[med-svn] [Git][med-team/pscan-tfbs][master] 2 commits: Update salsa URL
Steffen Möller
gitlab at salsa.debian.org
Thu May 3 11:09:35 BST 2018
Steffen Möller pushed to branch master at Debian Med / pscan-tfbs
Commits:
510829c9 by Steffen Moeller at 2018-05-03T00:01:07+02:00
Update salsa URL
- - - - -
d817b511 by Steffen Moeller at 2018-05-03T12:03:20+02:00
Added man page
- - - - -
3 changed files:
- debian/changelog
- debian/control
- + debian/pscan.1
Changes:
=====================================
debian/changelog
=====================================
--- a/debian/changelog
+++ b/debian/changelog
@@ -2,6 +2,7 @@ pscan-tfbs (1.4-1) UNRELEASED; urgency=low
[ Steffen Moeller ]
* Initial release (Closes: #673182)
+ * Added man page
* Homepage claims that version 1.4 exists but I can not find it
(Andreas Tille Mon, 18 Dec 2017 21:19:24 +0100)
=====================================
debian/control
=====================================
--- a/debian/control
+++ b/debian/control
@@ -5,9 +5,9 @@ Section: science
Priority: optional
Build-Depends: debhelper (>= 10),
libgsl-dev
-Standards-Version: 4.1.1
-Vcs-Browser: https://anonscm.debian.org/cgit/debian-med/pscan-tfbs.git
-Vcs-Git: https://anonscm.debian.org/git/debian-med/pscan-tfbs.git
+Standards-Version: 4.1.3
+Vcs-Browser: https://salsa.debian.org/med-team/pscan-tfbs
+Vcs-Git: https://salsa.debian.org/med-team/pscan-tfbs.git
Homepage: http://www.beaconlab.it/pscan
Package: pscan-tfbs
=====================================
debian/pscan.1
=====================================
--- /dev/null
+++ b/debian/pscan.1
@@ -0,0 +1,179 @@
+.\" Hey, EMACS: -*- nroff -*-
+.\" (C) Created by 2018 Steffen Moeller <moeller at debian.org> from the output of pscan -h
+.\"
+.TH PSCAN 1 "May 3 2018"
+.\" Please adjust this date whenever revising the manpage.
+.\"
+.\" Some roff macros, for reference:
+.\" .nh disable hyphenation
+.\" .hy enable hyphenation
+.\" .ad l left justify
+.\" .ad b justify to both left and right margins
+.\" .nf disable filling
+.\" .fi enable filling
+.\" .br insert line break
+.\" .sp <n> insert n+1 empty lines
+.\" for manpage-specific macros, see man(7)
+.SH NAME
+pscan \- detection of transcription factor binding sites in DNA sequences
+.SH SYNOPSIS
+.B pscan -q multifastafile -p multifastafile
+.RI [options]
+.br
+.B pscan -p multifastafile
+.RI [options]
+.br
+.B pscan -q multifastafile -M matrixfile
+.RI [options]
+
+.SH DESCRIPTION
+.hy
+.B Pscan
+inspects the upstream non-coding regions of many genes to derive subsequences
+that are characteristic for the binding of proteins, i.e. transcription factors,
+that control the tissue- and situation-dependent expression of a gene.
+The tool is supported by the JASPAR database and other data that is downloadable
+from the tool's home page.
+.no
+.PP
+.hy
+The command line tool
+.B pscan
+is meant for bulk submission. The tool is also offered with a web
+interface that has all auxillary data updated.
+.no
+.SH OPTIONS
+.hy
+.B pscan
+options only have single dashes (`-') and (with notable
+exceptions) followed by a single letter. Options are case-sensitive.
+A summary of options is included below.
+.no
+.TP
+.B \-h
+Show summary of options similar to this man page.
+.TP
+.B \-v
+Show version of program.
+.TP
+.B \-q
+.RI file
+Specify the multifasta file containing the foreground sequences.
+.TP
+.B \-p
+.RI file
+Specify the multifasta file containing the background sequences.
+.TP
+.B \-m
+.RI file
+Use it if the background data are already available in a file (see -g option).
+.TP
+.B \-M
+.RI file
+Scan the foreground sequences using only the Jaspar/Transfac matrix file contained in the specified file.
+.TP
+.B \-l
+.RI file
+Use the matrices contained in that file (for matrix file format see below).
+.TP
+.B \-N
+.RI name
+Use only the matrix with that name (usable only in association with -l).
+.TP
+.B \-ss
+Perform single strand only analysis.
+.TP
+.B \-rs
+Perform single strand only analysis on the reverse strand.
+.TP
+.B \-split
+.RI num1 num2
+Sequences are scanned only from position num1 and for num2 nucleotides.
