Bioinformatics/Sequence mutation: Difference between revisions
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=={{header|Nim}}==
<lang Nim>import random
import strformat
import strutils
type
# Enumeration type for bases.
Base {.pure.} = enum A, C, G, T, Other = "other"
# Sequence of bases.
DnaSequence = seq[Base]
# Kind of mutation.
Mutation = enum mutSwap, mutDelete, mutInsert
#---------------------------------------------------------------------------------------------------
proc newDnaSeq(length: Natural): DnaSequence =
## Create a DNA sequence of given length.
result = newSeqOfCap[Base](length)
for _ in 1..length:
result.add(Base(rand(3)))
#---------------------------------------------------------------------------------------------------
proc mutate(dnaSeq: var DnaSequence) =
## Mutate a sequence (it is changed in place).
# Choose randomly the position of mutation.
let idx = rand(dnaSeq.high)
# Choose randomly the kind of mutation.
let mut = Mutation(rand(ord(Mutation.high)))
# Apply the mutation.
case mut
of mutSwap:
let newBase = Base(rand(ord(Base.Other) - 1))
echo fmt"Changing base at position {idx + 1} from {dnaSeq[idx]} to {newBase}"
dnaSeq[idx] = newBase
of mutDelete:
echo fmt"Deleting base {dnaSeq[idx]} at position {idx + 1}"
dnaSeq.delete(idx)
of mutInsert:
let newBase = Base(rand(ord(Base.Other) - 1))
echo fmt"Inserting base {newBase} at position {idx + 1}"
dnaSeq.insert(newBase, idx)
#---------------------------------------------------------------------------------------------------
proc display(dnaSeq: DnaSequence) =
## Display a DNA sequence using EMBL format.
var counts: array[Base, Natural] # Count of bases.
for base in dnaSeq:
inc counts[base]
# Display the SQ line.
var sqline = fmt"SQ {dnaSeq.len} BP; "
for (base, count) in counts.pairs:
sqline &= fmt"{count} {base}; "
echo sqline
# Display the sequence.
var idx = 0
var row = newStringOfCap(80)
var remaining = dnaSeq.len
while remaining > 0:
row.setLen(0)
row.add(" ")
# Add groups of 10 bases.
for group in 1..6:
let nextIdx = idx + min(10, remaining)
for i in idx..<nextIdx:
row.add($dnaSeq[i])
row.add(' ')
dec remaining, nextIdx - idx
idx = nextIdx
if remaining == 0:
break
# Append the number of the last base in the row.
row.add(spaces(72 - row.len))
row.add(fmt"{idx:>8}")
echo row
# Add termination.
echo "//"
#———————————————————————————————————————————————————————————————————————————————————————————————————
randomize()
var dnaSeq = newDnaSeq(200)
echo "Initial sequence"
echo "———————————————\n"
dnaSeq.display()
echo "\nMutations"
echo "—————————\n"
for _ in 1..10:
dnaSeq.mutate()
echo "\nMutated sequence"
echo "————————————————\n"
dnaSeq.display()</lang>
{{out}}
<pre>Initial sequence
———————————————
SQ 200 BP; 53 A; 52 C; 45 G; 50 T; 0 other;
ATGGATAGAA TGGCACCTCA GTGTCACATG TCCTAGGCAC ATTCTACGTA CTAGTTTCTG 60
GAGGTCGATA AATACAAGAT GGAATACTCT TATCAACCGC TAGCAATGAA ACTTAGATAG 120
CCACCCCTCG ATCGCGGTTC GCTATGCGGC ATCGTCAACT GCGTCAAAGC ACTACGTCGT 180
TTCGTGACTG CCAGTCGAGC 200
//
Mutations
—————————
Inserting base A at position 121
Changing base at position 101 from T to G
Deleting base A at position 115
Changing base at position 126 from C to G
Deleting base T at position 155
Deleting base G at position 198
Deleting base T at position 159
Changing base at position 144 from A to T
Inserting base C at position 34
Changing base at position 127 from G to G
Mutated sequence
————————————————
SQ 198 BP; 52 A; 52 C; 46 G; 48 T; 0 other;
ATGGATAGAA TGGCACCTCA GTGTCACATG TCCCTAGGCA CATTCTACGT ACTAGTTTCT 60
GGAGGTCGAT AAATACAAGA TGGAATACTC TTATCAACCG CGAGCAATGA AACTTGATAG 120
ACCACCGCTC GATCGCGGTT CGCTTTGCGG CATCGCAACG CGTCAAAGCA CTACGTCGTT 180
TCGTGACTGC CAGTCGAC 198
//</pre>
=={{header|Perl}}==
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