How to convert a FASTA file to a pandas DataFrame?

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I'm trying to transfer a .fasta file into a .xls file so that I can conveniently color my phylogenetic tree.

import pandas as pd
import re
from Bio import SeqIO
s1 = {}
s2 = {}
with open('/Users/xxx.fasta') as seqF:
    for seqFP in SeqIO.parse(seqF,"fasta"):
        seq_id = seqFP.description
        seq_an = re.search(r"\[([^]]*)\]",seq_id)
        s1[seqFP.id] = seqFP.seq
        s2[seqFP.id] = seq_an
print(s2.values)

However when I tried to use the s1 to create a pd.Series, the sequence column shows like "(M, S, A, C, C, N, K, L, A, V, L, G, L, T, F, ...".

biopython pandas python
1 Answers

Using this FASTA file as an example:

import pandas as pd
import re
from Bio import SeqIO
from collections import defaultdict


data = defaultdict(list)
with open('nucleotide-sample.txt') as fp:
  for record in SeqIO.parse(fp,"fasta"):
    organism = re.search(r"\[([^]]*)\]", record.description).group(1)
    sequence = str(record.seq)
    data['organism'].append(organism)
    data['sequence'].append(sequence)

df = pd.DataFrame.from_dict(data)

Or, shorter but maybe less readable:

with open('nucleotide-sample.txt') as fp:
  records = [{'organism': re.search(r"\[([^]]*)\]", record.description).group(1), 
              'sequence': str(record.seq)} for record in SeqIO.parse(fp,"fasta")]

df = pd.DataFrame.from_records(records)

Both return the following DataFrame:

