about Blastx generated file

Question

[Kurban]

Hello,

I used blastx blasted my query file with a protein db file.

My query sequences more than 140000, so I just want to see aligned query sequences. but the result gives all the query , and their blast result as: aligned... or no hit was found , respectively. that makes selection of aligned query sequences from the blastx result file a tremendous work. so if I can only extract the aligned query sequences and their alignment information (e- value, score and aligned sequence) would simplify my job a lot.

This is the blastx out file:

Query= comp936_c0_seq10 len=156 path=[335:0-24 360:25-155]

Length=156

***** No hits found *****

Lambda      K        H        a         alpha
   0.318    0.134    0.401    0.792     4.96

Gapped
Lambda      K        H        a         alpha    sigma
   0.267   0.0410    0.140     1.90     42.6     43.6

Effective search space used: 21583458

Query= comp1863_c0_seq1 len=2184 path=[0:0-1278 1279:1279-1279
1280:1280-1303 1304:1304-2183]

Length=2184
                                                                      Score     E
Sequences producing significant alignments:                          (Bits)  Value

  FBpp0075807 FBgn0000404 symbol:CycA family:Transcription Cofact...   287    8e-89

> FBpp0075807 FBgn0000404 symbol:CycA family:Transcription Cofactors
species:Drosophila melanogaster
Length=491

 Score =  287 bits (735),  Expect = 8e-89, Method: Compositional matrix adjust.
Identities = 184/468 (39%), Positives = 261/468 (56%), Gaps = 50/468 (11%)
Frame = -3

Query  1810  MATINIHPDQENRV-PELRqkqannamaaqqKRTGLGLIDHN----KANKAVPKGKQ--P  1652
             MA+  IH D  N+  P ++               G G  + N    +AN AV  G    P
Sbjct  1     MASFQIHQDMSNKENPGIKIPAGVKNTKQPLAVIG-GKAEKNALAPRANFAVLNGNNNVP  59

Query  1651  LKESNLSNAR-VENIHVKEN------RKNVVVPVAQFEAFTVYED--DEQRARIDQKL-R  1502
                  +   R V N++V EN      + NVV  V QF+ F+VYED  D Q A   + L 
Sbjct  60    RPAGKVQVFRDVRNLNVDENVEYGAKKSNVVPVVEQFKTFSVYEDNNDTQVAPSGKSLAS  119

Query  1501  LISKSN--VYKGTAEDRFITKTELAEIERkkqlqklKELAEIPAVIEPKCENDPCTPMSI  1328
             L+ K N  V  G  +                     KEL +      P    D  +PMS+
Sbjct  120   LVDKENHDVKFGAGQ---------------------KELVDYDLDSTPMSVTDVQSPMSV  158

Query  1327  EK-LNDENAENDSSQLAEEVIRKNSNVKDL--------FFEMEEYRDDIYAYLREHELRH  1175
             ++ +      +D S   E  +     VK+L        F E+ +Y+ DI  Y RE E +H
Sbjct  159   DRSILGVIQSSDISVGTETGVSPTGRVKELPPRNDRQRFLEVVQYQMDILEYFRESEKKH  218

Query  1174  RPKPGYIVKQPDVTENMRAVLVDWLVEVTEEYKMQTETLYLAVNFIDRFLSYMSVVRAKL  995
             RPKP Y+ +Q D++ NMR++L+DWLVEV+EEYK+ TETLYL+V ++DRFLS M+VVR+KL
Sbjct  219   RPKPLYMRRQKDISHNMRSILIDWLVEVSEEYKLDTETLYLSVFYLDRFLSQMAVVRSKL  278

Query  994   QLVGTAAMFIASKYEEIFPPDVSEFVYITDDTYDKHQVIRMEHLILRVLGFDLSVPTPLT  815
             QLVGTAAM+IA+KYEEI+PP+V EFV++TDD+Y K QV+RME +IL++L FDL  PT  
Sbjct  279   QLVGTAAMYIAAKYEEIYPPEVGEFVFLTDDSYTKAQVLRMEQVILKILSFDLCTPTAYV  338

