From 97f4fde6f4c8808960c748b71cf35393e3d08813 Mon Sep 17 00:00:00 2001
From: Jonathan Dursi <jonathan@dursi.ca>
Date: Thu, 5 Nov 2015 17:21:56 -0500
Subject: [PATCH 1/2] Modify readtofasta to work with both versions of fast5
 files

---
 readtofasta.py | 91 ++++++++++++++++++++++++++++----------------------
 1 file changed, 52 insertions(+), 39 deletions(-)

diff --git a/readtofasta.py b/readtofasta.py
index ab09c5a..dcdf8b0 100755
--- a/readtofasta.py
+++ b/readtofasta.py
@@ -5,63 +5,76 @@
 import sys
 import os
 
-def readevents(filename):
-    events = []
-    kmers = []
-    sds = []
-    f = h5py.File(filename,"r")
+def readfasta(filename, calls="2D"):
+    """
+    Reads the fastq from basecalled read, returns label and sequence
+    """
+    with h5py.File(filename, "r") as f:
+        calls_group = "BaseCalled_"+calls
+        eventpath = "/Analyses/Basecall_2D_000/"+calls_group
+        if not eventpath in f:
+            eventpath = "/Analyses/Basecall_1D_000/"+calls_group
 
-    calls = "BaseCalled_2D"
-    if not "Analyses" in f or not "Basecall_2D_000" in f["Analyses"] or not calls in f["Analyses"]["Basecall_2D_000"]:
-        raise KeyError("Not present in HDF5 file")
+        if not "Analyses" in f or not "Basecall_2D_000" in f["Analyses"] or not calls_group in f["Analyses"]["Basecall_2D_000"]:
+            raise KeyError("Not present in HDF5 file")
+        if not "Fastq" in f[eventpath]:
+            raise KeyError("Fastq not found in HDF5 file")
+        data = f["Analyses"]["Basecall_2D_000"][calls_group]["Fastq"]
 
-    if not "Fastq" in f["Analyses"]["Basecall_2D_000"][calls]:
-        raise KeyError("Fastq not found in HDF5 file")
-    data = f["Analyses"]["Basecall_2D_000"][calls]["Fastq"]
-    lines =  data[()].splitlines()
-    seq = lines[1].decode('utf-8')
-    label = lines[0][1:].strip()
-    labelSuffix = "_twodirections" 
-    label = label+labelSuffix
-    label = label.decode('utf-8')
+        lines = data[()].splitlines()
+
+        seq = lines[1].decode('utf-8')
+
+        label = lines[0][1:].strip()
+        label_suffix = "_twodirections" if calls == "2D" else calls
+        label = label+label_suffix
+        label = label.decode('utf-8')
 
     return label, seq
 
+def build_filelist(filenames):
+    """ If given a directory, descend into directory and generate 
+        list of files (but do not descend into subdirectories)."""
+    file_list = []
+    for filename in filenames:
+        if os.path.isfile(filename):
+            file_list.append(filename)
+        elif os.path.isdir(filename):
+            for f in os.listdir(filename):
+                pathname = os.path.join(filename, f)
+                if os.path.isfile(pathname) and pathname.endswith('.fast5'):
+                    file_list.append(pathname)
+    return file_list
+
 if __name__ == "__main__":
     parser = argparse.ArgumentParser()
 
-    parser.add_argument('infile', type=str)
-    parser.add_argument('-o','--output', type=argparse.FileType('w'), default=sys.stdout, help="Specify output file (default:stdout)") 
-    parser.add_argument('-l','--linelength', type=int, default=60)
+    parser.add_argument('infile', nargs="+", type=str)
+    parser.add_argument('-l', '--linelength', type=int, default=60)
+    parser.add_argument('-o', '--output', type=argparse.FileType('w'),
+                            default=sys.stdout,
+                            help="Specify output file (default:stdout)")
 
     args = parser.parse_args()
 
-    try:
-        if os.path.isfile(args.infile):
-            label, sequence = readevents(args.infile)
-            label += " "+arg.infile
-            seqs = [(label, seq)]
-        elif os.path.isdir(args.infile):
-            seqs = []
-            for f in os.listdir(args.infile):
-               pathname = os.path.join(args.infile, f)
-               if os.path.isfile(pathname) and pathname.endswith('.fast5'):
-                   label, sequence = readevents(pathname)
-                   seqs.append((label+" "+pathname, sequence))
-        else:
-            raise ValueError("Path is not a directory or file: "+args.infile)
-    except KeyError:
-        sys.exit(1)
+    files = build_filelist(args.infile)
+    seqs = []
+    for infile in files:
+        try:
+            label, sequence = readfasta(infile)
+            seqs.append((label+" "+infile, sequence))
+        except:
+            continue
 
     outf = args.output
-    infname = args.infile
     llen = args.linelength
 
     for label, sequence in seqs:
         print(">"+label, file=outf)
-        for i in range( len(sequence)//llen ):
+        nchunks = (len(sequence)+llen-1)/llen
+        for i in range(nchunks):
             lstart = i*llen
             lend = min(lstart + llen, len(sequence))
-            print( sequence[lstart:lend], file=outf )
+            print(sequence[lstart:lend], file=outf)
 
     sys.exit(0)

From 52661fbefd905c4dd0a04aa6a7cfb8aaf16ba8bb Mon Sep 17 00:00:00 2001
From: Jonathan Dursi <jonathan@dursi.ca>
Date: Thu, 5 Nov 2015 17:24:10 -0500
Subject: [PATCH 2/2] Explicitly integer division

---
 readtofasta.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/readtofasta.py b/readtofasta.py
index dcdf8b0..b1cc2b4 100755
--- a/readtofasta.py
+++ b/readtofasta.py
@@ -71,7 +71,7 @@ def build_filelist(filenames):
 
     for label, sequence in seqs:
         print(">"+label, file=outf)
-        nchunks = (len(sequence)+llen-1)/llen
+        nchunks = (len(sequence)+llen-1)//llen
         for i in range(nchunks):
             lstart = i*llen
             lend = min(lstart + llen, len(sequence))