organism sequence
0 organism=Carpodacus mexicanus CCTTTATCTAATCTTTGGAGCATGAGCTGGCATAGTTGGAACCGCCCTCAGCCTCCTCATCCGTGCAGAACTTGGACAACCTGGAACTCTTCTAGGAGACGACCAAATTTACAATGTAATCGTCACTGCCCACGCCTTCGTAATAATTTTCTTTATAGTAATACCAATCATGATCGGTGGTTTCGGAAACTGACTAGTCCCACTCATAATCGGCGCCCCCGACATAGCATTCCCCCGTATAAACAACATAAGCTTCTGACTACTTCCCCCATCATTTCTTTTACTTCTAGCATCCTCCACAGTAGAAGCTGGAGCAGGAACAGGGTGAACAGTATATCCCCCTCTCGCTGGTAACCTAGCCCATGCCGGTGCTTCAGTAGACCTAGCCATCTTCTCCCTCCACTTAGCAGGTGTTTCCTCTATCCTAGGTGCTATTAACTTTATTACAACCGCCATCAACATAAAACCCCCAACCCTCTCCCAATACCAAACCCCCCTATTCGTATGATCAGTCCTTATTACCGCCGTCCTTCTCCTACTCTCTCTCCCAGTCCTCGCTGCTGGCATTACTATACTACTAACAGACCGAAACCTAAACACTACGTTCTTTGACCCAGCTGGAGGAGGAGACCCAGTCCTGTACCAACACCTCTTCTGATTCTTCGGCCATCCAGAAGTCTATATCCTCATTTTAC
1 organism=uncultured bacillus sp. GGTAGGTACCGCCCTAAGNCTCCTAATCCGAGCAGAACTANGCCAACCCGGAGCCCTTCTGGGAGACGACCAAATCTACAACGTAGTCGTTACGGCCCACGCCTTCGTAATAATCTTTTTCATAGTAATGCCAATCATAATCGGAGGATTCGGGAACTGACTAGTTCCTCTAATGATTGGGGCCCCAGACATAGCATTCCCTCGAATAAACAACATAAGCTTTTGACTACTACCACCATCATTCCTACTCCTAATAGCCTCCTCAACAGTAGAAGCAGGAGCCGGAACCGGATGAACCGTGTACCCACCACTAGCTGGAAACCTGGCCCACGCCGGAGCCTCAGTAGACCTAGCTATCTTCTCCCTACACCTAGCAGGTATCTCATCCATCCTGGGGGCAATTAACTTCATTACAACAGCAATCAACATAAAACCACCCGCCCTCTCACAATACCAAACACCACTATTCGTGTGATCCGTCCTAATTACGGCCGTACTACTCCTACTATCTCTCCCAGTACTAGCCGCCGGTATCACCATGCTACTCACAGACCGCAACCTCAACACCACCTTCTTTGACCCAGCAGGAGGAGGAGACCCAGTACTATACCAGCACCTATTCTGATTCTTCGGACACCCAGAAGTCTACATCCTAATTCTC
2 organism=Phalaenopsis equestris var. leucaspis CCTATACCTAATTTTCGGCGCATGAGCCGGAATGGTGGGTACCGCTCTAAGCCTCCTCATTCGAGCAGAACTAGGCCAACCCGGAGCCCTTCTGGGAGACGACCAAGTCTACAACGTGGTTGTCACGGCCCATGCCTTCGTAATAATCTTCTTTATAGTTATGCCGATTATAATCGGAGGATTCGGAAACTGACTAGTCCCCCTAATAATCGGAGCCCCAGACATAGCATTTCCGCGAATAAACAACATAAGCTTCTGACTACTCCCACCATCATTCCTCCTCCTCTTAGCATCCTCCACAGTGGAAGCAGGCGTAGGTACAGGCTGAACAGTGTATCCCCCACTAGCTGGCAACCTAGCTCATGCCGGGGCCTCAGTCGACCTCGCAATCTTCTCCTTACACCTAGCTGGTATTTCCTCAATCCTCGGAGCAATTAACTTCATTACAACAGCAATTAACATGAAACCTCCTGCCCTCTCACAATACCAAACCCCACTATTCGTCTGATCAGTGTTAATTACTGCAGTCCTCCTTCTCCTTTCCCTTCCAGTTCTAGCTGCAGGAATCACAATGCTCCTCACAGACCGCAACCTCAACACCACATTCTTCGACCCTGCCGGAGGAGGAGATCCCGTCCTATATCAACATCTCTTCTGATTCTTCGGCCACCCAGAAGTCTACATCCTAATCCTC
