Improving code design of DNA alignment degapping

Question

This is a question regarding a more efficient code design:

Assume three aligned DNA sequences (seq1, seq2 and seq3; they are each strings) that represent two genes (gene1 and gene2). Start and stop positions of these genes are known relative to the aligned DNA sequences.

# Input
align = {"seq1":"ATGCATGC", # In seq1, gene1 and gene2 are of equal length
         "seq2":"AT----GC",
         "seq3":"A--CA--C"}
annos = {"seq1":{"gene1":[0,3], "gene2":[4,7]},
         "seq2":{"gene1":[0,3], "gene2":[4,7]},
         "seq3":{"gene1":[0,3], "gene2":[4,7]}}

I wish to remove the gaps (i.e., dashes) from the alignment and maintain the relative association of the start and stop positions of the genes.

# Desired output
align = {"seq1":"ATGCATGC", 
         "seq2":"ATGC",
         "seq3":"ACAC"}
annos = {"seq1":{"gene1":[0,3], "gene2":[4,7]},
         "seq2":{"gene1":[0,1], "gene2":[2,3]},
         "seq3":{"gene1":[0,1], "gene2":[2,3]}}

Obtaining the desired output is less trivial than it may seem. Below I wrote some (line-numbered) pseudocode for this problem, but surely there is a more elegant design.

1  measure length of any aligned gene  # take any seq, since all seqs aligned
2  list_lengths = list of gene lengths  # order is important
3  for seq in alignment
4      outseq = ""
5      for each num in range(0, length(seq))  # weird for-loop is intentional
6          if seq[num] == "-"
7              current_gene = gene whose start/stop positions include num
8              subtract 1 from length of current_gene
9              subtract 1 from lengths of all genes following current_gene in list_lengths
10         else
11             append seq[num] to outseq
12     append outseq to new variable
13     convert gene lengths into start/stop positions and append ordered to new variable

Can anyone give me suggestions/examples for a shorter, more direct code design?

Answer 1

This answer handles your updated annos dictionary from the comment to cdlanes answer. That answer leaves the annos dictionary with the incorrect index of [2,1] for seq2 gene2. My proposed solution will remove the gene entry from the dictionary if the sequence contains ALL gaps in that region. Also to note, if a gene contains only one letter in the final align, then anno[geneX] will have equal indices for start and stop --> See seq3 gene1 from your commented annos.

align = {"seq1":"ATGCATGC",
         "seq2":"AT----GC",
         "seq3":"A--CA--C"}

annos = {"seq1":{"gene1":[0,3], "gene2":[4,7]},
         "seq2":{"gene1":[0,3], "gene2":[4,7]},
         "seq3":{"gene1":[0,3], "gene2":[4,7]}}


annos3 = {"seq1":{"gene1":[0,2], "gene2":[3,4], "gene3":[5,7]}, 
          "seq2":{"gene1":[0,2], "gene2":[3,4], "gene3":[5,7]}, 
          "seq3":{"gene1":[0,2], "gene2":[3,4], "gene3":[5,7]}}

import re
for name,anno in annos.items():
    # indices of gaps removed usinig re
    removed = [(m.start(0)) for m in re.finditer(r'-', align[name])]

    # removes gaps from align dictionary
    align[name] = re.sub(r'-', '', align[name])

    build_dna = ''
    for gene,inds in anno.items():

        start_ind = len(build_dna)+1

        #generator to sum the num '-' removed from gene
        num_gaps = sum(1 for i in removed if i >= inds[0] and i <= inds[1])

        # build the de-gapped string
        build_dna+= align[name][inds[0]:inds[1]+1].replace("-", "")

        end_ind = len(build_dna)

        if num_gaps == len(align[name][inds[0]:inds[1]+1]): #gene is all gaps
            del annos[name][gene] #remove the gene entry
            continue
        #update the values in the annos dictionary
        annos[name][gene][0] = start_ind-1
        annos[name][gene][1] = end_ind-1

Results:

In [3]: annos
Out[3]:  {'seq1': {'gene1': [0, 3], 'gene2': [4, 7]},
          'seq2': {'gene1': [0, 1], 'gene2': [2, 3]},
          'seq3': {'gene1': [0, 1], 'gene2': [2, 3]}}

Results from the 3 gene annos above. Just replace the annos variable:

In [5]: annos3
Out[5]:  {'seq1': {'gene1': [0, 2], 'gene2': [3, 4], 'gene3': [5, 7]},
          'seq2': {'gene1': [0, 1], 'gene3': [2, 3]},
          'seq3': {'gene1': [0, 0], 'gene2': [1, 2], 'gene3': [3, 3]}}

Answer 2

The following matches the output of example program for both test cases:

align = {"seq1":"ATGCATGC",
         "seq2":"AT----GC",
         "seq3":"A--CA--C"}

annos = {"seq1":{"gene1":[0,3], "gene2":[4,7]},
         "seq2":{"gene1":[0,3], "gene2":[4,7]},
         "seq3":{"gene1":[0,3], "gene2":[4,7]}}

(START, STOP) = (0, 1)

for alignment, sequence in align.items():
    new_sequence = ''
    gap = 0

    for position, codon in enumerate(sequence):
        if '-' == codon:
            for gene in annos[alignment].values():
                if gene[START] > (position - gap):
                    gene[START] -= 1
                if gene[STOP] >= (position - gap):
                    gene[STOP] -= 1
            gap += 1
        else:
            new_sequence += codon

    align[alignment] = new_sequence

The result of running this:

python3 -i test.py
>>> align
{'seq2': 'ATGC', 'seq1': 'ATGCATGC', 'seq3': 'ACAC'}
>>> 
>>> annos
{'seq1': {'gene1': [0, 3], 'gene2': [4, 7]}, 'seq2': {'gene1': [0, 1], 'gene2': [2, 3]}, 'seq3': {'gene1': [0, 1], 'gene2': [2, 3]}}
>>> 

I hope this is still elegant, direct, short and Pythonic enough!