Examples

It’s often easies to see how to use code through some well-worked examples. Here we provide some simple examples that illustrate how protfasta can be used to read and write FASTA files.

read_fasta examples

Some possible exampls of reading FASTA files using protfasta:

Example 1: Simple read in FASTA file

import protfasta

sequences = protfasta.read_fasta('inputfile.fasta')

Example 2: Simple read in FASTA file and ignore duplicate FASTA records and return a nested-list of residues

import protfasta

sequences = protfasta.read_fasta('inputfile.fasta',
                                 expect_unique_header=False,
                                 return_list=True,
                                 duplicate_record_action='ignore')

Example 3: Read in FASTA file and correct invalid residues using standard error correction dictionary

import protfasta

sequences = protfasta.read_fasta('inputfile.fasta',
                                 invalid_sequence_action='convert')

Example 4: Read in FASTA file and correct invalid residues using a custom dictionary

import protfasta

CD = {'U':'G', '-':''}
sequences = protfasta.read_fasta('inputfile.fasta',
                                 invalid_sequence_action='convert',
                                 correction_dictionary=CD)

Example 5: Read in FASTA file quickly without error checking By default **protfasta performs a bunch of sanity checking. In general this probably doesn’t need to be done every time if you KNOW a file is safe. To cancel any sanity checking and read in at maximum efficiency the following options can be provided:

import protfasta

sequences = protfasta.read_fasta('inputfile.fasta',
                                 invalid_sequence_action='ignore',
                                 duplicate_record_action='ignore',
                                 duplicate_sequence_action='ignore',
                                 expect_unique_header=False)

write_fasta examples

# input example using a sequence dictionary
import protfasta

sequence_in = {'seq1': 'MEEPQSDPSVEPPLS', 'seq2': 'DEAPRMPEAAPPVAPA'}
protfasta.write_fasta(sequence_in, 'example.fasta')

# input example using a sequence list
import protfasta

sequence_in = [['seq1','MEEPQSDPSVEPPLS'], ['seq2', 'DEAPRMPEAAPPVAPA']]
protfasta.write_fasta(sequence_in, 'example.fasta')