3 organism=uncultured archaeon CATGAGCTGGAATAGTAGGTACCGCCCTAAGCCTCCTAATTCGAGCAGAGCTAGGCCAACCCGGAGCCCTACTGGGAGACGACCAAATCTACAACGTAGTCGNCACGGCCCATGCTTTTGTAATAATCTTCTTCATAGTAATGCCAATCATAATCGGAGGGTTTGGAAACTGACTGGTCCCCCTAATAATTGGAGCTCCAGACATAGCATTCCCCCGAATAAACAACATGAGTTTCTGACTACTTCCCCCATCATTCCTACTACTAATAGCCTCCTCAACAGTAGAAGCAGGCGTTGGAACAGGATGAACCGTATATCCACCACTAGCCGGAAACCTAGCCCATGCAGGAGCCTCAGTAGACCTAGCTATCTTCTCCCTACACCTAGCAGGTATCTCCTCCATCCTAGGGGCAATCAACTTCATTACAACAGCAATCAACATAAAACCACCCGCCCTATCACAATACCAAACACCACTATTCGTATGATCCGTCCTAATCACAGCCGTACTACTCCTCCTATCACTCCCAGTGCTAGCTGCTGGAATTACCATGCTACTTACAGACCGCAACCTCAACACTACCTTCTTTGACCCAGCAGGGGGAGGAGACCCAGTGCTATACCAACATCTATTCTGATTCTTCGGACACCCAGAAGTTTACATCCTAATTCTC
4 organism=Influenza A virus CCTATACCTAATTTTCGGCGCATGAGCCGGAATAGTGGGTACCGCCCTAAGCCTCCTCATTCGAGCAGAACTAGGCCAACCCGGAGCCCTTCTGGGAGACGACCAAGTCTATAACGTAGTTGTCACGGCCCATGCCTTCGTAATAATTTTCTTTATAGTTATGCCGATTATAATCGGAGGATTCGGAAACTGACTAGTCCCCCTAATAATCGGAGCCCCAGACATAGCATTCCCACGAATAAACAACATAAGCTTCTGACTACTCCCACCATCATTCCTTCTCCTCCTAGCATCCTCCACAGTCGAAGCAGGCGTAGGTACAGGCTGAACAGTATACCCCCCACTAGCTGGCAACCTAGCTCACGCCGGAGCCTCAGTCGACCTCGCAATCTTCTCTCTACACCTAGCTGGTATTTCCTCAATCCTCGGAGCAATCAACTTCATTACAACAGCAATTAACATAAAACCTCCTGCCCTCTCACAATACCAAACCCCACTGTTCGTCTGATCCGTCCTAATCACTGCAGTCCTCCTGCTCCTTTCCCTTCCAGTTCTAGCTGCAGGAATCACAATACTCCTCACAGACCGCAACCTAAACACCACATTCTTCGACCCTGCTGGAGGAGGAGATCCCGTCCTATATCAACACCTTTTCTGATTCTTCGGCCACCCAGAAGTCTACATCCTAATCNTC
5 organism=Vireo gilvus CATGAGCTGGAATAGTAGGTACCGCCCTAAGCCTCCTAATTCGAGCAGAGCTAGGCCAACCCGGAGCCCTACTGGGAGACGACCAAATCTACAACGTAGTCGTCACGGCCCATGCTTTTGTAATAATCTTCTTCATAGTAATGCCAATCATAATCGGAGGGTTTGGAAACTGACTGGTCCCCCTAATAATTGGAGCTCCAGACATAGCATTCCCCCGAATAAACAACATGAGTTTCTGACTACTTCCCCCATCATTCCTACTACTAATAGCCTCCTCAACAGTAGAAGCAGGCGTTGGAACAGGATGAACTGTATACCCGCCACTAGCCGGTAACCTAGCCCATGCAGGAGCCTCAGTAGACCTAGCTATCTTCTCCCTACACCTAGCAGGTATCTCCTCCATCCTAGGGGCAATCAACTTCATTACAACAGCAATCAACATAAAACCACCCGCCCTATCACAATACCAAACACCACTATTCGTATGATCCGTCCTAATCACAGCCGTACTACTCCTCCTATCACTCCCAGTGCTAGCTGCTGGAATTACCATGCTACTTACAGACCGCAACCTCAACACTACCTTCTTTGACCCAGCAGGGGGAGGAGACCCAGTGCTATACCAACATCTATTCTGATTCTTCGGACACCCAGAAGTTTACATCCTAATTCTC
6 organism=Pelecanus erythrorhynchos TAGTTGGAACAGCCCTCAGCCTACTCATCCGAGCAGAACTAGGCCAACCCGGAACCCTCCTGGGAGATGACCAAATCTACAATGTAATCGTCACTGCCCATGCCTTCGTAATAATCTTCTTCATAGTAATACCAGTCATAATTGGAGGCTTCGGAAACTGACTAGTCCCCCTCATAATCGGCGCTCCAGACATAGCATTCCCACGTATAAACAACATAAGCTTCTGACTCCTACCCCCATCCTTCCTACTCCTCCTAGCCTCATCCACAGTGGAAGCAGGCGCAGGAACAGGATGAACGGTGTACCCCCCACTAGCTGGCAACCTAGCCCATGCCGGAGCCTCAGTAGATCTAGCTATTTTCTCACTCCACTTAGCAGGGGTATCCTCTATTCTAGGTGCAATCAATTTCATCACAACCGCCATCAACATAAAACCACCAGCCCTATCACAATATCAAACTCCATTATTCGTGTGATCCGTACTCATCACTGCCGTCCTACTACTATTATCCCTCCCAGTCCTAGCCGCCGGCATCACTATGCTCCTCACAGACCGAAATCTGAACACTACATTCTTCGACCCCGCTGGAGGAGGAGACCCAGTCCTATACCAACACTTATTCTGGTTTTTCGGCCACCCAGAAGTTTACATCCTAATTCTC
