Ubuntu Manpage: parseblast - Filtering High-scoring Segment Pairs (HSPs) from WU/NCBI BLAST.

NAME

       parseblast - Filtering High-scoring Segment Pairs (HSPs) from WU/NCBI BLAST.

SYNOPSIS

       parseblast [options] <results.from.blast>

DESCRIPTION

This manual page documents briefly the parseblast command.

Different output options are available, the most important here are those allowing to write HSPs in GFF
format (GFFv1, GFFv2 or APLOT). Sequences can be included in the GFF records as a comment field.
Furthermore, this script can output also the alignments for each HSP in ALN, MSF or tabular formats.

NOTE - If first line from blast program output (the one containing which flavour has been run, say here
BLASTN, BLASTP, BLASTX, TBLASTN or TBLASTX), is missing, the program assumes that it contains BLASTN HSP
records. So that, ensure that you feed the parseblast script with a well formatted BLAST file. Sometimes
there are no spaces between the HSP coords and its sequence, as it sometimes happens in Web-Blast or
Paracel-Blast outputs. Now those records are processed ok and that HSP is retrieved as well as "standard"
ones.

WARNING - Frame fields from GFF records generated with parseblast contain BLAST frame (".","1","2","3")
instead of the GFF standard values (".","0","1","2"). As the frame for reverse strand must be
recalculated from the original sequence length, we suggest users to post-process the GFF output from this
script with a suitable filter that fix the frames (in case that the program that is going to use the GFF
records will not work with the original BLAST frames). We provide the command-line option "--no-frame" to
set frames to "." (meaning that there is no frame).

OPTIONS

parseblast prints output in "HSP" format by default (see below). It takes input from <STDIN> or
single/multiple files, and writes its output to <STDOUT>, so user can redirect to a file but he also
could use the program as a filter within a pipe. "-N", "-M", "-P", "-G", "-F", "-A" and "-X" options
(also the long name versions for each one) are mutually exclusive, and their precedence order is shown
above.

GFF OPTIONS:

-G, --gff
Prints output in GFFv1 format.

-F, --fullgff
Prints output in GFFv2 "alignment" format ("target").

-A, --aplot
Prints output in pseudo-GFF APLOT "alignment" format.

-S, --subject
Projecting GFF output by SUBJECT (default by QUERY).

-Q, --sequence
Append query and subject sequences to GFF record.

-b, --bit-score
Set <score> field to Bits (default Alignment Score).

-i, --identity-score
Set <score> field to Identities (default Alignment).

-s, --full-scores
Include all scores for each HSP in each GFF record.

-u, --no-frame
Set all frames to "." (GFF for not available frames).

-t, --compact-tags
Target coords+strand+frame in short form (NO GFFv2!).

ALIGNMENT OPTIONS:

-P, --pairwise
Prints pairwise alignment for each HSP in TBL format.

-M, --msf
Prints pairwise alignment for each HSP in MSF format.

-N, --aln
Prints pairwise alignment for each HSP in ALN format.

-W, --show-coords
Adds start/end positions to alignment output.

GENERAL OPTIONS:

-X, --expanded
Expanded output (producing multiline output records).

-c, --comments
Include parameters from blast program as comments.

-n, --no-comments
Do not print "#" lines (raw output without comments).

-v, --verbose
Warnings sent to <STDERR>.

--version
Prints program version and exits.

-h, --help
Shows this help and exits.

OUTPUT FORMATS:

        "S_" stands for "Subject_Sequence" and "Q_" for "Query_Sequence". <Program> name  is  taken  from  input
       blast  file. <Strands> are calculated from <start> and <end> positions on original blast file. <Frame> is
       obtained from the blast file if is present else is set to ".". <SCORE>  is  set  to  Alignment  Score  by
       default, you can change it with "-b" and "-i".
        If  "-S"  or "--subject" options are given, then QUERY fields are referred to SUBJECT and SUBJECT fields
       are relative to QUERY (this only available for GFF output records).
        Dots ("...") mean that record description continues in the following line, but such record is printed as
       a single line record by parseblast.

       [HSP] <- (This is the DEFAULT OUTPUT FORMAT)
        <Program> <DataBase> : ...
          ... <IdentityMatches> <Min_Length> <IdentityScore> ...
          ... <AlignmentScore> <BitScore> <E_Value> <P_Sum> : ...
          ... <Q_Name> <Q_Start> <Q_End> <Q_Strand> <Q_Frame> : ...
          ... <S_Name> <S_Start> <S_End> <S_Strand> <S_Frame> : <S_FullDescription>

       [GFF]
        <Q_Name> <Program> hsp <Q_Start> <Q_End> <SCORE> <Q_Strand> <Q_Frame> <S_Name>

       [FULL GFF] <- (GFF showing alignment data)
        <Q_Name> <Program> hsp <Q_Start> <Q_End> <SCORE> <Q_Strand> <Q_Frame> ...
          ... Target "<S_Name>" <S_Start> <S_End> ...
          ... E_value <E_Value> Strand <S_Strand> Frame <S_Frame>

       [APLOT] <- (GFF format enhanced for APLOT program)
        <Q_Name>:<S_Name> <Program> hsp <Q_Start>:<S_Start> <Q_End>:<S_End> <SCORE> ...
          ... <Q_Strand>:<S_Strand> <Q_Frame>:<S_Frame> <BitScore>:<HSP_Number> ...
          ... # E_value <E_Value>

       [EXPANDED]
        MATCH(<HSP_Number>): <Q_Name> x <S_Name>
        SCORE(<HSP_Number>): <AlignmentScore>
        BITSC(<HSP_Number>): <BitScore>
        EXPEC(<HSP_Number>): <E_Value> Psum(<P_Sum>)
        IDENT(<HSP_Number>): <IdentityMatches>/<Min_Length> : <IdentityScore> %
        T_GAP(<HSP_Number>): <TotalGaps(BothSeqs)>
        FRAME(<HSP_Number>): <Q_Frame>/<S_Frame>
        STRND(<HSP_Number>): <Q_Strand>/<S_Strand>
        MXLEN(<HSP_Number>): <Max_Length>
        QUERY(<HSP_Number>): length <Q_Length> : gaps <Q_TotalGaps> : ...
          ... <Q_Start> <Q_End> : <Q_Strand> : <Q_Frame> : <Q_FullSequence>
        SBJCT(<HSP_Number>): length <S_Length> : gaps <S_TotalGaps> : ...
          ... <S_Start> <S_End> : <S_Strand> : <S_Frame> : <S_FullSequence>

AUTHOR