Recent changes to bictools - Python

bictools - Python modified by Giese, Sven

Giese, Sven — Thu, 05 Mar 2015 15:15:34 -0000

--- v5
+++ v6
@@ -23,14 +23,25 @@
 >bictools-bic_CSV --infile input.txt --outfile output.csv

 ###### 2) bictools-bic_DB ###### 
+
 Command line tool to create customized databases from biceps results. The input requires the biceps search results, the target databases and a desired output directory. The biceps search results can either be a directory or a single file.

-Main script with many important parameters (e.g. FDR, mass filter, maximum number of mutations). It is also possible to use the decoy free estimation of false positives via CurveFDP. This requires a working installation of R. Moreover, the "bic_cutoff.R" file needs to be downloaded from the project homepage and passed as an argument.
+Main script with many important parameters (e.g. FDR, mass filter, maximum number of mutations). It is also possible to use the decoy free estimation of false positives via CurveFDP. This requires a working installation of R. Moreover, the "bic_cutoff.R" file needs to be downloaded from the project homepage and passed as an argument. However, FDR estimation within BICEPS is not necessary but has an influence on the results.

 >Usage:
-> python bic_DB.py --in_bic Biceps.Results.HCT_all.txt 
+> bictools-bic_DB --in_bic Biceps.Results.HCT_all.txt 
 > --in_db HS_reviewed_19092014.fasta
 > --out_dir /home/results

 ###### 3) bictools-bic_evaluate ######

+A script to evaluate and filter search identifications on a customized variant database. The input files are OpenMS result files (can be created via KNIME), processed biceps files (output from bictools-bic_DB), a fasta database as used in the initial biceps call.
+
+>Usage:
+> bictools-bic_evaluate --in_oms /home/bick/test/TextExporterOutput/ --in_bic /home/bick/test/
+> --in_db /home/bick/test/db.fasta
+
+
+##### Script location #####
+
+On linux the scripts are usually installed to the python path that is probably already in your path variable. On Windows you should find the scripts in the python/Lib/site-packages/bictools folder. Note, the package is not tested under Windows / OSX.

bictools - Python modified by Giese, Sven

Giese, Sven — Thu, 05 Mar 2015 15:03:59 -0000

--- v4
+++ v5
@@ -1,4 +1,4 @@
-bictools Tutorial
+bictools overview
 ===========================

 For this tutorial you need a working installation of python with all packages listed at the previous page. If you are on Windows "Anaconda" is a very easy way to get a working python installation. On Linux and Windows packages can usually be installed via pip or setup tools.
@@ -15,12 +15,22 @@

 There are two parts of bictools: First, a very small API to access and deal with BICEPS identifications. Second, a few command line scripts that get installed automatically. We will only focus on the scripts and how to use them. Each script has a short command line interface with short help messages and examples. The scripts that are available are:

-#### 1) bictools-bic_CSV#### 
+###### 1) bictools-bic_CSV ######

 A small script that converts BICEPS result files into proper table-like result files. This is handy if you want to process the data in Excel / R / python.

-#### 2) bictools-bic_DB#### 
-#### 3) bictools-bic_evaluate#### 
+>Usage:
+>bictools-bic_CSV --infile input.txt --outfile output.csv

+###### 2) bictools-bic_DB ###### 
+Command line tool to create customized databases from biceps results. The input requires the biceps search results, the target databases and a desired output directory. The biceps search results can either be a directory or a single file.

-#### What can you do with bictools ####
+Main script with many important parameters (e.g. FDR, mass filter, maximum number of mutations). It is also possible to use the decoy free estimation of false positives via CurveFDP. This requires a working installation of R. Moreover, the "bic_cutoff.R" file needs to be downloaded from the project homepage and passed as an argument.
+
+>Usage:
+> python bic_DB.py --in_bic Biceps.Results.HCT_all.txt 
+> --in_db HS_reviewed_19092014.fasta
+> --out_dir /home/results
+
+###### 3) bictools-bic_evaluate ######
+

bictools - Python modified by Giese, Sven

Giese, Sven — Thu, 05 Mar 2015 14:48:49 -0000

--- v3
+++ v4
@@ -8,19 +8,19 @@

 To install bictools (not yet part of PyPi, sorry!) you have to download the dist package from the bictools project homepage. Installation is as easy as:

-#pip install bictools-0.1dev.tar.gz
+>pip install bictools-0.1dev.tar.gz

 #### What can you do with bictools ####

 There are two parts of bictools: First, a very small API to access and deal with BICEPS identifications. Second, a few command line scripts that get installed automatically. We will only focus on the scripts and how to use them. Each script has a short command line interface with short help messages and examples. The scripts that are available are:

-1) bictools-bic_CSV
+#### 1) bictools-bic_CSV#### 

 A small script that converts BICEPS result files into proper table-like result files. This is handy if you want to process the data in Excel / R / python.

-2) bictools-bic_DB
-3) bictools-bic_evaluate
+#### 2) bictools-bic_DB#### 
+#### 3) bictools-bic_evaluate#### 

 #### What can you do with bictools ####

bictools - Python modified by Giese, Sven

Giese, Sven — Thu, 05 Mar 2015 14:46:58 -0000

--- v2
+++ v3
@@ -8,7 +8,7 @@

 To install bictools (not yet part of PyPi, sorry!) you have to download the dist package from the bictools project homepage. Installation is as easy as:

-# pip install bictools-0.1dev.tar.gz
+#pip install bictools-0.1dev.tar.gz

 #### What can you do with bictools ####

bictools - Python modified by Giese, Sven

Giese, Sven — Thu, 05 Mar 2015 14:46:37 -0000

--- v1
+++ v2
@@ -1 +1,26 @@
-Help page to execute bictools-python scripts.
+bictools Tutorial
+===========================
+
+For this tutorial you need a working installation of python with all packages listed at the previous page. If you are on Windows "Anaconda" is a very easy way to get a working python installation. On Linux and Windows packages can usually be installed via pip or setup tools.
+
+
+#### Installing bictools ####
+
+To install bictools (not yet part of PyPi, sorry!) you have to download the dist package from the bictools project homepage. Installation is as easy as:
+
+# pip install bictools-0.1dev.tar.gz
+
+
+#### What can you do with bictools ####
+
+There are two parts of bictools: First, a very small API to access and deal with BICEPS identifications. Second, a few command line scripts that get installed automatically. We will only focus on the scripts and how to use them. Each script has a short command line interface with short help messages and examples. The scripts that are available are:
+
+1) bictools-bic_CSV
+
+A small script that converts BICEPS result files into proper table-like result files. This is handy if you want to process the data in Excel / R / python.
+
+2) bictools-bic_DB
+3) bictools-bic_evaluate
+
+
+#### What can you do with bictools ####

bictools - Python modified by Giese, Sven

Giese, Sven — Thu, 05 Mar 2015 12:22:02 -0000

Help page to execute bictools-python scripts.