support of multiple width values 1 per fasta

README.md

@@ -1,2 +1,2 @@
-# biomisc [![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.5795517.svg)](https://doi.org/10.5281/zenodo.5795517)
+# biomisc 
 collection of  miscellaneous command line bioinformatic scripts(see the wiki page for documentation and depedences) 

fasta_manipulation/fasta_formatter.py

@@ -2,13 +2,15 @@
 import os
 import argparse
 from Bio import SeqIO
+import pandas as pd
 import sys
 # input parameters
 ap = argparse.ArgumentParser(description="changes the width of sequences line in 1 or many FASTA files")
 ap.add_argument("-in", "--input", required=False, help="input fasta file")
+ap.add_argument("-txt", "--txt", required=False, help="input txt file with 2 columns 1) file name (without extension), 2) width")
 ap.add_argument("-out", "--output", required=False, help="output fasta file")
 ap.add_argument("-width", "--width", required=False, type=int, default=80, help="number of characters per line. Default 80")
-ap.add_argument("-pro", "--program", required=False, type=int, default=1, help="program to choose. 1) one input/output fasta file, 2) many input/output fasta files. Default is 1")
+ap.add_argument("-pro", "--program", required=False, type=int, default=1, help="program to choose. 1) one input/output fasta file, 2) many input/output fasta files, 3) .txt file with fasta file names and width for each file. Default is 1")
 args = vars(ap.parse_args())
 # main
 # create function to split the input sequence based on a specific number of characters
@@ -21,7 +23,7 @@ def split_every_width(s,w): return [s[i:i+w] for i in range(0,len(s),w)]
             print(">"+record.id)
             print('\n'.join(split_every_width(str(record.seq), args['width']))) # add characters in new line after the number of characters surpasses the input width 
     sys.stdout.close()
-else:
+elif args['program'] == 2:
     # import each fasta file from the working directory
     for filename in sorted(os.listdir(str(os.getcwd()))):
         if filename.endswith(".fa") or filename.endswith(".fasta"):
@@ -31,4 +33,19 @@ def split_every_width(s,w): return [s[i:i+w] for i in range(0,len(s),w)]
                     print(">"+record.id)
                     print('\n'.join(split_every_width(str(record.seq), args['width']))) # add characters in new line after the number of characters surpasses the input width 
             sys.stdout.close()
+else:
+    df = pd.read_csv(args['txt'], header=None, sep="\t")
+    # select ids and widths columns, convert to lists
+    headers = df.iloc[:,0].values.tolist()
+    widths = df.iloc[:,1].values.tolist()
+    # iter elements on pairs to export to fasta
+    for (a,b) in zip(headers, widths):
+        # export to new fasta files with the user imported width value
+        sys.stdout = open(''.join([str(a),"_","w",str(b),".fasta"]), 'a')
+        for record in SeqIO.parse(''.join([str(a),".fasta"]),'fasta'):
+            print(">"+record.id)
+            print('\n'.join(split_every_width(str(record.seq), int(b)))) # add characters in new line after the number of characters surpasses the input width 
+        sys.stdout.close()
+
+