Reorganize imports

Author: saketkc

ribotricer/bam.py

@@ -13,6 +13,7 @@
 # MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
 # GNU General Public License for more details.
 
+from .common import is_read_uniq_mapping
 from collections import Counter
 from collections import defaultdict
 
@@ -21,8 +22,6 @@
 
 tqdm.pandas()
 
-from .common import is_read_uniq_mapping
-
 
 def split_bam(bam_path, protocol, prefix, read_lengths=None):
     """Split bam by read length and strand

ribotricer/common.py

@@ -113,7 +113,7 @@ def _clean_input(comma_string):
 
 def collapse_coverage_to_codon(coverage):
     """Collapse nucleotide level coverage to codon level.
-  
+
   Parameters
   ----------
   coverage: list

ribotricer/count_orfs.py

@@ -88,7 +88,7 @@ def count_orfs_codon(
 ):
     """
     Create genewise codon summaries  
-    
+
     Parameters
     ----------
     ribotricer_index: str

ribotricer/detect_orfs.py

@@ -13,6 +13,23 @@
 # MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
 # GNU General Public License for more details.
 
+from .statistics import coherence
+from .plotting import plot_metagene
+from .plotting import plot_read_lengths
+from .orf import ORF
+from .metagene import align_metagenes
+from .metagene import metagene_coverage
+from .infer_protocol import infer_protocol
+from .const import MINIMUM_DENSITY_OVER_ORF
+from .const import MINIMUM_READS_PER_CODON
+from .const import MINIMUM_VALID_CODONS_RATIO
+from .const import MINIMUM_VALID_CODONS
+from .const import CUTOFF
+from .common import parent_dir
+from .common import mkdir_p
+from .common import collapse_coverage_to_codon
+from .bam import split_bam
+from quicksect import Interval, IntervalTree
 from collections import Counter
 from collections import defaultdict
 import datetime
@@ -21,24 +38,7 @@
 from tqdm.autonotebook import tqdm
 
 tqdm.pandas()
-from quicksect import Interval, IntervalTree
 
-from .bam import split_bam
-from .common import collapse_coverage_to_codon
-from .common import mkdir_p
-from .common import parent_dir
-from .const import CUTOFF
-from .const import MINIMUM_VALID_CODONS
-from .const import MINIMUM_VALID_CODONS_RATIO
-from .const import MINIMUM_READS_PER_CODON
-from .const import MINIMUM_DENSITY_OVER_ORF
-from .infer_protocol import infer_protocol
-from .metagene import metagene_coverage
-from .metagene import align_metagenes
-from .orf import ORF
-from .plotting import plot_read_lengths
-from .plotting import plot_metagene
-from .statistics import coherence
 
 # Required for IntervalTree
 STRAND_TO_NUM = {"+": 1, "-": -1}

ribotricer/infer_protocol.py

@@ -41,7 +41,7 @@ def infer_protocol(bam, gene_interval_tree, prefix, n_reads=20000):
     -------
     protocol: string
               forward/reverse
-    
+
     The strategy to do this is simple: keep a track
     of mapped reads and their strand and then tally 
     if the location of their mapping has a gene defined
@@ -52,7 +52,7 @@ def infer_protocol(bam, gene_interval_tree, prefix, n_reads=20000):
     Higher proportion of (++, --) implies forward protocol
     Higher proportion of (+-, -+) implies reverse protocol
     Equal proportion of the above two scenairos implies unstranded protocol.
-    
+
     """
     iteration = 0
     bam = pysam.AlignmentFile(bam, "rb")

ribotricer/learn_cutoff.py

@@ -166,8 +166,8 @@ def determine_cutoff_bam(
                            List of 'yes/no/reverse' 
   rna_stranded_protocols: list
                            List of 'yes/no/reverse' 
-  
-  
+
+
   Returns
   -------
   cutoff: float

ribotricer/metagene.py

@@ -13,6 +13,9 @@
 # MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
 # GNU General Public License for more details.
 
+from .statistics import coherence
+from .interval import Interval
+from .const import CUTOFF, TYPICAL_OFFSET
 import sys
 from collections import Counter, OrderedDict
 
@@ -22,10 +25,6 @@
 
 tqdm.pandas()
 
-from .const import CUTOFF, TYPICAL_OFFSET
-from .interval import Interval
-from .statistics import coherence
-
 
 def next_genome_pos(ivs, max_positions, leader, trailer, reverse=False):
     if len(ivs) == 0:

ribotricer/orf_seq.py

@@ -13,17 +13,15 @@
 # MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
 # GNU General Public License for more details.
 
+from .fasta import FastaReader
+from .interval import Interval
 import pandas as pd
 import sys
 from tqdm.autonotebook import tqdm
 
 tqdm.pandas()
 
 
-from .interval import Interval
-from .fasta import FastaReader
-
-
 def translate_nt_to_aa(seq):
     codon_table = {
         "ATA": "I",
@@ -108,7 +106,7 @@ def translate_nt_to_aa(seq):
 
 def orf_seq(ribotricer_index, genome_fasta, saveto, translate=False):
     """Generate sequence for ribotricer annotation.
-  
+
   Parameters
   -----------
 

ribotricer/prepare_orfs.py

@@ -34,7 +34,7 @@ def tracks_to_ivs(tracks):
     ----------
     tracks: List[GTFTrack]
             list of gtf tracks
-    
+
     Returns
     -------
     intervals: List[Interval]
@@ -228,7 +228,7 @@ def check_orf_type(orf, cds_orfs):
     otype: str
            Type of the candidate ORF
 
-    This method uses a fail-sast strategy 
+    This method uses a fail-fast strategy
     and hence multiple returns. 
     """
     if orf.gid not in cds_orfs:

ribotricer/utils.py

@@ -357,7 +357,7 @@ def _nucleotide_to_codon_profile(profile):
 
 def summarize_profile_to_codon_level(detected_orfs, saveto):
     """Collapse nucleotide level profiles in ribotricer to codon leve.
-  
+
   Parameters
   ----------
   ribotricer_output: string
@@ -407,7 +407,7 @@ def translate(seq):
 
 def learn_ribotricer_cutoff(roc_input_file):
     """Learn ribotricer phase score cutoff 
-  
+
   Parameters
   ----------
   roc_input_file: str