def MakeGeneraFastas(fin_taxonomy,fin_repset):
global repsetdic,taxdic,taxgendic,repsetIDlist,repgenlist,generaSeqIDdic
fin_repset = open(fin_repset,"U")
fin_taxonomy = open(fin_taxonomy,"U")
repsetdic = {}
for label, seq in parse_fasta(fin_repset,ignore_comment=True):
repsetdic[label] = seq
taxdic = {}
taxgendic = {}
for line in fin_taxonomy:
line = line.split("\t")
accessionID = line[0]
taxonomyline = line[1]
genus = taxonomyline.split(";")
genus = genus[-2]
if genus[0:3] == "g__":
genus = genus[3:]
taxgendic[accessionID] = genus
taxdic[accessionID] = taxonomyline
fin_taxonomy.close()
fin_repset.close()
repsetIDlist = []
repsetIDlist = repsetdic.keys()
repgenlist = []
for i in repsetIDlist:
genus = taxgendic[i]
if genus not in repgenlist:
repgenlist.append(genus)
generaSeqIDdic = {}
for m in repgenlist:
IDnumlist = []
generaSeqIDdic[m] = IDnumlist
for key in taxgendic:
if key in repsetIDlist:
try:
g = taxgendic[key]
generaSeqIDdic[g].append(key)
except:
continue
from skbio.sequence import BiologicalSequence
for genus in generaSeqIDdic:
fout = open("g__"+genus+"_seqs.fasta","w")
seqlist = []
seqlist = generaSeqIDdic[genus]
for i in seqlist:
seq = repsetdic[i]
t = BiologicalSequence(seq,id=i)
line = (t.to_fasta(terminal_character=""))
fout.write(line)
fout.write("\n")
fout.close()
cwd = os.getcwd()
for file in os.listdir(cwd):
if os.path.getsize(file) < 1:
os.remove(file)
return repsetdic,taxdic,taxgendic,repsetIDlist,repgenlist,generaSeqIDdic
def make_genera_fastas(fin_taxonomy, fin_repset):
"""Takes ITS fasta file representative sequences and sorts the
OTUs/species into their corresponding genus file. This allows
OTUs to be compared to other OTUs from the same genus.
Parameters
----------
repsetdic : dict
A dictionary containing the label (key)
and sequence (value) from ITS representative sequences file.
repgenlist : list
A list that contains all unique genera from ITS fasta file.
taxgendic: dict
A dictionary containing accession ID (key) and genus only
from the Unite taxonomy file. ***** not used currently
repsetIDlist : list
A list that contains all of the IDs from the representative ITS
sequences.
Returns
----------
Examples
----------
Input is a representative sequence fasta file where each sequence
corresponds to one representative for all of the OTUs in each
cluster. Each sequence has an accession ID that corresponds to
one sequence in the Unite database.
Example of one representative fasta sequence from the input
fasta file:
>>AB015922 Some_comment_ie_sample_location
CAGAGCCAAGAGATCCGTTGTTGAAAGTTTTTTCAATTCAAGAATAAAACTTAGACTGCAAAG
ACAACATGAGTTTGGTTTGGGTCTTTGGCGGACACGCTCCAGCCGAAGCCGGTGGGCGGCCGA
CGCCAGTCCTCACGAACAGCGCCGACGTAGCCCGGCCCGCCAAAGCAACAAGATATAAATCGA
CACGGGTGGGAGGGTCGACCCAGCACGC
Example of a taxonomy line:
AY880934 k__Fungi;p__Basidiomycota;c__Agaricomycetes;
o__Thelephorales;f__Thelephoraceae;g__Thelephora;
s__Thelephora_terrestris
This code identifies the genus of all OTUs by looking at the
accession number from the fasta sequence, then looking at the
Unite taxonomy file and identifying the genus the sequence
belongs to. The OTUs then get sorted into genus files that
have one or more OTUs/species per file.
