[med-svn] [Git][med-team/genomethreader][master] add manpage texts
Sascha Steinbiss
gitlab at salsa.debian.org
Fri Jan 10 13:35:33 GMT 2020
Sascha Steinbiss pushed to branch master at Debian Med / genomethreader
Commits:
0445cb85 by Sascha Steinbiss at 2020-01-10T14:35:08+01:00
add manpage texts
- - - - -
3 changed files:
- + debian/man_src/align_dna.1.adoc
- debian/man_src/gth.1.adoc
- + debian/man_src/gthbssmbuild.1.adoc
Changes:
=====================================
debian/man_src/align_dna.1.adoc
=====================================
@@ -0,0 +1,25 @@
+# align_dna(1)
+
+## NAME
+
+align_dna - spliced align genomic sequence with cDNA
+
+## SYNOPSIS
+
+*align_dna* [option ...] -datapath dir -bssmfile file
+
+## OPTIONS
+
+*-genreverse*::
+ align reverse strand of genomic sequence
+ default: no
+
+*-genrange*::
+ set aligned genomic range
+ default: undefined
+
+*-help*::
+ display help and exit
+
+*-version*::
+ display version information and exit
=====================================
debian/man_src/gth.1.adoc
=====================================
@@ -2,7 +2,7 @@
## NAME
-gth - calculate genome structures
+gth - predict genome structures
## SYNOPSIS
@@ -16,12 +16,17 @@ alignments to consensus spliced alignments.
## OPTIONS
--genomic specify input files containing genomic sequences
- mandatory option
--cdna specify input files containing cDNA/EST sequences
--protein specify input files containing protein sequences
--species specify species to select splice site model which is most
- appropriate; possible species:
+*-genomic* <file>::
+ specify input files containing genomic sequences (mandatory option)
+
+*-cdna* <file>::
+ specify input files containing cDNA/EST sequences
+
+*-protein* <file>::
+ specify input files containing protein sequences
+
+*-species* <species>::
+ specify species to select splice site model which is most appropriate; possible species:
"human"
"mouse"
"rat"
@@ -35,87 +40,376 @@ alignments to consensus spliced alignments.
"rice"
"medicago"
default: undefined
--bssm read bssm parameter from file in the path given by the
- environment variable BSSMDIR
- default: undefined
--scorematrix read amino acid substitution scoring matrix from file in the
+
+*-bssm*::
+ read bssm parameter from file in the path given by the environment variable BSSMDIR, default: undefined
+
+*-scorematrix*::
+ read amino acid substitution scoring matrix from file in the
path given by the environment variable GTHDATADIR
default: BLOSUM62
--translationtable set the codon translation table used for codon translation in
- matching, DP, and output
- default: 1
--f analyze only forward strand of genomic sequences
- default: no
--r analyze only reverse strand of genomic sequences
- default: no
--cdnaforward align only forward strand of cDNAs
- default: no
--frompos analyze genomic sequence from this position
- requires -topos or -width; counting from 1 on
- default: 0
--topos analyze genomic sequence to this position
- requires -frompos; counting from 1 on
- default: 0
--width analyze only this width of genomic sequence
- requires -frompos
- default: 0
--v be verbose
- default: no
--xmlout show output in XML format
- default: no
--gff3out show output in GFF3 format
- default: no
--md5ids show MD5 fingerprints as sequence IDs
- default: no
--o redirect output to specified file
- default: undefined
--gzip write gzip compressed output file
- default: no
--bzip2 write bzip2 compressed output file
- default: no
--force force writing to output file
- default: no
--gs2out output in old GeneSeqer2 format
- default: no
--minmatchlen specify minimum match length (cDNA matching)
- default: 20
--seedlength specify the seed length (cDNA matching)
- default: 18
--exdrop specify the Xdrop value for edit distance extension (cDNA
- matching)
- default: 2
--prminmatchlen specify minimum match length (protein matches)
- default: 24
--prseedlength specify seed length (protein matching)
- default: 10
--prhdist specify Hamming distance (protein matching)
- default: 4
--gcmaxgapwidth set the maximum gap width for global chains
- defines approximately the maximum intron length
- set to 0 to allow for unlimited length
- in order to avoid false-positive exons (lonely exons) at the
- sequence ends, it is very important to set this parameter
- appropriately!
- default: 1000000
--gcmincoverage set the minimum coverage of global chains regarding to the
- reference sequence
- default: 50
--paralogs compute paralogous genes (different chaining procedure)
- default: no
--introncutout enable the intron cutout technique
- default: no
--fastdp use jump table to increase speed of DP calculation
- default: no
--autointroncutout set the automatic intron cutout matrix size in megabytes and
- enable the automatic intron cutout technique
- default: 0
--intermediate stop after calculation of spliced alignments and output
- results in reusable XML format. Do not process this output
- yourself, use the ``normal'' XML output instead!
- default: no
--first set the maximum number of spliced alignments per genomic DNA
- input. Set to 0 for unlimited number.
