CLI Usage¶
1. CLIs Overview¶
CLI |
Usage |
|---|---|
Make a server to quickly find where DNA occurs in genome |
|
A client for the genomic finding program that produces a .psl file |
|
Convert fasta to 2bit format |
|
Convert 2bit to fasta format |
We can get completion for current shell via pxblat --install-completion.
The help message is got from
$ pxblat -h
Usage: pxblat [OPTIONS] COMMAND [ARGS]...
╭─ Options ────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────╮
│ --install-completion Install completion for the current shell. │
│ --show-completion Show completion for the current shell, to copy it or customize the installation. │
│ --help -h Show this message and exit. │
╰──────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────╯
╭─ Commands ───────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────╮
│ client A client for the genomic finding program that produces a .psl file │
│ fatotwobit Convert DNA from fasta to 2bit format │
│ server Make a server to quickly find where DNA occurs in genome │
│ twobittofa Convert all or part of .2bit file to fasta │
╰──────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────╯
YangyangLi 2023 yangyang.li@northwstern.edu
1.1 Server¶
$ pxblat server -h
Usage: pxblat server [OPTIONS] COMMAND [ARGS]...
Make a server to quickly find where DNA occurs in genome
╭─ Options ────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────╮
│ --help -h Show this message and exit. │
╰──────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────╯
╭─ Commands ───────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────╮
│ files To get input file list │
│ start To set up a server │
│ status To figure out if server is alive, on static instances get usage statics │
│ stop To remove a server │
╰──────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────╯
Start a server¶
$ pxblat server start localhost 650000 twobit.2bit
$ pxblat server start -h
Usage: pxblat server start [OPTIONS] HOST PORT TWO_BIT
To set up a server.
gfServer start host port file(s)
where the files are .2bit or .nib format files specified relative to the current directory
╭─ Arguments ───────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────╮
│ * host TEXT [default: None] [required] │
│ * port INTEGER [default: None] [required] │
│ * two_bit FILE Two bit file [default: None] [required] │
╰───────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────╯
╭─ Options ─────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────╮
│ --tile-size INTEGER Size of n-mers to index. Default is 11 for nucleotides, 4 for proteins (or translated nucleotides). [default: 11] │
│ --stepSize INTEGER Spacing between tiles. Default is tileSize. [default: 11] │
│ --min-match INTEGER Number of n-mer matches that trigger detailed alignment. Default is 2 for nucleotides, 3 for proteins. [default: 2] │
│ --trans Translate database to protein in 6 frames. │
│ --log TEXT Keep a log file that records server requests. [default: None] │
│ --mask Use masking from .2bit file. │
│ --repMatch INTEGER Number of occurrences of a tile (n-mer) that triggers repeat masking the tile. Default is 1024. [default: 0] │
│ --noSimpRepMask Suppresses simple repeat masking. │
│ --maxDnaHits INTEGER Maximum number of hits for a DNA query that are sent from the server. [default: 100] │
│ --maxTransHits INTEGER Maximum number of hits for a translated query that are sent from the server. [default: 200] │
│ --maxNtSize INTEGER Maximum size of untranslated DNA query sequence. [default: 40000] │
│ --perSeqMax FILE File contains one seq filename (possibly with ':seq' suffix) per line. [default: None] │
│ --canStop If set, a quit message will actually take down the server. │
│ --indexFile FILE Index file create by gfServer index. [default: None] │
│ --timeout INTEGER Timeout in seconds. [default: 90] │
│ --help -h Show this message and exit. │
╰───────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────╯
Get files of a running server¶
$ pxblat server files localhost 650000
$ pxblat server files -h
Usage: pxblat server files [OPTIONS] HOST PORT
To get input file list.
╭─ Arguments ───────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────╮
│ * host TEXT [default: None] [required] │
│ * port INTEGER [default: None] [required] │
╰───────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────╯
╭─ Options ─────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────╮
│ --help -h Show this message and exit. │
╰───────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────╯
Get status of a running server¶
$ pxblat server status localhost 650000
$ pxblat server status -h
Usage: pxblat server status [OPTIONS] HOST PORT
To figure out if server is alive, on static instances get usage statics.
