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python_one_week_4_biologists_solutions
Commits
6fd6a91f
Commit
6fd6a91f
authored
Mar 19, 2019
by
Blaise Li
Browse files
Adding an example of usage of SeqIO.
parent
ad4915a7
Pipeline
#10532
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in 22 seconds
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source/_static/code/seq_io.py
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6fd6a91f
#!/usr/bin/env python3
"""Example of use of SeqIO from biopython
Here, we parse a fasta file, put the records in a list, search for a motif in
the sequence of the first record, and create a subsequence around this motif.
"""
from
Bio
import
SeqIO
records
=
list
(
SeqIO
.
parse
(
fasta_filename
,
"fasta"
))
records
# [SeqRecord(seq=Seq('GCCTCGGCCTCTGCATAAATAAAAAAAATTAGTCAGCCATGGGGCGGAGAATGG...GCG', SingleLetterAlphabet()), id='gi|965480|gb|J02400.1|SV4CG', name='gi|965480|gb|J02400.1|SV4CG', description='gi|965480|gb|J02400.1|SV4CG Simian virus 40 complete genome', dbxrefs=[])]
sequence
=
records
[
0
].
seq
sequence
# Seq('GCCTCGGCCTCTGCATAAATAAAAAAAATTAGTCAGCCATGGGGCGGAGAATGG...GCG', SingleLetterAlphabet())
motif
=
"TAAAT"
sequence
.
find
(
motif
)
# 15
motif_pos
=
sequence
.
find
(
motif
)
subseq_start
=
motif_pos
-
10
subseq_end
=
motif_pos
+
len
(
motif
)
+
11
subseq
=
sequence
[
subseq_start
:
subseq_end
]
subseq
# Seq('GGCCTCTGCATAAATAAAAAAAATTA', SingleLetterAlphabet())
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