- default: 0
--help display help for basic options and exit
--help+ display help for all options and exit
--version display version information and exit
+
+*-translationtable*::
+ set the codon translation table used for codon translation in
+ matching, DP, and output
+ default: 1
+
+*-f*::
+ analyze only forward strand of genomic sequences
+ default: no
+
+*-r*::
+ analyze only reverse strand of genomic sequences
+ default: no
+
+*-cdnaforward*::
+ align only forward strand of cDNAs
+ default: no
+
+*-frompos*::
+ analyze genomic sequence from this position
+ requires -topos or -width; counting from 1 on
+ default: 0
+
+*-topos*::
+ analyze genomic sequence to this position
+ requires -frompos; counting from 1 on
+ default: 0
+
+*-width*::
+ analyze only this width of genomic sequence
+ requires -frompos
+ default: 0
+
+*-v*::
+ be verbose
+ default: no
+
+*-xmlout*::
+ show output in XML format
+ default: no
+
+*-gff3out*::
+ show output in GFF3 format
+ default: no
+
+*-md5ids*::
+ show MD5 fingerprints as sequence IDs
+ default: no
+
+*-o*::
+ redirect output to specified file
+ default: undefined
+
+*-gzip*::
+ write gzip compressed output file
+ default: no
+
+*-bzip2*::
+ write bzip2 compressed output file
+ default: no
+
+*-force*::
+ force writing to output file
+ default: no
+
+*-skipalignmentout*::
+ skip output of spliced alignments
+ default: no
+
+*-mincutoffs*::
+ show full spliced alignments
+ i.e., cutoffs mode for leading and terminal bases is MINIMAL
+ default: no
+
+*-showintronmaxlen*::
+ set the maximum length of a fully shown intron
+ If set to 0, all introns are shown completely
+ default: 120
+
+*-minorflen*::
+ set the minimum length of an ORF to be shown
+ default: 64
+
+*-startcodon*::
+ require than an ORF must begin with a start codon
+ default: no
+
+*-finalstopcodon*::
+ require that the final ORF must end with a stop codon
+ default: no
+
+*-showseqnums*::
+ show sequence numbers in output
+ default: no
+
+*-pglgentemplate*::
+ show genomic template in PGL lines
+ (switch off for backward compatibility)
+ default: yes
+
+*-gs2out*::
+ output in old GeneSeqer2 format
+ default: no
+
+*-maskpolyatails*::
+ mask poly(A) tails in cDNA/EST files
+ default: no
+
+*-proteinsmap*::
+ specify smap file used for protein files
+ default: protein
+
+*-noautoindex*::
+ do not create indices automatically
+ except for the .dna.* files used for the DP.
+ existence is not tested before an index is actually used!
+ default: no
+
+*-createindicesonly*::
+ stop program flow after the indices have been created
+ default: no
+
+*-skipindexcheck*::
+ skip index check (in preprocessing phase)
+ default: no
+
+*-minmatchlen*::
+ specify minimum match length (cDNA matching)
+ default: 20
+
+*-seedlength*::
+ specify the seed length (cDNA matching)
+ default: 18
+
+*-exdrop*::
+ specify the Xdrop value for edit distance extension (cDNA
+ matching)
+ default: 2
+
+*-prminmatchlen*::
+ specify minimum match length (protein matches)
+ default: 24
+
+*-prseedlength*::
+ specify seed length (protein matching)
+ default: 10
+
+*-prhdist*::
+ specify Hamming distance (protein matching)
+ default: 4
+
+*-online*::
+ run the similarity filter online without using the complete
+ index (increases runtime)
+ default: no
+
+*-inverse*::
+ invert query and index in vmatch call
+ default: no
+
+*-exact*::
+ use exact matches in the similarity filter
+ default: no
+
+*-gcmaxgapwidth*::
+ set the maximum gap width for global chains
+ defines approximately the maximum intron length
+ set to 0 to allow for unlimited length
+ in order to avoid false-positive exons (lonely exons) at the
+ sequence ends, it is very important to set this parameter
+ appropriately!
