#!/usr/bin/env python3
from fasta import FASTAReader
import sys
target = FASTAReader(open(sys.argv[1]))
query = FASTAReader(open(sys.argv[2]))
k = int(sys.argv[3])
kmers = {}
for ident1, sequence1 in target:
sequence1 = sequence1.upper()
for i in range(0, len(sequence1) - k + 1):
kmer1 = sequence1[i:i + k]
if kmer1 in kmers:
kmers[kmer1].append((ident1, i))
else:
kmers[kmer1] = [(ident1, i)]
for ident2, sequence2 in query:
sequence2 = sequence2.upper()
for a in range(0, len(sequence2) - k + 1):
kmer2 = sequence2[a:a + k]
if kmer2 in kmers:
print(kmers[kmer2], str(a), kmer2)
#!/usr/bin/env python3
import sys
from fasta import FASTAReader
f = sys.stdin
reader = FASTAReader(f)
contigs = []
for indent, sequence in reader:
contigs.append(sequence)
contigs = sorted(contigs, reverse=True)
print(len(contigs))
sequence_length = []
for sequence in contigs:
sequence_length.append(len(sequence))
print(min(sequence_length))
print(max(sequence_length))
print(sum(sequence_length) / len(contigs))
print(sum(sequence_length) / 2)
sorted_length = sorted(sequence_length, reverse=True)
count = 0
for i, item in enumerate(sorted_length):
count += item
if count >= (sum(sequence_length) / 2):
break
#!/usr/bin/env python3
"""match extender"""
from fasta import FASTAReader
import sys
target = FASTAReader(open(sys.argv[1])) #subset.fa
query = FASTAReader(open(sys.argv[2])) #droYak2_seq.fa
k = int(sys.argv[3])
kmers_from_target = {}
target_sequence = {}
for ident, sequence in target:
sequence = sequence.upper()
target_sequence[ident] = sequence
for i in range(0, len(sequence) - k + 1):
kmer = sequence[i:i + k]
if kmer in kmers_from_target:
kmers_from_target[kmer].append((ident, i))
else:
kmers_from_target[kmer] = [(ident, i)]
elongated_seq = []
for ident, sequence1 in query:
sequence1 = sequence1.upper()
for i in range(0, len(sequence) - k + 1):
kmer = sequence1[i:i + k]
if kmer in kmers_from_target:
for ident, j in kmers_from_target[kmer]:
#!/usr/bin/env python3
import sys
from fasta import FASTAReader
import math
import matplotlib.pyplot as plt
import statistics as stats
reader = FASTAReader(open(sys.argv[1])) #translated.out
protein_seq = []
for ident, sequence1 in reader:
protein_seq.append(sequence1)
#print (protein_seq)
reader2 = FASTAReader(open(sys.argv[2])) #3_new_blast_output
nt_seq = []
for ident, sequence2 in reader2:
nt_seq.append(sequence2)
#print (nt_seq)
list1 = []
for sequence, protein in zip(nt_seq, protein_seq):
dna1 = ""
nt_pos = 0
for num, j in enumerate(protein):
# print(a)
if j == "-":
dna1 = dna1 + "---"
#!/usr/bin/env python3
import sys
from fasta import FASTAReader
import math
import matplotlib.pyplot as plt
import statistics as stats
reader = FASTAReader(open(sys.argv[1]))
reader2 = FASTAReader(open(sys.argv[2]))
my_prot_sequence = [] #protein
for ident, sequence in reader:
my_prot_sequence.append(sequence)
#print(my_sequence)
#quit()
my_sequence_nt = [] #nucleotide
for ident2, sequence2 in reader2:
my_sequence_nt.append(sequence2)
#print(my_sequence_nt)
newlist = []
#for m in my_sequence_nt:
#dna = my_sequence_nt[m]#you only need to do it in the query sequence
#store by sequence identity in dictionary
# for i in range(len(my_prot_sequence)):
#dna= str(dna)
for sequence, protein in zip(my_sequence_nt, my_prot_sequence):
gap_dna = ""
nucl_pos = 0
for num, a in enumerate(protein):
#!/usr/bin/env python3
"""
Commands: enter this argument:
./.py file subset.fa droYak2_seq.fa 11
script, target file, query file, and kmer number
"""
#use previously developed FASTAReader to make the work below easier.