╭─ Arguments ───────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────╮
│ * host TEXT [default: None] [required] │
│ * port INTEGER [default: None] [required] │
╰───────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────╯
╭─ Options ─────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────╮
│ --trans Translate database to protein in 6 frames. │
│ --help -h Show this message and exit. │
╰───────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────╯
Stop a running server¶
$ pxblat server stop localhost 650000
$ pxblat server stop -h
Usage: pxblat server stop [OPTIONS] HOST PORT
To remove a server.
╭─ Arguments ───────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────╮
│ * host TEXT [default: None] [required] │
│ * port INTEGER [default: None] [required] │
╰───────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────╯
╭─ Options ─────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────╮
│ --help -h Show this message and exit. │
╰───────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────╯
1.2 Client¶
$ pxblat client localhost 65000 twobit_dir fasta1.fa out.psl
$ pxblat client -h
Usage: pxblat client [OPTIONS] HOST PORT SEQDIR INFASTA OUTPSL
A client for the genomic finding program that produces a .psl file.
╭─ Arguments ───────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────╮
│ * host TEXT The name of the machine running the gfServer [default: None] [required] │
│ * port INTEGER The same port that you started the gfServer with [default: None] [required] │
│ * seqdir PATH The path of the .2bit or .nib files relative to the current dir [default: None] [required] │
│ * infasta PATH Fasta format file. May contain multiple records [default: None] [required] │
│ * outpsl PATH where to put the output [default: None] [required] │
╰───────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────╯
╭─ Options ─────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────╮
│ --type -t TEXT Database type. Type is one of: dna, prot, dnax [default: dna] │
│ --qtype -q TEXT Query type. Type is one of: dna, rna, prot, dnax, rnax [default: dna] │
│ --prot Synonymous with -t=prot -q=prot. │
│ --dots INTEGER Output a dot every N query sequences. [default: 0] │
│ --nohead Suppresses 5-line psl header. │
│ --minScore INTEGER Sets minimum score. This is twice the matches minus the mismatches minus some sort of gap penalty. │
│ Default is 30. │
│ [default: 30] │
│ --minIdentity INTEGER Sets minimum sequence identity (in percent). Default is 90 for nucleotide searches, 25 for protein or │
│ translated protein searches. │
│ [default: 90.0] │
│ --out TEXT Controls output file format. Type is one of: psl, pslx, axt, maf, sim4, wublast, blast, blast8, blast9 │
│ [default: psl] │
│ --maxIntron INTEGER Sets maximum intron size. Default is 750000. [default: 750000] │
│ --genome TEXT dynamic │
│ --genomeDataDir TEXT dynamic │
│ --help -h Show this message and exit. │
╰───────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────╯
1.3 fatotwobit¶
$ pxblat fatotwobit in.fa out.2bit
$ pxblat fatotwobit -h
Usage: pxblat fatotwobit [OPTIONS] in.fa [inf2.fa in3.fa ...] out.2bit
Convert DNA from fasta to 2bit format.
╭─ Arguments ───────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────╮
│ * infa in.fa [inf2.fa in3.fa ...] The fasta files [required] │
│ * out2bit out.2bit The output file [required] │
╰───────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────╯
╭─ Options ─────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────╮
│ --long Use 64-bit offsets for index. Allow for twoBit to contain more than 4Gb of sequence. │
│ --nomask Ignore lower-case masking in fa file. │
│ --stripVersion Strip off version number after '.' for GenBank accessions. │
│ --ignoreDups Convert first sequence only if there are duplicate sequence names. Use 'twoBitDup' to find duplicate sequences. │
│ --help -h Show this message and exit. │
╰───────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────╯
1.4 twobittofa¶
$ pxblat twobittofa input.2bit out.fa
$ pxblat twobittofa -h
Usage: pxblat twobittofa [OPTIONS] input.2bit out.fa
Convert all or part of .2bit file to fasta.
╭─ Arguments ───────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────╮
│ * input2bit input.2bit The input 2bit file [default: None] [required] │
│ * outputfa out.fa The output fasta file [required] │
╰───────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────╯
╭─ Options ─────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────╮
│ --seq TEXT Restrict this to just one sequence. │
│ --start INTEGER Start at given position in sequence (zero-based). [default: 0] │
│ --end INTEGER End at given position in sequence (non-inclusive). [default: 0] │
│ --seqList TEXT File containing list of the desired sequence names │
│ --noMask Convert sequence to all upper case. │
│ --bpt TEXT Use bpt index instead of built-in one. │
│ --bed TEXT Grab sequences specified by input.bed. │
│ --bedPos With -bed, use chrom:start-end as the fasta ID in output.fa. │
│ --udcDir TEXT Place to put cache for remote bigBed/bigWigs. │
│ --help -h Show this message and exit. │
╰───────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────╯
2. Reference¶
pxblat¶
Version: 1.2.8
Usage
pxblat [OPTIONS] COMMAND [ARGS]...