7 organism=Hippodamia tredecimpunctata tibialis TAGTTGGAACAGCCCTCAGCCTACTCATCCGAGCAGAACTAGGCCAACCCGGAACCCTCCTGGGAGATGACCAAATCTACAATGTAATCGTCACTGCCCATGCCTTCGTAATAATCTTCTTCATAGTAATACCAGTCATAATTGGAGGCTTCGGAAACTGACTAGTCCCCCTCATAATCGGCGCTCCAGACATAGCATTCACAACATAAGCTTCTGACTCCTACCCCCATCCTTCCTACTCCTCCTAGCCTCATCCACAGTGGAAGCAGGCGCAGGAACAGGATGAACGGTGTACCCCCCACTAGCTGGCAACCTAGCCCATGCCGGAGCCTCAGTAGATCTAGCTATTTTCTCACTCCACTTAGCAGGGGTATCCTCTATTCTAGGTGCAATCAATTTCATCACAACCGCCATCAACATAAAACCACCAGCCCTATCACAATATCAAACTCCATTATTCGTGTGATCCGTACTCATCACTGCCGTCCTACTACTATTATCCCTCCCAGTCCTAGCCGCCGGCATCACTATGCTCCTCACAGACCGAAATCTGAACACTACATTCTTCGACCCCGCTGGAGGAGGAGACCCAGTCCTATACCAACACTTATTCTGGTTTTTCGGCCACCCAGAAGTTTACATCCTAATTCTC
8 organism=Petunia integrifolia subsp. inflata TAGTTGGAACAGCCCTCAGCCTACTCATCCGAGCAGAACTAGGCCAACCCGGAACCCTCCTGGGAGATGACCAAATCTACAATGTAATCGTCACTGCCCATGCCTTCGTAATAATCTTCTTCATAGTAATACCAGTCATAATTGGAGGCTTCGGAAACTGACTAGTCCCCCTCATAATCGGCGCTCCAGACATAGCATTCCCACGTATAAACAACATAAGCTTCTGACTCCTACCCCCATCCTTCCTACTCCTCCTAGCCTCATCCACAGTGGAAGCAGGCGCAGGAACAGGATGAACGGTGTACCCCCCACTAGCTGGCAACCTAGCCCATGCCGGAGCCTCAGTAGATCCATCAACATAAAACCACCAGCCCTATCACAATATCAAACTCCATTATTCGTGTGATCCGTACTCATCACTGCCGTCCTACTACTATTATCCCTCCCAGTCCTAGCCGCCGGCATCACTATGCTCCTCACAGACCGAAATCTGAACACTACATTCTTCGACCCCGCTGGAGGAGGAGACCCAGTCCTATACCAACACTTATTCTGGTTTTTCGGCCACCCAGAAGTTTACATCCTAATTCTC
9 organism=Fusarium oxysporum f. tuberosi TAGTTGGAACAGCCCTCAGCCTACTCATCCGAGCAGAACTAGGCCAACCCGGAACCCTCCTGGGAGATGAATTGGAGGCTTCGGAAACTGACTAGTCCCCCTCATAATCGGCGCTCCAGACATAGCATTCCCACGTATAAACAACATAAGCTTCTGACTCCTACCCCCATCCTTCCTACTCCTCCTAGCCTCATCCACAGTGGAAGCAGGCGCAGGAACAGGATGAACGGTGTACCCCCCACTAGCTGGCAACCTAGCCCATGCCGGAGCCTCAGTAGATCTAGCTATTTTCTCACTCCACTTAGCAGGGGTATCCTCTATTCTAGGTGCAATCAATTTCATCACAACCGCCATCAACATAAAACCACCAGCCCTATCACAATATCAAACTCCATTATTCGTGTGATCCGTACTCATCACTGCCGTCCTACTACTATTATCCCTCCCAGTCCTAGCCGCCGGCATCACTATGCTCCTCACAGACCGAAATCTGAACACTACATTCTTCGACCCCGCTGGAGGAGGAGACCCAGTCCTATACCAACACTTATTCTGGTTTTTCGGCCACCCAGAAGTTTACATCCTAATTCTC
10 organism=Dendroica tigrina TAGTTGGAACAGCCCTCAGCCTACTCATCCGAGCAGAACTAGGCCAACCCGGAACCCTCCTGGGAGATGACCAAATCTACAATGTAATCGTCACTGCCCATGCCTTCGTAATAATCTTCTTCATAGTAATACCAGTCATAATTGGAGGCTTCGGAAACTGACTAGTCCCCCTCATAATCGGCGCTCCAGACATAGCATTCCCACGTATAAACAACATAAGCTTCTGACTCCTACCCCCATCCTTCCTACTCCTCCTAGCCTCATCCACAGTGGAAGCAGGCGCAGGAACAGGATGAACGGTGTACCCCCCACTAGCTGGCAACCTAGCCCATGCCGGAGCCTCAGTAGATCTAGCTATTTTCTCACTCCACTTAGCAGGGGTATCCTCTATTCTAGGTGCAATCAATTTCATCACAACCGCCATCAACATAAAACCACCAGCCCTATCACAATATCAAACTCCATTATTCGTGTGATCCGTACTCATCAC
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