from fasta import FASTAReader
import sys
#add our files
target = FASTAReader(open(sys.argv[1])) # this is target (subset.fa)
query = FASTAReader(open(sys.argv[2])) # this is query file
k = int(sys.argv[3]) # this is the length of kmer
#initialize dictionary that holds the kmer (sequence) as the key and a tuple that contains the name
target_dictionary = {}
#for loop to go through target file
for name_t, sequence_t in target:
for i in range(0, len(sequence_t) - k + 1):
#set kmer_t length and make letters IN CAPS
kmer_t = sequence_t[i:i + k].upper()
#since we are using a dictionary, add name_t and i into the values section and assign it to specific kmer_t
target_tuple = (name_t, i)
if kmer_t in target_dictionary:
target_dictionary[kmer_t].append(target_tuple)
else:
target_dictionary[kmer_t] = [target_tuple]
#!/usr/bin/env python3
"""
Usage: ./02_nt.py new_blast_output.fa aa_alignment.out week5_query.fa
"""
import sys
from fasta import FASTAReader
import numpy as np
import matplotlib.pyplot as plt
import math
dna_reader = FASTAReader(open(sys.argv[1]))
dna_sequence = []
blast_dnaid = []
for ident, sequence in dna_reader:
dna_sequence.append(sequence)
blast_dnaid.append(ident)
# dna = dna_sequence[0]
# print(len(dna))
protein_reader = FASTAReader(open(sys.argv[2]))
protein_sequence = []
for ident, sequence in protein_reader:
protein_sequence.append(sequence)
# print(len(protein_sequence))
l = len(protein_sequence)
aligned_dna = {}
Commands:
k The length of the seeds used to find exact matches
"""
# ______________________________________________________________________________
# This section is copied from the kmer_matcher. Finds all matches
import sys
from fasta import FASTAReader
k = int(sys.argv[3])
target_kmers = {}
for ident, sequence in FASTAReader(open(sys.argv[1])):
target_kmers[ident] = {}
sequence = sequence.upper()
for i in range(0, len(sequence) - k + 1):
kmer = sequence[i:i + k]
target_kmers[ident].setdefault(kmer, set())
target_kmers[ident][kmer].add(str(i))
query_file = open(sys.argv[2])
query_seq = ''
for line in query_file:
if line.startswith('>'):
continue
query_seq += line.strip()
query_kmers = {}
#!/usr/bin/env python3
import sys
from fasta import FASTAReader
import numpy as np
import matplotlib.pyplot as plt
f = open(sys.argv[1])
f2 = open(sys.argv[2])
reader = FASTAReader(f)
reader2 = FASTAReader(f2)
count = 0
protein_seq = {}
for ident, seq in reader:
count += 1
ident = count
protein_seq[ident] = seq
count2 = 0
nt_seq = {}
for ident, seq in reader2:
count2 += 1
ident = count2
nt_seq[ident] = seq
new_seq = {}
for ident in protein_seq:
pseq = protein_seq[ident]
nseq = nt_seq[ident]
#!/usr/bin/env python3
"""
Count all kmers in a FASTA file
"""
from fasta import FASTAReader
import sys
reader1 = FASTAReader( open(sys.argv[1]) ) #This is a function that returns an object AND was generated by us
k = int(sys.argv[2])
reader2 = FASTAReader( open(sys.argv[3]) )
#query to 1 k to 2 and target to 3
kmers = {}
for ident, sequence in reader1:
for i in range( 0, len(sequence) - k + 1 ):
kmer = sequence[i:i+k]
if kmer in kmers:
kmers[kmer].append((i, ident))
else:
kmers[kmer] = [(i, ident)]
extk = {}
for ident1, sequence1 in reader2:
for i in range( 0, len(sequence1) - k + 1 ):
kmerQ = sequence1[i:i+k]
if kmerQ in kmers:
print(i, kmerQ, kmers[kmerQ])
