blast

$ module load BLAST/2.15.0

# 对核酸序列构建索引
$ makeblastdb -in ref.fa -dbtype nucl -parse_seqids

# 对氨基酸序列构建索引
$ makeblastdb -in prot.fa -dbtype prot -parse_seqids

# 生成的索引文件
ref.fa
ref.fa.nhr
ref.fa.nin
ref.fa.nog
ref.fa.nsd
ref.fa.nsi
ref.fa.nsq

$ blastn -db ref.fa -outfmt 6 -num_threads 6 -evalue 0.001 -query query.fa -out blast_out

$ blastn -subject ref.fa -outfmt 6 -num_threads 6  -query query.fa -out blast_out

$ blastn -task blastn-short  -outfmt 6 -num_threads 6 -word_size 4 -gapopen 1 -gapextend 1  -db ref.fa -query query.fa -out blast_out

   alignment view options:
     0 = Pairwise,
     1 = Query-anchored showing identities,
     2 = Query-anchored no identities,
     3 = Flat query-anchored showing identities,
     4 = Flat query-anchored no identities,
     5 = BLAST XML,
     6 = Tabular,
     7 = Tabular with comment lines,
     8 = Seqalign (Text ASN.1),
     9 = Seqalign (Binary ASN.1),
    10 = Comma-separated values,
    11 = BLAST archive (ASN.1),
    12 = Seqalign (JSON),
    13 = Multiple-file BLAST JSON,
    14 = Multiple-file BLAST XML2,
    15 = Single-file BLAST JSON,
    16 = Single-file BLAST XML2,
    17 = Sequence Alignment/Map (SAM),
    18 = Organism Report

[00] Query id
[01] Subject id
[02] % identity
[03] alignment length
[04] mismatches
[05] gap openings
[06] q. start
[07] q. end
[08] s. start
[09] s. end
[10] e-value
[11] bit score

The supported format specifiers for options 6, 7 and 10 are:
        qseqid means Query Seq-id
           qgi means Query GI
          qacc means Query accession
       qaccver means Query accession.version
          qlen means Query sequence length
        sseqid means Subject Seq-id
     sallseqid means All subject Seq-id(s), separated by a ';'
           sgi means Subject GI
        sallgi means All subject GIs
          sacc means Subject accession
       saccver means Subject accession.version
       sallacc means All subject accessions
          slen means Subject sequence length
        qstart means Start of alignment in query
          qend means End of alignment in query
        sstart means Start of alignment in subject
          send means End of alignment in subject
          qseq means Aligned part of query sequence
          sseq means Aligned part of subject sequence
        evalue means Expect value
      bitscore means Bit score
         score means Raw score
        length means Alignment length
        pident means Percentage of identical matches
        nident means Number of identical matches
      mismatch means Number of mismatches
      positive means Number of positive-scoring matches
       gapopen means Number of gap openings
          gaps means Total number of gaps
          ppos means Percentage of positive-scoring matches
        frames means Query and subject frames separated by a '/'
        qframe means Query frame
        sframe means Subject frame
          btop means Blast traceback operations (BTOP)
        staxid means Subject Taxonomy ID
      ssciname means Subject Scientific Name
      scomname means Subject Common Name
    sblastname means Subject Blast Name
     sskingdom means Subject Super Kingdom
       staxids means unique Subject Taxonomy ID(s), separated by a ';'
             (in numerical order)
     sscinames means unique Subject Scientific Name(s), separated by a ';'
     scomnames means unique Subject Common Name(s), separated by a ';'
    sblastnames means unique Subject Blast Name(s), separated by a ';'
             (in alphabetical order)
    sskingdoms means unique Subject Super Kingdom(s), separated by a ';'
             (in alphabetical order) 
        stitle means Subject Title
    salltitles means All Subject Title(s), separated by a '<>'
       sstrand means Subject Strand
         qcovs means Query Coverage Per Subject
       qcovhsp means Query Coverage Per HSP
        qcovus means Query Coverage Per Unique Subject (blastn only)
   When not provided, the default value is:
   'qaccver saccver pident length mismatch gapopen qstart qend sstart send
   evalue bitscore', which is equivalent to the keyword 'std'
   The supported format specifier for option 17 is:
            SQ means Include Sequence Data
            SR means Subject as Reference Seq

from Bio.Blast import NCBIXML

# 读取 BLAST XML 文件
result_handle = open(blast_output)
blast_records = NCBIXML.parse(result_handle)

data = []
for blast_record in blast_records:
    for alignment in blast_record.alignments:
        for hsp in alignment.hsps:
            align_item = hsp.query + "\n" + hsp.match + "\n" + hsp.sbjct 
            row_data = {
                'col1': blast_record.query,
                'col2': alignment.hit_id,
                'col4': hsp.identities,
                'col5': hsp.align_length,
                'col6': hsp.query_start,
                'col7': hsp.query_end,
                'col8': hsp.sbjct_start,
                'col9': hsp.sbjct_end,
                'col10': align_item
            }
            data.append(row_data)