PARSEBLAST(1)

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>

SEE ALSO
ali2gff(1), blat2gff(1), gff2aplot(1), sim2gff(1).

AUTHOR
parseblast was written by Josep F. Abril <abril@imim.es>.

This manual page was written by Nelson A. de Oliveira <naoliv@gmail.com>, for the Debian project (but may be used by others).