transform_bc.py missing?

[afvallejo]

Hi, Thank you very much for this amzing work, I was trying to use your pipeline, however seem like the transform_bc.py file is mising from the repository. Could you please let me know how can i get tha file? or how to format the BC for the input

best

Andres

[Psy-Fer]

Hello,

I'll add the file in when I get the chance tomorrow. But here is a quick copy/paste with my phone that should work.

import sys

filename = sys.argv[1]
header = int(sys.argv[2])

head = False
if header:
    head = True

count = 0
# first = '\t'.join(['index', 'fwd_bc', 'rev_bc', 'gene_num', 'UMI_num'])
first = '\t'.join(['index', 'fwd_bc', 'rev_bc'])
print first
with open(filename, 'r') as f:
    for l in f:
        if head:
            head = False
            continue
        count += 1
        l = l.strip('\r\n')
        l = l.strip('\r')
        l = l.strip('\n')
        l = l.split(',')
        l = [i.strip('"') for i in l]
        l[0] = l[0].split('-')[0]
        rev = []
        for i in l[0]:
            if i == 'A':
                rev.append('T')
            elif i == 'T':
                rev.append('A')
            elif i == 'G':
                rev.append('C')
            elif i == 'C':
                rev.append('G')
            else:
                print >> sys.stderr, "Something is wrong, try again", l
        out = ''.join(rev[::-1])
        # print '\t'.join([str(count), l[0], out, l[1], l[2]])
        print '\t'.join([str(count), l[0], out])

[afvallejo]

Many thanks James, I will try it best Andres

…

On Mon, 21 Jun 2021 at 11:17, James Ferguson ***@***.***> wrote: Hello, I'll add the file in when I get the chance tomorrow. But here is a quick copy/paste with my phone that should work. import sys filename = sys.argv[1] header = int(sys.argv[2]) head = False if header: head = True count = 0 # first = '\t'.join(['index', 'fwd_bc', 'rev_bc', 'gene_num', 'UMI_num']) first = '\t'.join(['index', 'fwd_bc', 'rev_bc']) print first with open(filename, 'r') as f: for l in f: if head: head = False continue count += 1 l = l.strip('\r\n') l = l.strip('\r') l = l.strip('\n') l = l.split(',') l = [i.strip('"') for i in l] l[0] = l[0].split('-')[0] rev = [] for i in l[0]: if i == 'A': rev.append('T') elif i == 'T': rev.append('A') elif i == 'G': rev.append('C') elif i == 'C': rev.append('G') else: print >> sys.stderr, "Something is wrong, try again", l out = ''.join(rev[::-1]) # print '\t'.join([str(count), l[0], out, l[1], l[2]]) print '\t'.join([str(count), l[0], out]) — You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub <#1 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AIVOOMRFF3MCBKB5QFJAHFLTT4GSJANCNFSM47BIPXTA> .

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[jkbenotmane]

What should be the input for this? The Barcodes from cellranger?
Best wishes

[Psy-Fer]

Hello,

This was built to accommodate the ever changing and bug ridden formats I was given from the illumina/cell ranger side of things.

But I'll upload a simplified version now, that takes a flat list of barcodes, for example, the input file would look like this:

AAACAACGAATAGTTC
AAACAAGTATCTCCCA
AAACAATCTACTAGCA
AAACACCAATAACTGC
AAACAGAGCGACTCCT
AAACAGCTTTCAGAAG
AAACAGGGTCTATATT
AAACAGTGTTCCTGGG
AAACATGGTGAGAGGA
AAACATTTCCCGGATT

And the output would be in the format needed for the demultiplexing.

James F.

[Psy-Fer]

Alright, so if you have barcodes that look like this in a file

filtered_pass_barcodes.txt

AAACCTGAGCACACAG
AAACCTGAGCGTAGTG
AAACCTGAGGCTACGA
AAACCTGCAAGACACG
AAACCTGCATGAACCT
AAACCTGGTTCGAATC
AAACGGGAGAGAGCTC
AAACGGGAGGTACTCT
AAACGGGAGTGTCCCG
AAACGGGTCTTTACAC

then you do

python barcode_transform.py filtered_pass_barcodes.txt > transformed_barcodes.tsv

Then you can use this file for the demultiplexing.