+ default: 1000000
+
+*-gcmincoverage*::
+ set the minimum coverage of global chains regarding to the
+ reference sequence
+ default: 50
+
+*-paralogs*::
+ compute paralogous genes (different chaining procedure)
+ default: no
+
+*-enrichchains*::
+ enrich genomic sequence part of global chains with additional
+ matches
+ default: no
+
+*-introncutout*::
+ enable the intron cutout technique
+ default: no
+
+*-fastdp*::
+ use jump table to increase speed of DP calculation
+ default: no
+
+*-autointroncutout*::
+ set the automatic intron cutout matrix size in megabytes and
+ enable the automatic intron cutout technique
+ default: 0
+
+*-icinitialdelta*::
+ set the initial delta used for intron cutouts
+ default: 50
+
+*-iciterations*::
+ set the number of intron cutout iterations
+ default: 2
+
+*-icdeltaincrease*::
+ set the delta increase during every iteration
+ default: 50
+
+*-icminremintronlen*::
+ set the minimum remaining intron length for an intron to be
+ cut out
+ default: 10
+
+*-nou12intronmodel*::
+ disable the U12-type intron model
+ default: no
+
+*-u12donorprob*::
+ set the probability for perfect U12-type donor sites
+ default: 0.99
+
+*-u12donorprob1mism*::
+ set the prob. for U12-type donor w. 1 mismatch
+ default: 0.90
+
+*-probies*::
+ set the initial exon state probability
+ default: 0.50
+
+*-probdelgen*::
+ set the genomic sequence deletion probability
+ default: 0.03
+
+*-identityweight*::
+ set the pairs of identical characters weight
+ default: 2.00
+
+*-mismatchweight*::
+ set the weight for mismatching characters
+ default: -2.00
+
+*-undetcharweight*::
+ set the weight for undetermined characters
+ default: 0.00
+
+*-deletionweight*::
+ set the weight for deletions
+ default: -5.00
+
+*-dpminexonlen*::
+ set the minimum exon length for the DP
+ default: 5
+
+*-dpminintronlen*::
+ set the minimum intron length for the DP
+ default: 50
+
+*-shortexonpenal*::
+ set the short exon penalty
+ default: 100.00
+
+*-shortintronpenal*::
+ set the short intron penalty
+ default: 100.00
+
+*-wzerotransition*::
+ set the zero transition weights window size
+ default: 80
+
+*-wdecreasedoutput*::
+ set the decreased output weights window size
+ default: 80
+
+*-leadcutoffsmode*::
+ set the cutoffs mode for leading bases
+ can be either RELAXED, STRICT, or MINIMAL
+ default: RELAXED
+
+*-termcutoffsmode*::
+ set the cutoffs mode for terminal bases
+ can be either RELAXED, STRICT, or MINIMAL
+ default: STRICT
+
+*-cutoffsminexonlen*::
+ set the cutoffs minimum exon length
+ default: 5
+
+*-scoreminexonlen*::
+ set the score minimum exon length
+ default: 50
+
+*-minaveragessp*::
+ set the minimum average splice site prob.
+ default: 0.50
+
+*-duplicatecheck*::
+ criterion used to check for spliced alignment duplicates,
+ choose from none|id|desc|seq|both
+ default: both
+
+*-minalignmentscore*::
+ set the minimum alignment score for spliced alignments to be
+ included into the set of spliced alignments
+ default: 0.00
+
+*-maxalignmentscore*::
+ set the maximum alignment score for spliced alignments to be
+ included into the set of spliced alignments
+ default: 1.00
+
+*-mincoverage*::
+ set the minimum coverage for spliced alignments to be
+ included into the set of spliced alignments
+ default: 0.00
+
+*-maxcoverage*::
+ set the maximum coverage for spliced alignments to be
+ included into the set of spliced alignments
+ default: 9999.99
+
+*-intermediate*::
+ stop after calculation of spliced alignments and output
+ results in reusable XML format. Do not process this output
+ yourself, use the ``normal'' XML output instead!
+ default: no
+
+*-sortags*::
+ sort alternative gene structures according to the weighted
+ mean of the average exon score and the average splice site
+ probability
+ default: no
+
+*-sortagswf*::
+ set the weight factor for the sorting of AGSs
+ default: 1.00
+
+*-exondistri*::
+ show the exon length distribution
+ default: no
+
+*-introndistri*::
+ show the intron length distribution
+ default: no
+
+*-refseqcovdistri*::
+ show the reference sequence coverage distribution
+ default: no
+
+*-first*::
+ set the maximum number of spliced alignments per genomic DNA
+ input. Set to 0 for unlimited number.
+ default: 0
+
+*-help*::
+ display help for basic options and exit
+
+*-help+*::
+ display help for all options and exit
+
+*-version*::
+ display version information and exit
=====================================
debian/man_src/gthbssmbuild.1.adoc
=====================================
@@ -0,0 +1,46 @@
+# gthbssmbuild(1)
+
+## NAME
+
+gthbssmbuild - build splice site model
+
+## SYNOPSIS
+
+*gthbssmbuild* [option ...] genomic_file cDNA_file
+
+## DESCRIPTION
+
+Build a BSSM file from a directory tree containing the training data.
+
+## OPTIONS
+
+
+*-bssmfile*::
+ specify name of BSSM file to store parameters in
+ default: undefined
+
+*-datapath*::
+ specify root of species-specific training data directory tree
+ default: undefined
+
+*-gtdonor*::
+ train GT donor model
+ default: no
+
+*-gcdonor*::
+ train GC donor model
+ default: no
+
+*-agacceptor*::
+ train AG acceptor model
+ default: no
+
+*-gzip*::
+ use gzip'ed input files
+ default: no
+
+*-help*::
+ display help and exit
+
+*-version*::
+ display version information and exit
View it on GitLab: https://salsa.debian.org/med-team/genomethreader/commit/0445cb851591fe89bce32cc0e862179470ca869d
--
View it on GitLab: https://salsa.debian.org/med-team/genomethreader/commit/0445cb851591fe89bce32cc0e862179470ca869d
You're receiving this email because of your account on salsa.debian.org.
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://alioth-lists.debian.net/pipermail/debian-med-commit/attachments/20200110/641a8f70/attachment-0001.html>
More information about the debian-med-commit
mailing list