Better setup.py with installation of scripts

README.md

@@ -11,6 +11,9 @@ Read our [short SUPPA tutorial on an example dataset](https://github.com/comprna
 
    * [Overview](#overview)
    * [Installation](#installation)
+     * [From the tar.gz archive](#from-the-targz-archive)
+     * [Using pip](#using-pip)
+     * [Using bioconda](#using-bioconda)
    * [Command and subcommand structure](#command-and-subcommand-structure)
    * [Generation of transcript events and local alternative splicing events](#generation-of-transcript-events-and-local-alternative-splicing-events)
       * [Input files](#input-files)
@@ -72,10 +75,34 @@ SUPPA has been developed in Python 3.4.
 
 If necessary, to install python3 we recommend to download from the official site https://www.python.org/downloads/ the corresponding version for your OS.
 
+## From the tar.gz archive
+
+Uncompress the archive using:
+```
+tar xvzf SUPPA-2.3.tar.gz
+cd SUPPA
+```
+
+As root/administrator, you can install with:
+```
+python3 setup.py install
+```
+or as a non-privilegied user for a user specific install:
+```
+python3 setup.py install --user
+```
+in this case, on a unix-like environment, the executable are installed by default in `~/.local/bin`. You can add this path to the shell search path with (Bash shell):
+
+```
+if ! grep -q 'PATH.*~/\.local/bin' ~/.bashrc ; then echo 'export PATH=$PATH:~/.local/bin' >>~/.bashrc; fi
+```
+
+## Using pip
+
 A installation using pip is available using the next command:
 
 ```
-pip install SUPPA==2.2.1 
+pip install SUPPA==2.3 
 ```
 By default SUPPA is installed into the Python package library directory. The following command can be executed to obtain the directory location:
 
@@ -85,6 +112,8 @@ pip show SUPPA
 
 SUPPA is ready to use. Once downloaded, it can be used directly from the command line by specifying the absolute path to the SUPPA executable (suppa.py).
 
+## Using bioconda
+
 Another option is via bioconda (thanks to Devon Ryan)
 
 ```
@@ -98,7 +127,7 @@ conda install -c bioconda suppa
 SUPPA works with a command/subcommand structure:
 
 ```
-python3.4 suppa.py subcommand options
+python3 suppa2.py subcommand options
 
 ```
 where the subcommand can be one of these five:
@@ -165,7 +194,7 @@ The *generateEvents* operation uses the lines where the feature (column 3) is "e
 To generate the events from the GTF file one has to run the following command:
 
 ```
-python3.4 suppa.py generateEvents [options]
+python3 suppa2.py generateEvents [options]
 ```
 List of options available:
 
@@ -202,13 +231,13 @@ List of options available:
 The command line to generate local AS events will be of the form:
 
 ```
-python3.4 suppa.py generateEvents -i <input-file.gtf> -o <output-file> -f ioe -e <list-of-events>
+python3 suppa2.py generateEvents -i <input-file.gtf> -o <output-file> -f ioe -e <list-of-events>
 ```
 
 The command to generate the transcript "events" would be of the form:
 
 ```
-python3.4 suppa.py generateEvents -i <input-file.gtf> -o <output-file> -f ioi 
+python3 suppa2.py generateEvents -i <input-file.gtf> -o <output-file> -f ioi 
 ```
 
 ## Output files
@@ -377,7 +406,7 @@ transcript3 <expression>  <expression>  <expression>  <expression>
 At the moment the PSI per transcript isoform is calculated in the following way:
 
 ```
-python3.4 suppa.py psiPerIsoform [options]
+python3 suppa2.py psiPerIsoform [options]
 ```
 List of options available:
 
@@ -394,15 +423,15 @@ List of options available:
 An example of the usage of the program is:
 
 ```
-python3.4 suppa.py psiPerIsoform -g <gtf-file> -e <expression-file> -o <output-file>
+python3 suppa2.py psiPerIsoform -g <gtf-file> -e <expression-file> -o <output-file>
 ```
 
 ### **PSI per local event** ###
 
 To calculate the PSI value for each event from the *ioe* and the *transcript expression file* one has to run the following command:
 
