Merge pull request #11 from Takadonet/remove_fastqs

Reduce repo size from 191M to 919k.

README.md

@@ -39,39 +39,39 @@ profile	Neisseria_spp/neisseria.txt
 
 ### Predict:
 
-* Extract all the read files to a folder (say ./example/) such that fastq files are in the folder as :
+* Download example read datasets with bash script download_example_reads.sh . After download is complete, tests/fastqs folder will contain the following files:
 ```
-example/ERR026529_1.fastq
-example/ERR026529._2fastq
-example/ERR027250_1.fastq
-example/ERR027250_2.fastq
-example/ERR036104_1.fastq
-example/ERR036104_2.fastq
+tests/fastqs/ERR026529_1.fastq
+tests/fastqs/ERR026529_2.fastq
+tests/fastqs/ERR027250_1.fastq
+tests/fastqs/ERR027250_2.fastq
+tests/fastqs/ERR036104_1.fastq
+tests/fastqs/ERR036104_2.fastq
 ```
 * Predict:
 
 #### Single sample :
 ```
-./stringMLST.py --predict -1 example/ERR026529_1.fastq -2 example/ERR026529_2.fastq -k 35 -P NM 	
+./stringMLST.py --predict -1 tests/fastqs/ERR026529_1.fastq -2 tests/fastqs/ERR026529_2.fastq -k 35 -P NM 	
 ```
 #### Batch mode (all the samples together):
 ```
-./stringMLST.py --predict -d ./example/ -k 35 -P NM	
+./stringMLST.py --predict -d ./tests/fastqs/ -k 35 -P NM	
 ```
 #### List mode:
 Create a list file (list_paired.txt) as :
 ```
-example/ERR026529_1.fastq	example/ERR026529_2.fastq
-example/ERR027250_1.fastq	example/ERR027250_2.fastq
-example/ERR036104_1.fastq	example/ERR036104_2.fastq
+tests/fastqs/ERR026529_1.fastq	tests/fastqs/ERR026529_2.fastq
+tests/fastqs/ERR027250_1.fastq	tests/fastqs/ERR027250_2.fastq
+tests/fastqs/ERR036104_1.fastq	tests/fastqs/ERR036104_2.fastq
 ```
 Run the tool as:
 ```
 ./stringMLST.py --predict -l list_paired.txt -k 35 -P NM
 ```
 #### Working with gziped files
 ```
-stringMLST.py --predict -1 example/ERR026529_1.fq.gz -2 example/ERR026529_2.fq.gz -p --prefix <prefix for the database> -k <k-mer size> -o <output file name>
+stringMLST.py --predict -1 tests/fastqs/ERR026529_1.fq.gz -2 tests/fastqs/ERR026529_2.fq.gz -p --prefix <prefix for the database> -k <k-mer size> -o <output file name>
 ```
 ## Usage Documentation
 

download_example_reads.sh

@@ -0,0 +1,22 @@
+#!/bin/bash
+
+testdir='tests/fastqs'
+
+echo -e "Downloading fastq files from EBI..."
+
+wget ftp://ftp.sra.ebi.ac.uk/vol1/fastq/ERR026/ERR026529/ERR026529_1.fastq.gz -P $testdir
+wget ftp://ftp.sra.ebi.ac.uk/vol1/fastq/ERR026/ERR026529/ERR026529_2.fastq.gz -P $testdir
+wget ftp://ftp.sra.ebi.ac.uk/vol1/fastq/ERR027/ERR027250/ERR027250_1.fastq.gz -P $testdir
+wget ftp://ftp.sra.ebi.ac.uk/vol1/fastq/ERR027/ERR027250/ERR027250_2.fastq.gz -P $testdir
+wget ftp://ftp.sra.ebi.ac.uk/vol1/fastq/ERR036/ERR036104/ERR036104_1.fastq.gz -P $testdir
+wget ftp://ftp.sra.ebi.ac.uk/vol1/fastq/ERR036/ERR036104/ERR036104_2.fastq.gz -P $testdir
+
+echo -e "Done downloading.\n\n"
+
+for file in `ls $testdir/*` ; do
+    echo -e "Attempting to unzip $file..."
+    gunzip $file;
+    echo -e "Done unzipping $file.\n"
+done
+
+echo -e "Done downloading and extrating test read files."

tests/fastqs/.desc

@@ -0,0 +1 @@
+location of downloaded test fastq files