+.TP
+.B \-trashn
+Discards sequences containing "N".
+.TP
+.B \-n
+Oligos containing "N" will not be discarded. Instead a "N" will obtain an "average" score.
+.TP
+.B \-g
+.hy
+If a background sequences file is used than a file will be written containing the data calculated
+for that background sequences and the current set of matrices.
+From now on one can use that file (-m option) instead of the sequences file for faster processing.
+.nh
+.TP
+.B \-ui file
+An index of the background file will be used to avoid duplicated sequences.
+.TP
+.B \-bi
+Build an index of the background sequences file (to be used later with the -ui option).
+This is useful when you have duplicated sequences in your background that may introduce a bias in your results.
+
+.SH NOTES
+.hy
+The sequences to be used with Pscan have to be promoter sequences.
+To obtain meaningful results it's critical that the background and the foreground sequences are consistent between them either in size
+and in position (with respect to the transcription start site). For optimal results the foreground set should be a subset of the background set.
+.no
+.PP
+If the "-l" option is not used Pscan will try to find Jaspar/Transfac matrix files in the current folder.
+Jaspar files have ".pfm" extension while Transfac ones have ".pro" extension.
+If Jaspar matrix files are used than a file called "matrix_list.txt" must be present in the same folder.
+That file contains required info about the matrices in the ".pfm" files.
+
+.SH EXAMPLES
+
+.B 1)
+pscan -p human_450_50.fasta -bi
+.PP
+.hy
+This command will scan the file "human_450_50.fasta" using the matrices in the current folder.
+It is handy to use that command the first time one uses a set of matrices with a given background sequences file.
+A file called human_450_50.short_matrix will be written and it can be used from now on every time you want to use
+the same background sequences with the same set of matrices. A file called human_450_50.index will be written too
+and it will be useful every time you will use the same background file.
+.no
+.PP
+.B 2)
+pscan \-q human_nfy_targets.fasta \-m human_450_50.short_matrix \-ui human_450_50.index
+.PP
+.hy
+This command will scan the file human_nfy_targets.fasta searching for over-represented binding sites (with respect
+to the preprocessed background contained in the "human_450_50.short_matrix" file) using the matrices in the current folder.
+Please note that the query file "human_nfy_targets.fasta" must be a subset of the sequences contained in the background file "human_450_50.fasta"
+in order to use the index file with the "-ui" option. This means that both the sequences and their FASTA headers used in the query file must appear
+in the background file as well. Using the "-ui" option when the sequences contained in the query file are not a subset of the background file will
+have undefined/unpredictable outcomes.
+The output will be a file called "human_nfy_targets.fasta.res" where you will find all the used matrices sorted by ascending P-value.
+The lower the P-value obtained by a matrix, the higher are the chances that the transcription factor associated to that matrix
+is a regulator of the input promoter sequences.
+The fields of the output are the following: "Transcription Factor Name", "Matrix ID", "Z Score", "Pvalue", "Foreground Average", "Background Average".
+.no
+.PP
+.B 3)
+pscan -q human_nfy_targets.fasta -M MA0108.pfm
+.PP
+.hy
+This command will scan the sequences file "human_nfy_targets.fasta" using the matrix contained in "MA0108.pfm".
+The result will be written in a file called "human_nfy_targets.fasta.ris" where you will find the sequences in input
+sorted by a descending score (between 1 and 0). The higher the score, the better is the oligo found with respect to the used matrix.
+The fields of the output are the following: "Sequence Header", "Score", "Position from the end of sequence", "Oligo that obtained the score",
+"Strand where the oligo was found".
+.no
+.PP
+.B 4)
+pscan -p human_450_50.fasta -bi -l matrixfile.wil
+.PP
+.hy
+This command is like Example #1 with the difference that the matrices set to be used is the one contained in the "matrixfile.wil" file.
+Please look at the "example_matrix_file.wil" file included in this Pscan distribution to see the correct format for matrices file.
+.no
+.PP
+.B 5)
+pscan -q human_nfy_targets.fasta -l matrixfile.wil -N MATRIX1
+.PP
+This command is like Example #3 but it will use the matrix called "MATRIX1" contained in the "matrixfile.wil" file.
+.SH SEE ALSO
+.BR
+For info on how Pscan works pleare refer to the paper.
View it on GitLab: https://salsa.debian.org/med-team/pscan-tfbs/compare/a46fc1679e4c718b6f96684deeb684f0bc5d198d...d817b5116c282f32dbd60cb11cb0e119e6e32937
---
View it on GitLab: https://salsa.debian.org/med-team/pscan-tfbs/compare/a46fc1679e4c718b6f96684deeb684f0bc5d198d...d817b5116c282f32dbd60cb11cb0e119e6e32937
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