome chromosome:ASM294v2:MT:1:19431:1"

Test assembly

Working parameters for sequence assembly in the file S_pombe_genome.fasta

For the 1st sequence: MT dna:chromosome chromosome:ASM294v2:MT:1:19431:1

NB_NUCL 10
READ_LENGTH 1000
READ_OVERLAP_LENGTH 50

$ ./projet_fasta -a data/S_pombe_complet.fasta -c "MT dna:chromosome chromosome:ASM294v2:MT:1:19431:1"

Analyse des séquences du fichier...
Taille de la séquence étudiée pour l'assemblage: 20128 nucléotides
Génération des reads...

 100 % [===============================================>]

Nombre de reads générés: 388

***************** ASSEMBLAGE DU GENOME *****************

Le génome a bien été assemblé !

############## RAPPORT D'ACTIVITE DU PROGRAMME ##############
    Temps d'analyse des séquences du fichier: 38.14 secondes
    Temps d'assemblage du génome: 30.48 secondes

For the 3rd sequence: MTR dna:chromosome chromosome:ASM294v2:MTR:1:20128:1

NB_NUCL 10
READ_LENGTH 1000
READ_OVERLAP_LENGTH 50

$ ./projet_fasta -a data/S_pombe_complet.fasta -c "MTR"

Analyse des séquences du fichier...
Taille de la séquence étudiée pour l'assemblage: 20128 nucléotides
Génération des reads...

 100 % [===============================================>]

Nombre de reads générés: 402

***************** ASSEMBLAGE DU GENOME *****************

Le génome a bien été assemblé !

############## RAPPORT D'ACTIVITE DU PROGRAMME ##############
    Temps d'analyse des séquences du fichier: 39.09 secondes
    Temps d'assemblage du génome: 32.87 secondes