#Script to combine exon and intron alignments for a gene and generate a RAxML partition file.

# Seth's edit: specify all three codon positions as separate partitions (as recommended by PartitionFinder)

# also: write to 'exons_only.fasta/partition' if no intron file exists

import sys,os

from Bio import SeqIO

from Bio.Seq import Seq

from Bio.SeqRecord import SeqRecord

if len(sys.argv) < 4:

print("Usage: python combine_alignments.py exon.fasta intron.fasta[or any value if no intron] geneName")

sys.exit(1)

exon_fn = sys.argv[1]

intron_fn = sys.argv[2]

geneName = sys.argv[3]

exon_dict = SeqIO.to_dict(SeqIO.parse(exon_fn,'fasta'))

exonLength = len(next(exon_dict.itervalues()))

if os.path.isfile(intron_fn):

with open("{}.combined.fasta".format(geneName),'w') as outfile:

for seq in SeqIO.parse(intron_fn,'fasta'):

intronLength = len(seq)

sampleID = seq.id.split("-")[0]

newseq = exon_dict[sampleID].seq + seq.seq

outfile.write(">{}\n{}\n".format(sampleID,newseq))

partition = """DNA, codon1 = 1-{}\\3

DNA, codon2 = 2-{}\\3

DNA, codon3 = 3-{}\\3

DNA, intron = {}-{}

""".format(exonLength, exonLength, exonLength, exonLength+1,exonLength+intronLength)

with open("{}.combined.partition".format(geneName),'w') as partitionfile:

partitionfile.write(partition)

else:

with open("{}.exon_only.fasta".format(geneName),'w') as outfile:

for sampleID in exon_dict:

newseq = exon_dict[sampleID].seq

outfile.write(">{}\n{}\n".format(sampleID,newseq))

partition = """DNA, codon1 = 1-{}\\3

DNA, codon2 = 2-{}\\3

DNA, codon3 = 3-{}\\3

""".format(exonLength, exonLength, exonLength)

with open("{}.exon_only.partition".format(geneName),'w') as partitionfile:

partitionfile.write(partition)