Options
- --install-completion¶
Install completion for the current shell.
- --show-completion¶
Show completion for the current shell, to copy it or customize the installation.
YangyangLi 2026 yangyang.li@northwstern.edu
client¶
A client for the genomic finding program that produces a .psl file.
Usage
pxblat client [OPTIONS] HOST PORT SEQDIR INFASTA OUTPSL
Options
- --minScore <minnScore>¶
Sets minimum score. This is twice the matches minus the mismatches minus some sort of gap penalty. Default is 30.
- Default:¶
30
- --minIdentity <minIdentity>¶
Sets minimum sequence identity (in percent). Default is 90 for nucleotide searches, 25 for protein or translated protein searches.
- Default:¶
90.0
- --out <out>¶
Controls output file format. Type is one of: psl, pslx, axt, maf, sim4, wublast, blast, blast8, blast9
- Default:¶
'psl'
Arguments
- HOST¶
Required argument
The name of the machine running the gfServer
- PORT¶
Required argument
The same port that you started the gfServer with
- SEQDIR¶
Required argument
The path of the .2bit or .nib files relative to the current dir
- INFASTA¶
Required argument
Fasta format file. May contain multiple records
- OUTPSL¶
Required argument
where to put the output
fatotwobit¶
Convert DNA from fasta to 2bit format.
Usage
pxblat fatotwobit [OPTIONS] in.fa [inf2.fa in3.fa ...] out.2bit
Options
- --long¶
Use 64-bit offsets for index. Allow for twoBit to contain more than 4Gb of sequence.
- Default:¶
False
- --ignoreDups¶
Convert first sequence only if there are duplicate sequence names. Use ‘twoBitDup’ to find duplicate sequences.
- Default:¶
False
Arguments
- in.fa [inf2.fa in3.fa ...]¶
Required argument(s)
The fasta files
- out.2bit¶
Required argument
The output file
server¶
Make a server to quickly find where DNA occurs in genome
Usage
pxblat server [OPTIONS] COMMAND [ARGS]...
files¶
To get input file list.
Usage
pxblat server files [OPTIONS] HOST PORT
Arguments
- HOST¶
Required argument
- PORT¶
Required argument
start¶
To set up a server.
gfServer start host port file(s)
where the files are .2bit or .nib format files specified relative to the current directory
Usage
pxblat server start [OPTIONS] HOST PORT TWO_BIT
Options
- --tile-size <tileSize>¶
Size of n-mers to index. Default is 11 for nucleotides, 4 for proteins (or translated nucleotides).
- Default:¶
11
- --min-match <minMatch>¶
Number of n-mer matches that trigger detailed alignment. Default is 2 for nucleotides, 3 for proteins.
- Default:¶
2
- --log <log>¶
Keep a log file that records server requests.
- --repMatch <repMatch>¶
Number of occurrences of a tile (n-mer) that triggers repeat masking the tile. Default is 1024.
- Default:¶
0
- --maxDnaHits <maxDnaHits>¶
Maximum number of hits for a DNA query that are sent from the server.
- Default:¶
100
- --maxTransHits <maxTransHits>¶
Maximum number of hits for a translated query that are sent from the server.
- Default:¶
200
- --perSeqMax <perSeqMax>¶
File contains one seq filename (possibly with ‘:seq’ suffix) per line.
Arguments
- HOST¶
Required argument
- PORT¶
Required argument
- TWO_BIT¶
Required argument
Two bit file
status¶
To figure out if server is alive, on static instances get usage statics.
Usage
pxblat server status [OPTIONS] HOST PORT
Options
Arguments
- HOST¶
Required argument
- PORT¶
Required argument
stop¶
To remove a server.
Usage
pxblat server stop [OPTIONS] HOST PORT
Arguments
- HOST¶
Required argument
- PORT¶
Required argument
twobittofa¶
Convert all or part of .2bit file to fasta.
Usage
pxblat twobittofa [OPTIONS] input.2bit out.fa
Options
Arguments
- input.2bit¶
Required argument
The input 2bit file
- out.fa¶
Required argument
The output fasta file