[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

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