 ```
-python3.4 suppa.py psiPerEvent [options]
+python3 suppa2.py psiPerEvent [options]
 
 ```
 List of options available:
@@ -422,7 +451,7 @@ List of options available:
 An example of the usage of the program is:
 
 ```
-python3.4 suppa.py psiPerEvent --ioe-file <ioe-file> --expression-file <expression-file> -o <output-file> 
+python3 suppa2.py psiPerEvent --ioe-file <ioe-file> --expression-file <expression-file> -o <output-file> 
 ```
 
 ### **Output files** ###
@@ -456,7 +485,7 @@ ENSG00000000419.12;SE:chr20:50940933-50941105:50941209-50942031:-       0.023022
 Transcript expression files used with SUPPA typically come from calculations with multiple samples. To facilitate the generation of a single file with all the transcript expression values for all samples, SUPPA distribution includes a program to combine multiple simple transcript expression files into one single file:
 
 ```
-python3.4 suppa.py joinFiles [options]
+python3 suppa2.py joinFiles [options]
 ```
 
 
@@ -474,7 +503,7 @@ where the options are:
 We show below an example of the usage of the program for reading multiple output files from Sailfish to join together the 3rd column, given that all files have in the first column the transcript ids (which are kept for the output):
 
 ```
-python3.4 suppa.py joinFiles -f tpm -i sample1.tpm sample2.tpm sample3.tpm -o all_samples_tpms  
+python3 suppa2.py joinFiles -f tpm -i sample1.tpm sample2.tpm sample3.tpm -o all_samples_tpms  
 ```
 
 The output will look like an expression file with multiple files as described above.
@@ -521,7 +550,7 @@ where the expression values are given in TPM units.
 ### **Command and options** ###
 To calculate the dpsi from the *ioe*, *psi* and the *expression file* one has to run the following command:
 ```
-python3.4 suppa.py diffSplice [options]
+python3 suppa2.py diffSplice [options]
 ```
 
 List of options available:
@@ -564,15 +593,15 @@ List of options available:
 An example of the usage of the program with transcripts is, indicating that replicates are paired (-pa), to apply a multple testing correction (-gc) and perform pairwise comparison between all conditions (-c):
 
 ```
-python3.4 suppa.py diffSplice --method <empirical> --input <ioi-file> --psi <Cond1.psi> <Cond2.psi> --expression-file <Cond1_expression-file> <Cond2_expression-file> --area <1000> --lower-bound <0.05> -pa -gc -c -o <output-file>
+python3 suppa2.py diffSplice --method <empirical> --input <ioi-file> --psi <Cond1.psi> <Cond2.psi> --expression-file <Cond1_expression-file> <Cond2_expression-file> --area <1000> --lower-bound <0.05> -pa -gc -c -o <output-file>
 ```
 
 ### **Differential splicing with local events** ###
 
 An example of the usage of the program with local events, applying a multple testing correction (-gc):
 
 ```
-python3.4 suppa.py diffSplice --method <empirical> --input <ioe-file> --psi <Cond1.psi> <Cond2.psi> --expression-file <Cond1_expression-file> <Cond2_expression-file> --area <1000> --lower-bound <0.05> -gc -o <output-file>
+python3 suppa2.py diffSplice --method <empirical> --input <ioe-file> --psi <Cond1.psi> <Cond2.psi> --expression-file <Cond1_expression-file> <Cond2_expression-file> --area <1000> --lower-bound <0.05> -gc -o <output-file>
 ```
 
 ### **Output files** ###
@@ -661,7 +690,7 @@ event3    <psi_value> <psi_value> <psi_value> <psi_value> <psi_value> <psi_value
 SUPPA will use the psivec file to cluster events according to the PSI values across samples using those events that show significant change in at least one pairwise comparison using the dpsi file. Two methods are available: DBSCAN and OPTICS. Both methods require as input the minimum number of events in a cluster. OPTICS also requires as the maximum reachability distance (s), which represents the maximum distance in PSI space of an event to a cluster  To perform the clustering from the *dpsi* and the *psivec* one has to run the following command:
 
 ```
-python3.4 suppa.py clusterEvents [options]
+python3 suppa2.py clusterEvents [options]
 
 ```
 List of options available:
@@ -693,7 +722,7 @@ List of options available:
 An example of the usage of the program is:
 
