Some docs, simple test for FASTA loading

SamStudio8 · Aug 7, 2015 · df17caf · df17caf
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diff --git a/docs/advanced.rst b/docs/advanced.rst
@@ -1,6 +1,6 @@
-==============
-Advanced Usage
-==============
+======================
+Advanced Package Usage
+======================
 
 The following assumes basic Python programming experience (and
 that you have installed Goldilocks and familiarised yourself

diff --git a/docs/examples.rst b/docs/examples.rst
diff --git a/docs/index.rst b/docs/index.rst
@@ -13,7 +13,8 @@ Contents:
 
    readme
    installation
-   examples
+   cli
+   basic
    advanced
    exporting
    plotting

diff --git a/goldilocks/goldilocks.py b/goldilocks/goldilocks.py
@@ -193,14 +193,14 @@ def __init__(self, strategy, data, length, stride, is_pos=False, is_faidx=False,
         # Read data
         self.groups = data
         self.max_chr_max_len = None
-        self.fa_idx = {}
 
         for group in self.groups:
             if self.IS_FAI:
                 self.groups[group]["seq"] = {}
                 #TODO Close f
                 #TODO Assume for now records in each input faidx are ordered zipwise
                 for i, line in enumerate(open(self.groups[group]["idx"])):
+                    i += 1
                     self.groups[group]["seq"][i] = {}
                     fields = line.strip().split("\t")
 
@@ -297,7 +297,6 @@ def census_slide(work_q):
 
                 i = work_block["i"]
                 zeropos_start = work_block["s0"]
-                #onepos_end = work_block["e1"]
                 track = work_block["t"]
                 track_id = work_block["tid"]
                 group = work_block["g"]
@@ -362,7 +361,6 @@ def census_slide(work_q):
                         wwork_block = {
                             "i": region_i,
                             "s0": zeropos_start,
-                            #"e1": onepos_end,
                             "t": track,
                             "tid": track_id,
                             "g": group,
@@ -378,7 +376,6 @@ def census_slide(work_q):
         for _ in range(self.PROCESSES):
             p = Process(target=census_slide,
                         args=(work_queue,))
-            #p.daemon = True
             processes.append(p)
 
         for p in processes:

diff --git a/tests/dat/my_other_sequence.fa b/tests/dat/my_other_sequence.fa
@@ -0,0 +1,4 @@
+>hoothoot
+AAACCCNNNTTTAAACCCGGGNNNAAACCCGGGTTTNNNCCCGGGTTT
+>meowmeow
+GCGTNANNGANGGCTANTCTANAGCNNTTTCTNTNNGCANCANTTGNN
diff --git a/tests/dat/my_other_sequence.fa.fai b/tests/dat/my_other_sequence.fa.fai
@@ -0,0 +1,2 @@
+hoothoot	48	10	48	49
+meowmeow	48	69	48	49
diff --git a/tests/dat/my_sequence.fa b/tests/dat/my_sequence.fa
@@ -0,0 +1,4 @@
+>hoothoot
+AAACCCNNNTTTAAACCCGGGNNNAAACCCGGGTTTNNNCCCGGGTTT
+>meowmeow
+GCGTNANNGANGGCTANTCTANAGCNNTTTCTNTNNGCANCANTTGNN
diff --git a/tests/dat/my_sequence.fa.fai b/tests/dat/my_sequence.fa.fai
@@ -0,0 +1,2 @@
+hoothoot	48	10	48	49
+meowmeow	48	69	48	49