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