# HG changeset patch
# User devteam
# Date 1727957515 0
# Node ID 5cbde03c110344653d68a790018f2f697d9997c5
# Parent  7d37cfda8e0080c7db796fc35001a30d7191bdfd
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/fasta_compute_length commit 9f0b8eb9fd7cf9e2513e7c822767153dbd4bc3b2

diff -r 7d37cfda8e00 -r 5cbde03c1103 fasta_compute_length.py
--- a/fasta_compute_length.py	Mon Mar 02 06:46:51 2020 -0500
+++ b/fasta_compute_length.py	Thu Oct 03 12:11:55 2024 +0000
@@ -1,10 +1,47 @@
 #!/usr/bin/env python
 """
-Uses fasta_to_len converter code.
+Input: fasta, int
+Output: tabular
+Return titles with lengths of corresponding seq
 """
 
 import sys
-from utils.fasta_to_len import compute_fasta_length
 
 
-compute_fasta_length(sys.argv[1], sys.argv[2], sys.argv[3], sys.argv[4] == 'id_only')
+def compute_fasta_length(fasta_file, out_file, keep_first_char, keep_first_word=False):
+    keep_first_char = int(keep_first_char)
+    fasta_title = ''
+    seq_len = 0
+
+    # number of char to keep in the title
+    if keep_first_char == 0:
+        keep_first_char = None
+    else:
+        keep_first_char += 1
+
+    first_entry = True
+    with open(fasta_file) as in_fh, open(out_file, 'w') as out_fh:
+        for line in in_fh:
+            line = line.strip()
+            if not line or line.startswith('#'):
+                continue
+            if line[0] == '>':
+                if first_entry is False:
+                    if keep_first_word:
+                        fasta_title = fasta_title.split()[0]
+                    out_fh.write("%s\t%d\n" % (fasta_title[1:keep_first_char], seq_len))
+                else:
+                    first_entry = False
+                fasta_title = line
+                seq_len = 0
+            else:
+                seq_len += len(line)
+
+        # last fasta-entry
+        if keep_first_word:
+            fasta_title = fasta_title.split()[0]
+        out_fh.write("%s\t%d\n" % (fasta_title[1:keep_first_char], seq_len))
+
+
+if __name__ == "__main__":
+    compute_fasta_length(sys.argv[1], sys.argv[2], sys.argv[3], sys.argv[4] == 'id_only')
diff -r 7d37cfda8e00 -r 5cbde03c1103 fasta_compute_length.xml
--- a/fasta_compute_length.xml	Mon Mar 02 06:46:51 2020 -0500
+++ b/fasta_compute_length.xml	Thu Oct 03 12:11:55 2024 +0000
@@ -1,8 +1,11 @@
-<tool id="fasta_compute_length" name="Compute sequence length" version="1.0.3" profile="16.04">
+<tool id="fasta_compute_length" name="Compute sequence length" version="1.0.4" profile="22.04">
     <description></description>
     <requirements>
-        <requirement type="package" version="3.7">python</requirement>
+        <requirement type="package" version="3.12">python</requirement>
     </requirements>
+    <required_files>
+        <include path="fasta_compute_length.py"/>
+    </required_files>
     <command>
     #if $ref.ref_source == 'dbkey':
         cp '${ref.index.fields.len_path}' '$output'
diff -r 7d37cfda8e00 -r 5cbde03c1103 utils/__init__.py
diff -r 7d37cfda8e00 -r 5cbde03c1103 utils/fasta_to_len.py
--- a/utils/fasta_to_len.py	Mon Mar 02 06:46:51 2020 -0500
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,47 +0,0 @@
-#!/usr/bin/env python
-"""
-Input: fasta, int
-Output: tabular
-Return titles with lengths of corresponding seq
-"""
-
-import sys
-
-
-def compute_fasta_length(fasta_file, out_file, keep_first_char, keep_first_word=False):
-    keep_first_char = int(keep_first_char)
-    fasta_title = ''
-    seq_len = 0
-
-    # number of char to keep in the title
-    if keep_first_char == 0:
-        keep_first_char = None
-    else:
-        keep_first_char += 1
-
-    first_entry = True
-    with open(fasta_file) as in_fh, open(out_file, 'w') as out_fh:
-        for line in in_fh:
-            line = line.strip()
-            if not line or line.startswith('#'):
-                continue
-            if line[0] == '>':
-                if first_entry is False:
-                    if keep_first_word:
-                        fasta_title = fasta_title.split()[0]
-                    out_fh.write("%s\t%d\n" % (fasta_title[1:keep_first_char], seq_len))
-                else:
-                    first_entry = False
-                fasta_title = line
-                seq_len = 0
-            else:
-                seq_len += len(line)
-
-        # last fasta-entry
-        if keep_first_word:
-            fasta_title = fasta_title.split()[0]
-        out_fh.write("%s\t%d\n" % (fasta_title[1:keep_first_char], seq_len))
-
-
-if __name__ == "__main__":
-    compute_fasta_length(sys.argv[1], sys.argv[2], sys.argv[3], True)