CI
637ea108cd
Build pipeline: viash-hub.rnaseq.v0.3-6gfl7
Source commit: e21130ff7a
Source message: Bump version to v0.3.0
81 lines
2.8 KiB
Python
81 lines
2.8 KiB
Python
#!/usr/bin/env python3
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"""
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Read a custom fasta file and create a custom GTF containing each entry
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"""
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from itertools import groupby
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import logging
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import os
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import sys
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## VIASH START
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par = {
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"fasta": "testData/minimal_test/reference/genome.fasta",
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"gtf": "testData/minimal_test/reference/genes.gtf",
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"additional_fasta": "testData/minimal_test/reference/gfp.fa.gz",
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"biotype": "gene_biotype",
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"fasta_output": "genome_gfp.fasta",
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"gtf_output": "genome_gfp.gtf",
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}
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meta = {
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"functionality_name": "cat_additonal_fasta"
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}
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## VIASH END
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def fasta_iter(fasta_name):
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"""
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modified from Brent Pedersen
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Correct Way To Parse A Fasta File In Python
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given a fasta file. yield tuples of header, sequence
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Fasta iterator from https://www.biostars.org/p/710/#120760
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"""
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with open(fasta_name) as fh:
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# ditch the boolean (x[0]) and just keep the header or sequence since
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# we know they alternate.
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faiter = (x[1] for x in groupby(fh, lambda line: line[0] == ">"))
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for header in faiter:
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# drop the ">"
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headerStr = header.__next__()[1:].strip()
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# join all sequence lines to one.
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seq = "".join(s.strip() for s in faiter.__next__())
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yield (headerStr, seq)
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def fasta2gtf(fasta, output, biotype):
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fiter = fasta_iter(fasta)
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# GTF output lines
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lines = []
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attributes = 'exon_id "{name}.1"; exon_number "1";{biotype} gene_id "{name}_gene"; gene_name "{name}_gene"; gene_source "custom"; transcript_id "{name}_gene"; transcript_name "{name}_gene";\n'
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line_template = "{name}\ttransgene\texon\t1\t{length}\t.\t+\t.\t" + attributes
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for ff in fiter:
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name, seq = ff
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# Use first ID as separated by spaces as the "sequence name"
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# (equivalent to "chromosome" in other cases)
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seqname = name.split()[0]
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# Remove all spaces
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name = seqname.replace(" ", "_")
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length = len(seq)
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biotype_attr = ""
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if biotype:
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biotype_attr = f' {biotype} "transgene";'
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line = line_template.format(name=name, length=length, biotype=biotype_attr)
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lines.append(line)
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with open(output, "w") as f:
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f.write("".join(lines))
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add_name = os.path.basename(par['additional_fasta'])
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output = os.path.splitext(add_name)[0] + ".gtf"
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fasta2gtf(par['additional_fasta'], output, par['biotype'])
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with open(par['fasta'], 'r') as f1:
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content1 = f1.read()
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with open(par['additional_fasta'], 'r') as f2:
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content2 = f2.read()
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with open(par['fasta_output'], 'w') as f_out:
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f_out.write(content1 + content2)
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with open(par['gtf'], 'r') as g1:
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g_content1 = g1.read()
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with open(output, 'r') as g2:
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g_content2 = g2.read()
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with open(par['gtf_output'], 'w') as g_out:
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g_out.write(g_content1 + g_content2)
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