Merge pull request #5 from prophyle/travis

Fix testing using Travis

.gitignore

@@ -1,4 +1,5 @@
 prophasm
+README.html
 
 _*
 

.travis.yml

@@ -1,7 +1,6 @@
 language: cpp
 
 cache:
-  - brew
   - apt: true
 
 matrix:
@@ -13,23 +12,12 @@ matrix:
       install:
         - sudo add-apt-repository ppa:ubuntu-toolchain-r/test -y
         - sudo apt-get update
-        - sudo apt-get install g++-4.8 zlib1g-dev
-        - sudo update-alternatives --install /usr/bin/g++ g++ /usr/bin/g++-4.8 90
-        - sudo update-alternatives --install /usr/bin/gcc gcc /usr/bin/gcc-4.8 90
+        - sudo apt-get install zlib1g-dev
 
     - os: osx
       compiler: clang-3.7
-      before_install:
-        - brew update
-        - brew tap homebrew/versions
-      install:
-        - export CXX="clang++-3.7" CC="clang-3.7"
-        - brew install llvm37
+
 
 script:
   - make test
 
-cache:
-  directories:
-  - $HOME/miniconda
-

Makefile

@@ -1,4 +1,4 @@
-.PHONY: all help clean test prophasm
+.PHONY: all help clean test prophasm readme
 
 SHELL=/usr/bin/env bash -eo pipefail
 
@@ -10,12 +10,15 @@ prophasm:
 	$(MAKE) -C src
 
 help: ## Print help message
-	    @echo "$$(grep -hE '^\S+:.*##' $(MAKEFILE_LIST) | sed -e 's/:.*##\s*/:/' -e 's/^\(.\+\):\(.*\)/\\x1b[36m\1\\x1b[m:\2/' | column -c2 -t -s : | sort)"
+	@echo "$$(grep -hE '^\S+:.*##' $(MAKEFILE_LIST) | sed -e 's/:.*##\s*/:/' -e 's/^\(.\+\):\(.*\)/\\x1b[36m\1\\x1b[m:\2/' | column -c2 -t -s : | sort)"
 
 test:
 	$(MAKE) -C tests
 
+readme:
+	 md2html README.md > README.html
+
 clean: ## Clean
 	$(MAKE) -C src clean
 	$(MAKE) -C tests clean
-	rm -f prophasm
+	rm -f prophasm README.html

tests/tools/verify_output.py

@@ -1,14 +1,15 @@
-#! /usr/bin/env python3
-"""A program to verify output of prophyle-assembler.
+#! /usr/bin/env python2.7
+
+"""A program to verify output of prophasm.
 
 Author: Karel Brinda <[email protected]>
 
 Licence: MIT
 """
 
-import sys
+import collections
 import re
-from Bio import SeqIO
+import sys
 
 in1_fn = sys.argv[1]
 in2_fn = sys.argv[2]
@@ -26,6 +27,24 @@
     "T": "A",
 }
 
+def load_fasta(fn):
+    d=collections.defaultdict(list)
+    with open(fn) as f:
+        seqname="_"
+        for line in f:
+            line=line.strip()
+            if len(line)==0:
+                continue
+            if line[0]==">":
+                seqname, _, _ = line.partition(" ")
+            else:
+                d[seqname].append(line)
+    dd={}
+    for k in d:
+        dd[k]="".join(d[k])
+
+    return dd
+
 
 def reverse_complement_str(dna):
     reverse_complement = "".join([comp_dict[x] for x in dna[::-1]])
@@ -37,9 +56,9 @@ def get_canonical_kmers_from_fasta(fasta_fn, k):
 
     reg_splitting = re.compile("[^ACGT]")
     set_of_kmers = set()
-    fasta_sequences = SeqIO.parse(fasta_fn, 'fasta')
-    for fasta_seq in fasta_sequences:
-        name, sequence = fasta_seq.id, str(fasta_seq.seq).upper()
+    fasta_sequences = load_fasta(fasta_fn)
+    for name in fasta_sequences:
+        sequence = fasta_sequences[name].upper()
         sequences_ok = reg_splitting.split(sequence)
         for seq in sequences_ok:
             for i in range(len(seq) - k + 1):