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Add support for newer Biopython #48

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54 changes: 43 additions & 11 deletions mgefinder/fastatools.py
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Original file line number Diff line number Diff line change
Expand Up @@ -3,7 +3,10 @@
from Bio import SeqIO
from Bio.Seq import Seq
from Bio.SeqRecord import SeqRecord
from Bio.Alphabet import IUPAC
try:
from Bio.Alphabet import IUPAC
except ImportError:
IUPAC = None
from mgefinder.misc import revcomp


Expand All @@ -14,8 +17,13 @@ def write_sequences_to_fasta(sequences, fasta, names=None):
name = names[i]
else:
name = i
record = SeqRecord(Seq(sequences[i], IUPAC.IUPACAmbiguousDNA),

if IUPAC:
record = SeqRecord(Seq(sequences[i], IUPAC.IUPACAmbiguousDNA),
id=str(name), description=str(name))
else:
record = SeqRecord(Seq(sequences[i]), annotations={"molecule_type": "DNA"},
id=str(name), description=str(name))
outseqs.append(record)
with open(fasta, 'w') as output_handle:
SeqIO.write(outseqs, output_handle, 'fasta')
Expand All @@ -33,9 +41,15 @@ def write_termini_to_fasta(termini, fasta):
seq5p = row['seq_5p']
seq3p = row['seq_3p']

record5p = SeqRecord(Seq(seq5p, IUPAC.IUPACAmbiguousDNA),
if IUPAC:
record5p = SeqRecord(Seq(seq5p, IUPAC.IUPACAmbiguousDNA),
id=str(name5p), description=str(name5p))
record3p = SeqRecord(Seq(seq3p, IUPAC.IUPACAmbiguousDNA),
id=str(name3p), description=str(name3p))
else:
record5p = SeqRecord(Seq(seq5p), annotations={"molecule_type": "DNA"},
id=str(name5p), description=str(name5p))
record3p = SeqRecord(Seq(seq3p, IUPAC.IUPACAmbiguousDNA),
record3p = SeqRecord(Seq(seq3p), annotations={"molecule_type": "DNA"},
id=str(name3p), description=str(name3p))

outseqs.append(record5p)
Expand All @@ -54,9 +68,15 @@ def write_termini_to_paired_fasta(pairs, fasta_prefix):
seq5p = p['seq_5p']
seq3p = p['seq_3p']

record5p = SeqRecord(Seq(seq5p, IUPAC.IUPACAmbiguousDNA),
if IUPAC:
record5p = SeqRecord(Seq(seq5p, IUPAC.IUPACAmbiguousDNA),
id=str(name5p), description=str(name5p)+'_5p')
record3p = SeqRecord(Seq(revcomp(seq3p), IUPAC.IUPACAmbiguousDNA),
id=str(name3p), description=str(name3p)+'_3p')
else:
record5p = SeqRecord(Seq(seq5p), annotations={"molecule_type": "DNA"},
id=str(name5p), description=str(name5p)+'_5p')
record3p = SeqRecord(Seq(revcomp(seq3p), IUPAC.IUPACAmbiguousDNA),
record3p = SeqRecord(Seq(revcomp(seq3p)), annotations={"molecule_type": "DNA"},
id=str(name3p), description=str(name3p)+'_3p')

fiveprime_outseqs.append(record5p)
Expand All @@ -78,9 +98,15 @@ def write_termini_to_unpaired_fasta(pairs, fasta_prefix):
seq5p = p['seq_5p']
seq3p = p['seq_3p']

record5p = SeqRecord(Seq(seq5p, IUPAC.IUPACAmbiguousDNA),
if IUPAC:
record5p = SeqRecord(Seq(seq5p, IUPAC.IUPACAmbiguousDNA),
id=str(name5p), description=str(name5p)+'_5p')
record3p = SeqRecord(Seq(revcomp(seq3p), IUPAC.IUPACAmbiguousDNA),
record3p = SeqRecord(Seq(revcomp(seq3p), IUPAC.IUPACAmbiguousDNA),
id=str(name3p), description=str(name3p)+'_3p')
else:
record5p = SeqRecord(Seq(seq5p), annotations={"molecule_type": "DNA"},
id=str(name5p), description=str(name5p)+'_5p')
record3p = SeqRecord(Seq(revcomp(seq3p)), annotations={"molecule_type": "DNA"},
id=str(name3p), description=str(name3p)+'_3p')

fiveprime_outseqs.append(record5p)
Expand All @@ -101,13 +127,19 @@ def write_panisa_termini_to_fasta(termini, fasta):
seq5p = row['Left sequence']
seq3p = row['Right sequence']

record5p = SeqRecord(Seq(seq5p, IUPAC.IUPACAmbiguousDNA),
if IUPAC:
record5p = SeqRecord(Seq(seq5p, IUPAC.IUPACAmbiguousDNA),
id=str(name5p), description=str(name5p))
record3p = SeqRecord(Seq(seq3p, IUPAC.IUPACAmbiguousDNA),
record3p = SeqRecord(Seq(seq3p, IUPAC.IUPACAmbiguousDNA),
id=str(name3p), description=str(name3p))
else:
record5p = SeqRecord(Seq(seq5p), annotations={"molecule_type": "DNA"},
id=str(name5p), description=str(name5p))
record3p = SeqRecord(Seq(seq3p), annotations={"molecule_type": "DNA"},
id=str(name3p), description=str(name3p))

outseqs.append(record5p)
outseqs.append(record3p)

with open(fasta, 'w') as output_handle:
SeqIO.write(outseqs, output_handle, 'fasta')
SeqIO.write(outseqs, output_handle, 'fasta')