 ```
-python3.4 suppa.py clusterEvents --dpsi <dpsi-file> --psivec <psivec-file> --sig-threshold <0.05> --eps <0.05> --min-pts <20> --groups <1-3,4-6> -o <output-file> 
+python3 suppa2.py clusterEvents --dpsi <dpsi-file> --psivec <psivec-file> --sig-threshold <0.05> --eps <0.05> --min-pts <20> --groups <1-3,4-6> -o <output-file> 
 
 ```
 

scripts/Volcano_MA_plot.R → scripts/suppa2_Volcano_MA_plot.R

@@ -1,3 +1,5 @@
+#! /usr/bin/env Rscript
+
 library(scales)
 library(ggplot2)
 library(ggrepel)

scripts/format_Ensembl_ids.R → scripts/suppa2_format_Ensembl_ids.R

@@ -1,4 +1,5 @@
-#!/usr/bin/Rscript
+#! /usr/bin/env Rscript
+
 #with this script, running from bash, we want to format the ids fo the Ensembl transcripts for running SUPPA
 
 # Parse command line arguments

scripts/format_unique_fasta_RefSeq_annotation.py → scripts/suppa2_format_unique_fasta_RefSeq_annotation.py

@@ -1,3 +1,5 @@
+#! /usr/bin/env python3
+
 """
 @authors: Juan L. Trincado
 @email: [email protected]

scripts/generate_boxplot_event.py → scripts/suppa2_generate_boxplot_event.py

@@ -1,3 +1,5 @@
+#! /usr/bin/env python3
+
 # The next script will format a phenotype table (junctions, events, trasncripts...)
 # for runnning FastQTL analysis
 
@@ -159,4 +161,4 @@ def main():
 
 
 if __name__ == '__main__':
-    main()
+    main()

multipleFieldSelection.py → scripts/suppa2_multipleFieldSelection.py

@@ -1,3 +1,5 @@
+#! /usr/bin/env python3
+
 # -*- coding: utf-8 -*-
 """
 Created on Thu May 22 11:24:33 2014

scripts/split_file.R → scripts/suppa2_split_file.R

@@ -1,4 +1,4 @@
-#!/soft/R/R-3.1.0/bin/Rscript
+#! /usr/bin/env Rscript
 #Given two pairs of lists of samples, split [1] in two files with the samples indicated in [2] and [3]
 
 #[1] First argument: input file that we want to split
@@ -7,13 +7,17 @@
 #[4] Fourth argument: output file of the first condition
 #[5] Fifth argument: output file of the second condition
 
+## bug in setuptools, this script is recognized as python if not included
+## bugs #355, #1178
+data.frame(a="")$a
+
 # Parse command line arguments
 print("Parsing samples...")
 CHARACTER_command_args <- commandArgs(trailingOnly=TRUE)
 
 #Load the input file
 print(paste0("Loading ",CHARACTER_command_args[1],"..."))
-input_file <- read.table(CHARACTER_command_args[1],header=TRUE)
+input_file <- read.table(CHARACTER_command_args[1],row.names=1,header=TRUE, check.names=FALSE)
 
 #Load the list of samples of the first condition
 first_condition <- unlist(strsplit(CHARACTER_command_args[2],","))

setup.py

@@ -0,0 +1,36 @@
+#! /usr/bin/env python3
+
+from setuptools import setup, find_packages
+
+setup(
+    name='SUPPA',
+    packages=find_packages(),
+    scripts=['suppa2.py',
+             'scripts/suppa2_multipleFieldSelection.py',
+             'scripts/suppa2_format_Ensembl_ids.R',
+             'scripts/suppa2_split_file.R',
+             'scripts/suppa2_Volcano_MA_plot.R',
+             'scripts/suppa2_generate_boxplot_event.py',
+             'scripts/suppa2_format_unique_fasta_RefSeq_annotation.py'],
+    version='2.3',
+    description='A tool to study splicing across multiple conditions at high speed and accuracy.',
+    author='GP Alamancos',
+    author_email='[email protected]',
+    license='MIT',
+    url='https://github.com/comprna/SUPPA',
+    download_url='https://github.com/comprna/SUPPA/archive/v2.3.tar.gz',
+    keywords=['alternative', 'splicing', 'analysis', 'transcriptomics'],
+    classifiers=[
+        'Development Status :: 5 - Production/Stable',
+        'Topic :: Scientific/Engineering :: Bio-Informatics',
+        'Intended Audience :: Science/Research',
+        'License :: OSI Approved :: MIT License',
+        'Operating System :: POSIX :: Linux',
