v0.2

Bug fix (peptide sequences were not input in the reverse order, which resulted in short contigs)

Re-arranged the repo

README.md

@@ -2,7 +2,7 @@
 
 # PASS
 ## Proteome Assembler with Short Sequence peptide (PASS)
-## PASS v0.1 Rene L. Warren, 2015
+## PASS v0.2 Rene L. Warren, 2015-2018
 ## email: warrenlr at gmail.com
 
 
@@ -18,25 +18,31 @@ TRY IT OUT BY SIMPLY RUNNING:
 </pre>
 
 
+### What's new in v0.2 ?
+-----------
+
+Bug fix (peptide sequences were not input in the reverse order, which resulted in short contigs)
+
+
 ### Implementation and requirements
--------------------------------
+-----------
 
 PASS is implemented in PERL and runs on any OS where PERL is installed.
 
 
 ### Install
--------
+-----------
 
 Download the tar ball, gunzip and extract the files on your system using:
 
-gunzip pass_v0-1.tar.gz
-tar -xvf pass_v0-1.tar
+gunzip pass_v0-2.tar.gz
+tar -xvf pass_v0-2.tar
 
 Change the shebang line of PASS to point to the version of perl installed on your system and you're good to go.
 
 
 ### Documentation
--------------
+-----------
 
 Refer to the PASS.readme file on how to run PASS
 
@@ -56,11 +62,12 @@ Warren RL, Sutton GG, Jones SJM, Holt RA.  2007.  Assembling millions of short D
 
 
 ### Running PASS
-------------
+-----------
+
 <pre>
 e.g. ../PASS -f AAreadsLEN6-COV30.fa -m 4 -w 1 -o 1 -r 0.51 
 
-Usage: ./PASS [v0.1 peptide assembly]
+Usage: ./PASS [v0.2 peptide assembly]
 -f  File containing all the peptide reads (required)
 -w  Minimum depth of coverage allowed for contigs (e.g. -w 1 = process all reads, required)
     *The assembly will stop when 50+ contigs with coverage < -w have been seen.*
@@ -81,15 +88,18 @@ Usage: ./PASS [v0.1 peptide assembly]
 </pre>
 
 ### Test data
----------
+-----------
 
-Go to ./test
+Go to the test directory and execute the runme.sh bash script
 
-Run: ./runme.sh
+<pre>
+cd ./test
+./runme.sh
+</pre>
 
 
 ### How it works
-------------
+-----------
 
 A. Sequence Overlap
 
@@ -121,7 +131,7 @@ PASS doesn't not constrain the k-mer length derived from a target sequence for i
 
 
 ### Input sequences
----------------
+-----------
 
 amino acid sequences can be in lower caps as well
 <pre>
@@ -155,7 +165,7 @@ General points:
 
 
 ### Output files
-------------
+-----------
 
 Output file | Description
 ---|---
@@ -173,7 +183,7 @@ Output file (-c 1*) | Description
 
 
 #### Understanding the .contigs fasta header
----------------------------------------
+-----------
 
 e.g.
 <pre>
@@ -191,7 +201,7 @@ C = T / G
 
 
 #### Understanding the .coverage.csv file
-------------------------------------
+-----------
 
 e.g.
 <pre>
@@ -202,7 +212,7 @@ Each number represents the number of reads covering that amino acid at that posi
 
 
 #### Understanding the .readposition file
-------------------------------------
+-----------
 
 e.g.
 <pre>
@@ -224,16 +234,16 @@ In this order: read name [template th -p 1 :: name followed with 1 or 2, corresp
 
 
 #### PASS does not
---------------
+-----------
 
 1. Take into consideration quality scores.  It is up to the user to process the sequence data before assembly.
 2. Consider sequence read having any character other than A,R,N,D,C,Q,E,G,H,I,L,K,M,F,P,S,T,W,Y,V and will skip these reads entirely while reading the fasta file. 
 
 
 ### License
--------
+-----------
 
-PASS Copyright (c) 2015 Rene Warren.  All rights reserved.
+PASS Copyright (c) 2015-2018 Rene Warren.  All rights reserved.
 
 This program is free software; you can redistribute it and/or
 modify it under the terms of the GNU General Public License