"""
global repgenlist
fin_repset = open(fin_repset, "U")
fin_taxonomy = open(fin_taxonomy, "U")
repsetdic = {}
for label, seq in parse_fasta(fin_repset, ignore_comment=True):
repsetdic[label] = seq
taxgendic = {}
for line in fin_taxonomy:
line = line.split("\t")
accessionID = line[0]
taxonomyline = line[1]
genus = taxonomyline.split(";")
genus = genus[-2]
if genus.startswith("g__"):
genus = genus[3:]
taxgendic[accessionID] = genus
fin_taxonomy.close()
fin_repset.close()
repsetIDlist = []
repsetIDlist = repsetdic.keys()
repgenlist = []
for i in repsetIDlist:
genus = taxgendic[i]
if genus not in repgenlist:
repgenlist.append(genus)
generaSeqIDdic = {}
for m in repgenlist:
IDnumlist = []
generaSeqIDdic[m] = IDnumlist
for key in taxgendic:
if key in repsetIDlist:
try:
g = taxgendic[key]
generaSeqIDdic[g].append(key)
except:
continue
from skbio.sequence import BiologicalSequence
for genus in generaSeqIDdic:
fout = open("g__" + genus + "_seqs.fasta", "w")
seqlist = []
seqlist = generaSeqIDdic[genus]
for i in seqlist:
seq = repsetdic[i]
t = BiologicalSequence(seq, id=i)
line = (t.to_fasta(terminal_character=""))
fout.write(line)
fout.write("\n")
fout.close()
for file in os.listdir(cwd):
if os.path.getsize(file) < 1:
os.remove(file)
return repgenlist
def make_genera_fastas(fin_taxonomy,fin_repset):
"""Takes ITS fasta file representative sequences and sorts the
OTUs/species into their corresponding genus file. This allows
OTUs to be compared to other OTUs from the same genus.
Parameters
----------
repsetdic : dict
A dictionary containing the label (key)
and sequence (value) from ITS representative sequences file.
repgenlist : list
A list that contains all unique genera from ITS fasta file.
taxgendic: dict
A dictionary containing accession ID (key) and genus only
from the Unite taxonomy file. ***** not used currently
repsetIDlist : list
A list that contains all of the IDs from the representative ITS
sequences.
Returns
----------
Examples
----------
Input is a representative sequence fasta file where each sequence
corresponds to one representative for all of the OTUs in each
cluster. Each sequence has an accession ID that corresponds to
one sequence in the Unite database.
Example of one representative fasta sequence from the input
fasta file:
>>AB015922 Some_comment_ie_sample_location
CAGAGCCAAGAGATCCGTTGTTGAAAGTTTTTTCAATTCAAGAATAAAACTTAGACTGCAAAG
ACAACATGAGTTTGGTTTGGGTCTTTGGCGGACACGCTCCAGCCGAAGCCGGTGGGCGGCCGA
CGCCAGTCCTCACGAACAGCGCCGACGTAGCCCGGCCCGCCAAAGCAACAAGATATAAATCGA
CACGGGTGGGAGGGTCGACCCAGCACGC
Example of a taxonomy line:
AY880934 k__Fungi;p__Basidiomycota;c__Agaricomycetes;
o__Thelephorales;f__Thelephoraceae;g__Thelephora;
s__Thelephora_terrestris
This code identifies the genus of all OTUs by looking at the
accession number from the fasta sequence, then looking at the
Unite taxonomy file and identifying the genus the sequence
belongs to. The OTUs then get sorted into genus files that
have one or more OTUs/species per file.
"""
global repgenlist
fin_repset = open(fin_repset,"U")
fin_taxonomy = open(fin_taxonomy,"U")
repsetdic = {}
for label, seq in parse_fasta(fin_repset,ignore_comment=True):
repsetdic[label] = seq
taxgendic = {}
for line in fin_taxonomy:
line = line.split("\t")
accessionID = line[0]
taxonomyline = line[1]
genus = taxonomyline.split(";")
genus = genus[-2]
if genus.startswith("g__"):
genus = genus[3:]
taxgendic[accessionID] = genus
fin_taxonomy.close()
fin_repset.close()
repsetIDlist = []
repsetIDlist = repsetdic.keys()
repgenlist = []
for i in repsetIDlist:
genus = taxgendic[i]
if genus not in repgenlist:
repgenlist.append(genus)
generaSeqIDdic = {}
for m in repgenlist:
IDnumlist = []
generaSeqIDdic[m] = IDnumlist
for key in taxgendic:
if key in repsetIDlist:
try:
g = taxgendic[key]
generaSeqIDdic[g].append(key)
except:
continue
from skbio.sequence import BiologicalSequence
for genus in generaSeqIDdic:
fout = open("g__"+genus+"_seqs.fasta","w")
seqlist = []
seqlist = generaSeqIDdic[genus]
for i in seqlist:
seq = repsetdic[i]
t = BiologicalSequence(seq,id=i)
line = (t.to_fasta(terminal_character=""))
fout.write(line)
fout.write("\n")
fout.close()
for file in os.listdir(cwd):
if os.path.getsize(file) < 1:
os.remove(file)
return repgenlist
