Outputing a Blast result that includes global pairwise alignment

Question

[Nano]

I have made a Local Blast of one query file (containing thousands of sequences) against many individual database formatted files (each containing thousands of sequences). The result is good. Script below

#!/bin/bash
for file in *.fasta
do
  pb tblastn -query queryFile.fasta -dbnuc $file -out $file\.table -evalue 0.00001 -outfmt 6
done

The results in each file look like this:

BGIBMGA000034   c9147_g1_i1     33.95   162     97      2       42      193     120     605     1e-22   93.2
BGIBMGA000034   c13162_g1_i2    51.35   74      36      0       42      115     300     79      4e-20   84.0
BGIBMGA000034   c15905_g1_i1    36.00   125     79      1       44      167     493     119     4e-19   82.0
BGIBMGA000034   c15528_g1_i1    29.70   165     104     1       42      194     241     735     1e-15   75.1
BGIBMGA000034   c13162_g1_i3    42.65   68      39      0       129     196     2104    1901    2e-08   52.8
BGIBMGA000060   c15177_g1_i1    44.85   689     269     10      51      715     1423    3228    2e-177  561
BGIBMGA000060   c15177_g1_i1    37.74   106     61      1       286     386     1369    1686    2e-12   70.9
BGIBMGA000060   c15177_g1_i3    44.70   689     266     11      55      715     1435    3240    8e-176  556
BGIBMGA000060   c15177_g1_i3    37.74   106     61      1       286     386     1369    1686    2e-12   71.2
BGIBMGA000060   c15177_g1_i2    55.99   384     160     2       341     715     502     1653    3e-136  440
BGIBMGA000060   c15821_g1_i2    30.14   282     174     8       454     714     1955    2794    8e-24   108

The first columns are query IDs while the second column are matched IDs from database files, the values are normal Blast values.

Question: How can I get the code to also output the full sequence (including the header >xxx|yyy) of the matching database sequence as part of the result.

For example (output):

BGIBMGA000034   c9147_g1_i1     33.95   162     97      2       42      193     120     605     1e-22   93.2
>c9147_g1_i1
AGAGGACCATTGCACCGGGAAATTCCTCCCAATTGGGGTTCCAAAGGGGCCCCTTAAGGGAAGGAAGGTTTCCRCCGGCCTTTTTTCCCTTGGGGAAAGGGGTTTCCCCCAAGGTTCCAACCAATTGGGGGCCTTCTTTAAGGG........

Thanks

[Jenez]

You can't.

You need to run blastdbcmd to retrieve your sequences. Write the id's and the corresponding start and stop positions to a file and send that file as a query to blastdbcmd.

If I'm not mistaken I think the format of the query should be:

Accession_id_1 50 410

Accession_id_2 113 460