多重比对格式

from Bio import AlignIO

for multiple_alignment in AlignIO.parse("chr10.maf", "maf"):
    print("printing a new multiple alignment")

    for seqrec in multiple_alignment:
        print(
            "starts at %s on the %s strand of a sequence %s in length, and runs for %s bp"
            % (
                seqrec.annotations["start"],
                seqrec.annotations["strand"],
                seqrec.annotations["srcSize"],
                seqrec.annotations["size"],
            )
        )

# index mouse chr10 from UCSC and store it in a file for later use

from Bio.AlignIO import MafIO

# idx = MafIO.MafIndex(sqlite_file, maf_file, target_seqname)
idx = MafIO.MafIndex("chr10.mafindex", "chr10.maf", "mm9.chr10")

# count the number of bases in danRer5 (Zebrafish) that align to the
# Pcmt1 locus in mouse

from Bio.AlignIO.MafIO import MafIndex

idx = MafIndex("chr10.mafindex", "chr10.maf", "mm9.chr10")
results = idx.search([7350034], [7383048])

total_bases = 0

for multiple_alignment in results:
    for seqrec in multiple_alignment:
        if seqrec.id.startswith("danRer5"):
            # don't count gaps as bases
            total_bases += len(str(seqrec.seq).replace("-", ""))

print("a total of %s bases align" % total_bases)

# convert the alignment for mouse Foxo3 (NM_019740) from MAF to FASTA

from Bio import AlignIO

idx = AlignIO.MafIO.MafIndex("chr10.mafindex", "chr10.maf", "mm9.chr10")

multiple_alignment = idx.get_spliced(
    [41905591, 41916271, 41994621, 41996331],
    [41906101, 41917707, 41995347, 41996548],
    strand="+",
)

AlignIO.write(multiple_alignment, "mm9_foxo3.fa", "fasta")

# find every gene on chr10 in the current UCSC refGene database,
# retrieve its spliced multiple alignment, and write it to
# a FASTA file in the current directory
#
# depends: MySQLdb

import MySQLdb
from Bio import AlignIO

# connect to UCSC's live MySQL database
mysql_conn = MySQLdb.connect(
    host="genome-mysql.cse.ucsc.edu", user="genome", passwd="", db="mm9"
)

db_conn = mysql_conn.cursor(MySQLdb.cursors.DictCursor)

# load MAF index
idx = AlignIO.MafIO.MafIndex("chr10.mafindex", "chr10.maf", "mm9.chr10")

# fetch all records on chr10
db_conn.execute("SELECT * FROM refGene WHERE chrom = 'chr10'")

for record in db_conn.fetchall():
    multiple_alignment = idx.get_spliced(
        map(int, record["exonStarts"].split(",")[:-1]),
        map(int, record["exonEnds"].split(",")[:-1]),
        strand=record["strand"],
    )

    print("writing %s.fa" % record["name"])

    AlignIO.write(multiple_alignment, "%s.fa" % record["name"], "fasta")