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

parseblast [options] <results.from.blast>

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).

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.

"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>

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

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).