From 3c35250eb6394ec8d0e28e4391ec23f2223345c8 Mon Sep 17 00:00:00 2001
From: AndreaGuarracino
Date: Sat, 21 Nov 2020 21:21:36 +0100
Subject: generalized spoa workflow

---
 .../pangenome-generate/pangenome-generate_spoa.cwl      |  2 +-
 .../sort_fasta_by_quality_and_len.cwl                   |  2 ++
 .../pangenome-generate/sort_fasta_by_quality_and_len.py | 17 +++++++++++------
 3 files changed, 14 insertions(+), 7 deletions(-)

diff --git a/workflows/pangenome-generate/pangenome-generate_spoa.cwl b/workflows/pangenome-generate/pangenome-generate_spoa.cwl
index b623054..a46524a 100644
--- a/workflows/pangenome-generate/pangenome-generate_spoa.cwl
+++ b/workflows/pangenome-generate/pangenome-generate_spoa.cwl
@@ -42,7 +42,7 @@ outputs:
 #    outputSource: segment_components/colinear_components
 steps:
   dedup_and_sort_by_quality_and_len:
-    in: {readsFA: seqs}
+    in: {readsFA: seqs, reversed_sorting: 'true'}
     out: [sortedReadsFA, dups]
     run: sort_fasta_by_quality_and_len.cwl
   induceGraph:
diff --git a/workflows/pangenome-generate/sort_fasta_by_quality_and_len.cwl b/workflows/pangenome-generate/sort_fasta_by_quality_and_len.cwl
index 26c20e8..f8df786 100644
--- a/workflows/pangenome-generate/sort_fasta_by_quality_and_len.cwl
+++ b/workflows/pangenome-generate/sort_fasta_by_quality_and_len.cwl
@@ -5,6 +5,8 @@ hints:
     coresMin: 1
     ramMin: 3000
 inputs:
+    reversed_sorting:
+    inputBinding: {position: 3}
   readsFA:
     type: File
     inputBinding: {position: 2}
diff --git a/workflows/pangenome-generate/sort_fasta_by_quality_and_len.py b/workflows/pangenome-generate/sort_fasta_by_quality_and_len.py
index e836654..02ebf60 100644
--- a/workflows/pangenome-generate/sort_fasta_by_quality_and_len.py
+++ b/workflows/pangenome-generate/sort_fasta_by_quality_and_len.py
@@ -7,15 +7,17 @@ import os
 import sys
 import gzip
 
-#import xxhash # Faster library
+# import xxhash # Faster library
 import hashlib
 
+
 def open_gzipsafe(path_file):
     if path_file.endswith('.gz'):
-    	return gzip.open(path_file, 'rt')
+        return gzip.open(path_file, 'rt')
     else:
         return open(path_file)
 
+
 path_fasta = sys.argv[1]
 
 hash_to_count_and_headers_dict = {}
@@ -28,7 +30,7 @@ with open_gzipsafe(path_fasta) as f:
         header = fasta.strip('\n').split('\n')[0]
         sequence = ''.join(fasta.strip('\n').split('\n')[1:])
 
-        ##hash = xxhash.xxh64(sequence).hexdigest() # Faster library
+        # hash = xxhash.xxh64(sequence).hexdigest() # Faster library
         hash = hashlib.md5(sequence.encode('utf-8')).hexdigest()
 
         if hash not in hash_to_count_and_headers_dict:
@@ -38,15 +40,18 @@ with open_gzipsafe(path_fasta) as f:
             header_to_seq_dict[header] = sequence
 
             seq_len = len(sequence)
-            header_percCalledBases_seqLength_list.append([header, (seq_len - sequence.count('N'))/seq_len, seq_len])
+            header_percCalledBases_seqLength_list.append([header, (seq_len - sequence.count('N')) / seq_len, seq_len])
 
         hash_to_count_and_headers_dict[hash][0] += 1
         hash_to_count_and_headers_dict[hash][1].append(header)
 
-
 with open('dups.txt', 'w') as fw:
     for count, header_list in hash_to_count_and_headers_dict.values():
         fw.write('\t'.join([str(count), ', '.join(header_list)]) + '\n')
 
-for header, percCalledBases, seqLength_list in sorted(header_percCalledBases_seqLength_list, key=lambda x: (x[-2], x[-1]), reverse = True):
+reversed_sorting = True if len(sys.argv) > 2 and sys.argv[2].lower() == 'true' else False
+
+for header, percCalledBases, seqLength_list in sorted(
+        header_percCalledBases_seqLength_list, key=lambda x: (x[-2], x[-1]), reverse=reversed_sorting
+):
     sys.stdout.write('>{}\n{}\n'.format(header, header_to_seq_dict[header]))
-- 
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