Query  814   FINATCISAGLTEKTMYLAMYLSEIALLEVEPYLQFLPSVIASSAIALARHTLGEEAWND  635
             FIN   +   + EK  Y+ +Y+SE++L+E E YLQ+LPS+++S+++ALARH LG E W 
Sbjct  339   FINTYAVLCDMPEKLKYMTLYISELSLMEGETYLQYLPSLMSSASVALARHILGMEMWTP  398

Query  634   SLYKHTGYTLKQLQLCICFLYDMFVKAPNHPQHAIQDKYRSRKYMQVS  491
              L + T Y L+ L+  +  L      A      A+++KY    Y +V+
Sbjct  399   RLEEITTYKLEDLKTVVLHLCHTHKTAKELNTQAMREKYNRDTYKKVA  446

Lambda      K        H        a         alpha
   0.318    0.134    0.401    0.792     4.96

Gapped
Lambda      K        H        a         alpha    sigma
   0.267   0.0410    0.140     1.90     42.6     43.6

Effective search space used: 472565421

Query= comp1199_c0_seq1 len=1877 path=[19533:0-169 21522:170-173
19704:174-982 21495:983-986 20513:987-1876]

Length=1877

***** No hits found *****

Lambda      K        H        a         alpha
   0.318    0.134    0.401    0.792     4.96

Gapped
Lambda      K        H        a         alpha    sigma
   0.267   0.0410    0.140     1.90     42.6     43.6

Effective search space used: 397904649

Answer 1

[Ram]

You can use a simple BioPython script to convert your plain text result to tabular format, which will be easier to filter and process. Take a look here: http://biopython.org/DIST/docs/api/Bio.SearchIO.BlastIO-module.html

Or, you can edit my script (this one just filters out no-hits) to read plain text and write tabular. This is BioPerl though. https://github.com/RamRS/myPerlScripts/blob/master/filterBlastReport.pl

[Kurban]

Hello Mr.RamRS,

I tried your script , before any change it showed this result:

kurban@kurban-X550VC:~/Desktop/tf$ perl filterBlastReport.pl tf.blast
Getopt::ArgParse: Option in is required
kurban@kurban-X550VC:~/Desktop/tf$

kurban@kurban-X550VC:~/Desktop/tf$ perl filterBlastReport.pl --in tf.blast
filterBlastReport.pl: remove entries with no hits from BLAST output file
usage: filterBlastReport.pl [--help|-h] --in|-i

This script reads a BLAST results file as input\ and filters out query
sequences with no hits to the database. \ The results are written in plain text
format to output file.

optional arguments:
    --help, -h     ? show this help message and exit
    --in, -i IN      input BLAST results file

Then my friend changed the script little bit (I believe he change the line 21 if(scalar(@ARGV) != 2)), then it gives this:

kurban@kurban-X550VC:~/Desktop/tf$ perl changed.pl --in tf.blast
2Getopt::ArgParse::Namespace=HASH(0x2adfe78)
unknown option: fasta at changed.pl line 30.

I could not be able to find where is the problem.

[Ram]

Check the usage line, it needs the -i flag before the input file name :)

Run the script (the version before your friend changed it) like so:

perl filterBlastReport.pl -i tf.blast

You'd have to change the argparse code if you wanna use input files without the flag.

EDIT: The change your friend made just bypasses the line of code trying to warn you of an imminent failure - it does nothing to address the cause whatsoever :)

[Kurban]

I tried that commend line several times too before make any change of the script, and got the same result:

kurban@kurban-X550VC:~/Desktop/tf$ perl filterBlastReport.pl -i tf.blast
filterBlastReport.pl: remove entries with no hits from BLAST output file
usage: filterBlastReport.pl [--help|-h] --in|-i

This script reads a BLAST results file as input\ and filters out query
sequences with no hits to the database. \ The results are written in plain text
format to output file.

optional arguments:
    --help, -h     ? show this help message and exit
    --in, -i IN      input BLAST results file
kurban@kurban-X550VC:~/Desktop/tf$

[Ram]

I just fixed it - it should work fine now. Sorry for the inconvenience

[Kurban]

yes Sir, it runs perfect now.

no no, there has not been any inconvenience actually. your suggestion and scripts have been great help, thank you for your time and patience.

[Ram]

You're very welcome! Glad I could be of help, and thank you for finding the bug in my code.

[Ram]

That's weird. I guess the script is a bit buggy. I'll work on it and let you know once it is tweaked. It should not take me more than a couple of hours.