for taxa in taxalist:
taxainfo = {}
taxainfo['novel'] = record
taxainfo['taxa'] = taxa
taxainfo['taxid'] = ncbi.get_taxid(taxa)
taxainfo['blast_record'] = get_BLAST(taxainfo['taxid'], qseqid)
try:
taxainfo['sbjctseq'] = taxainfo['blast_record'].alignments[0].hsps[0].sbjct[:50]
print(taxainfo['sbjctseq'])
try:
taxainfo['GI'] = int(taxainfo['blast_record'].alignments[0].title.split('|')[1])
print("GI is: " + str(taxainfo['GI']))
except:
print("GI not valid for " + taxa + " : " + taxainfo['blast_record'].alignments[0].title.split('|')[1])
try:
taxainfo['seqdef'] = ncbi.get_gene_data(taxainfo['GI'])[0]['GBSeq_definition']
print('GBSeq_definition is ' + taxainfo['seqdef'])
except:
print("Unable to get GBSeq_definition")
try:
taxainfo['lineage'] = ncbi.get_lineage(taxainfo['taxid'])
except:
print("Unable to get Lineage")
try:
taxainfo['sequence'] = ncbi.get_gene_seq(taxainfo['GI'])
except:
print("unable to get sequence")
except:
print("No match found for " + taxa)
taxarecords.append(taxainfo)
handle = open('temp/' + record + '.pickle', 'w')
GROUP BY qseqid, genus
ORDER BY i.taxid, pident, coverage""")
#GROUP BY qseqid, i.taxid
results = dbconnection.cursor()
results.execute(query, (novelseq1, novelseq2, novelseq1, novelseq2))
results = list(results)
# get homolog data
homologs = ()
for homolog in results:
taxid = homolog[1]
sgi = homolog[4]
print(taxid)
lineage = ncbi.get_lineage(taxid)
sequence = ncbi.get_gene_seq(sgi)
seqdef = ncbi.get_gene_data(sgi)[0]['GBSeq_definition']
homologs = homologs + (homolog + (seqdef, lineage, sequence),)
# Build a fasta file from homolog seq
homologsRec1=[]
homologsRec2=[]
# Add novel sequences
handle = open("notes/transcriptome/BothNyAd.fa", "rU")
record_dict = SeqIO.to_dict(SeqIO.parse(handle, "fasta"))
handle.close()
sid = 'Diaphorina citri'
name = 'Diaphorina citri'
# Rename the novel sequence
record_dict[novelseq2].name = name
record_dict[novelseq2].id = sid
record_dict[novelseq1].description = novelseq1
record_dict[novelseq2].description = novelseq2
homologs = ()
for ataxa in list(alltaxa)[:4]:
print("lookup " + ataxa)
taxid = ncbi.get_taxid(ataxa)
print(ataxa + " tax id is " + str(taxid))
qseq1 = str(record_dict[novelseq2].seq)
blast_record = get_BLAST(taxid, qseq1)
try:
sbjctseq1 = blast_record.alignments[0].hsps[0].sbjct[:50]
sgi1 = blast_record.alignments[0].title.split('|')[1]
print("1", sbjctseq1)
seqdef1 = ncbi.get_gene_data(sgi1)[0]['GBSeq_definition']
lineage1 = ncbi.get_lineage(taxid)
sequence1 = ncbi.get_gene_seq(sgi1)
except:
print("No match")
sgi1 = 0
qseq2 = str(record_dict[novelseq1].seq)
blast_record = get_BLAST(taxid, qseq2)
try:
sbjctseq2 = blast_record.alignments[0].hsps[0].sbjct[:50]
sgi2 = blast_record.alignments[0].title.split('|')[1]
print("2", sbjctseq2)
seqdef2 = ncbi.get_gene_data(sgi2)[0]['GBSeq_definition']
lineage2 = ncbi.get_lineage(taxid)