+        'Programming Language :: Python :: 3.5'],
+    install_requires=['scipy>=0.15.1',
+                      'numpy>=1.11.0',
+                      'pandas>=0.18.0',
+                      'statsmodels>=0.6.1',
+                      'scikit-learn>=0.16.1'],
+    python_requires='>=3',
+)

lib/cluster_tools.py → suppa/cluster_tools.py

@@ -13,7 +13,7 @@
 from sklearn.cluster import DBSCAN
 from collections import defaultdict
 from sklearn.metrics import silhouette_score
-from lib.optics import *
+from .optics import *
 
 
 

lib/event.py → suppa/event.py

@@ -607,7 +607,7 @@ def process_events(my_gene, event, ioe_writer, gtf_writer, edge_len, th):
         gtf_writer.write(gtf_line, etype)
 
 # to avoid circular dependencies
-from lib.var_event import *
+from .var_event import *
 
 
 def create_event_classes(all_events, b_type):

eventClusterer.py → suppa/eventClusterer.py

@@ -9,7 +9,7 @@
 
 import os
 import logging
-from lib.cluster_tools import cluster_analysis
+from .cluster_tools import cluster_analysis
 from argparse import ArgumentParser, RawTextHelpFormatter
 
 

eventGenerator.py → suppa/eventGenerator.py

@@ -9,9 +9,9 @@
 import sys
 import logging
 from argparse import ArgumentParser, RawTextHelpFormatter
-from lib.tools import *
-from lib.gtf_store import *
-from lib.event import *
+from .tools import *
+from .gtf_store import *
+from .event import *
 
 # Setting argument parser
 # parser = argparse.ArgumentParser()

psiCalculator.py → suppa/psiCalculator.py

@@ -10,7 +10,7 @@
 import logging
 import numpy as np
 from argparse import ArgumentParser, RawTextHelpFormatter
-from lib.tools import *
+from .tools import *
 
 
 description = \
@@ -158,7 +158,7 @@ def main():
                 writer = Writer.getWriter("PSI")
                 logger.info("Generating output %s" % (output_file + ".psi"))
                 writer.openFile(output_file)
-                writer.writeLine("\t".join(col_ids), False)
+                writer.writeLine("\t".join(["Name"] + col_ids), False)
                 for key, value in sorted(psi_dictionary.items()):
                     logger.debug("Calculating psi for %s" % key)
                     psi_line = PsiWriter.lineGenerator(key, value, col_ids)
@@ -183,4 +183,4 @@ def main():
     logger.info("Done")
 
 if __name__ == '__main__':
-    main()
+    main()

psiPerGene.py → suppa/psiPerGene.py

@@ -10,8 +10,8 @@
 import sys
 import logging
 from argparse import ArgumentParser, RawTextHelpFormatter
-from lib.tools import *
-from lib.gtf_store import *
+from .tools import *
+from .gtf_store import *
 
 
 description = \

significanceCalculator.py → suppa/significanceCalculator.py

@@ -12,7 +12,7 @@
 
 import os
 import logging
-from lib.diff_tools import multiple_conditions_analysis
+from .diff_tools import multiple_conditions_analysis
 from argparse import *
 
 

lib/tools.py → suppa/tools.py

@@ -9,7 +9,7 @@
 import sys
 import logging
 from abc import ABCMeta, abstractmethod
-from lib.event import *
+from .event import *
 
 
 #Setting logging preferences
@@ -376,9 +376,9 @@ def readLine(self, header = True):
                 fields = line.rstrip("\n").split("\t")
                 if lineNumber == 0 and header: #Skip the header line
                     #Calculating the number of fields required
-                    min_fields = (len(line.rstrip("\n").split("\t")) + 1)
+                    min_fields = len(fields)
                     #Storing column_id for the expression fields
-                    colIds = fields
+                    colIds = fields[1:]
                     continue
                 if line.startswith('#'):
                     logger.debug("Line %i starts with #. Skipping line..." % (