Basic Python scripts to analyze fasta files

count_seqs

• script to count the number of sequences in a fasta file

biotools.sh

• shell script to install the latest release of some bioinformatics tools that i use using regular expressions

orf_finder

• python script to find the open reading frames in a fasta file

GC_content

• python script used to calculate the GC content of the sequences inside a fasta file
• output file is GC_content.txt

DNA2Protein.py

• translate fasta file sequences to protein (amino acids) based on the desired open reading frame
• run the script with python DNA2Protein.py or sudo chmod +x DNA2Protein.py in Linux then ./DNA2Protein.py - then enter the open reading frame you want to translate or press enter to translate all open reading frames - output file is translation.txt

6_frame_translation.py

• getting all the 6 reading frames (forward and reverse strands) from a fasta file

reverse_comp.py

• getting the reverse complement of the sequences in a fasta file
• output file is reverse_comp.txt

detect-N-repeats.py

• takes 2 inputs fasta file, the length of the repeat
• gives back an output file (repeats.txt) with all the repeats of the specified length and their number of occurrences - as a dictionary and the most frequent repeat of that length