def get_nr_sequences(fasta_file, genomes_list):
locus2genome = {}
for fasta in genomes_list:
genome = os.path.basename(fasta).split('.')[0]
for seq in SeqIO.parse(fasta, "fasta"):
locus2genome[seq.name] = genome
nr_fasta = open('nr.faa', 'w')
nr_mapping = open('nr_mapping.tab', 'w')
hsh_checksum_list = {}
records = SeqIO.parse(fasta_file, "fasta")
updated_records = []
for record in records:
# NOTE: the case is important for crc64, need to check whether it
# is necessary to make all entries lower/upper case to ensure consistency.
checksum = CheckSum.crc64(record.seq)
nr_mapping.write("%s\t%s\t%s\n" % (record.id,
checksum,
locus2genome[record.id]))
if checksum not in hsh_checksum_list:
hsh_checksum_list[checksum] = [record]
record.id = checksum
record.name = ""
updated_records.append(record)
else:
# NOTE: having same hash does not mean that the sequences are identical: as
# the hash space is smaller than the sequence space, it means that collision
# are unavoidable (but not probable) and record with same hashes should be compared
# https://www.uniprot.org/help/uniparc (sequence comparison)
#
# the list of records having the same checksum, but potentially,
# different sequences -> compare them: python does so
# comparing the sequences as strings, assuming a similar alphabet
lst_records = hsh_checksum_list[checksum]
sequence = record.seq
has_identical = False
for prev_record in lst_records:
if prev_record.seq == sequence:
has_identical = True
break
if not has_identical:
lst_records.append(record)
record.id = checksum + "-" + len(lst_records)
record.name = ""
updated_records.append(record)
SeqIO.write(updated_records, nr_fasta, "fasta")
print IUPACData.ambiguous_dna_complement #dictionary of complements
#and a lot more
from Bio.Data import CodonTable
print CodonTable.generic_by_id[2]
#SeqUtils. Several functions to deal with DNA and protein sequences.
#DNA utils
import Bio.SeqUtils as SeqUtils
print SeqUtils.GC('gacgatcggtattcgtag') #GC content
from Bio.SeqUtils import MeltingTemp
print MeltingTemp.Tm_staluc('tgcagtacgtatcgt') #DNA/RNA melting temperature
#checksum functions: short alphanumeric string signature of a file or sequence
#usually written in description of sequence
#cgc is a easy, weak, very used checksum (better crc32, crc64)
from Bio.SeqUtils import CheckSum
myseq='acaagatgccattgtcccccggcctcctgctgctgct'
print CheckSum.gcg(myseq)
print CheckSum.crc32(myseq)
print CheckSum.crc64(myseq)
print CheckSum.seguid(myseq)
#Protein utils
from Bio.SeqUtils import ProtParam
myprot=ProtParam.ProteinAnalysis('MLTNK')
print myprot.count_amino_acids()
print myprot.get_amino_acids_percent()
print myprot.molecular_weight()
print myprot.aromaticity()
print myprot.instability_index()
print myprot.flexibility()
print myprot.isoelectric_point()
print myprot.secondary_structure_fraction()
