how to read file into dictionary (seq_id and seq)?-CodePudding

I am trying to create a dictionary that has a seq_id and a list of sequences associated with that key. If anyone knows how to resolve this issue that would be much appreciated. Here is my code:

def __init__(self, file):
    sequences = {}
    with open(file) as handle:
        for seq_id, seq in SimpleFastaParser(handle):
            if seq_id in sequences:
                sequences[seq_id].append(seq)
            else:
                sequences[seq_id] = seq
    self.sequences = sequences

CodePudding user response：

Is it possible you just didn't make it a list (by using square brackets) in the else scenario?

Suggested code:

def __init__(self, file):
    sequences = {}
    with open(file) as handle:
        for seq_id, seq in SimpleFastaParser(handle):
            if seq_id in sequences:
                sequences[seq_id].append(seq)
            else:
                sequences[seq_id] = [seq]  ## Change made here
    self.sequences = sequences

CodePudding user response：

You'll find setdefault useful here as follows:

def __init__(self, file):
    self.sequences = {}
    with open(file) as handle:
        for seq_id, seq in SimpleFastaParser(handle):
            self.sequences.setdefault(seq_id, []).append(seq)

...or...

self.sequences = {seq_id: seq for seq_id, seq in SimpleFastaParser(handle)}