Mercurial > repos > ebi-gxa > salmon_kallisto_mtx_to_10x

annotate salmonKallistoMtxTo10x.py @ 2:40f7a3d18cf4 draft

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planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/salmon-kallisto-mtx-to-10x/.shed.yml commit 3fbbd818012005da4513271beda50df98d3c1cde-dirty
author ebi-gxa
date Fri, 08 Nov 2019 08:32:04 -0500
parents fe0fd27aba50
children 60fa6080f86f
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fe0fd27aba50 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/salmon-kallisto-mtx-to-10x/.shed.yml commit 023431ca119829efbde33c94d54e051fac24a1d5
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1 #!/usr/bin/env python
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3 # Alevin and Kallisto currently output MTX files and gene labels in a manner
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4 # inconsistent with the old-style 10X conventions. In both cases the matrix
fe0fd27aba50 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/salmon-kallisto-mtx-to-10x/.shed.yml commit 023431ca119829efbde33c94d54e051fac24a1d5
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5 # must be transposed, and gene indentifier columns duplicated
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6
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7 from __future__ import print_function
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8 from collections import defaultdict
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9 from struct import Struct
fe0fd27aba50 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/salmon-kallisto-mtx-to-10x/.shed.yml commit 023431ca119829efbde33c94d54e051fac24a1d5
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10 import pandas as pd
fe0fd27aba50 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/salmon-kallisto-mtx-to-10x/.shed.yml commit 023431ca119829efbde33c94d54e051fac24a1d5
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11 import gzip
fe0fd27aba50 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/salmon-kallisto-mtx-to-10x/.shed.yml commit 023431ca119829efbde33c94d54e051fac24a1d5
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12 import sys
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13 import os
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14 from scipy.io import mmread,mmwrite
fe0fd27aba50 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/salmon-kallisto-mtx-to-10x/.shed.yml commit 023431ca119829efbde33c94d54e051fac24a1d5
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15 from scipy.sparse import *
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16 from shutil import copyfile
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17 import pathlib
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18 import numpy as np
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19 import argparse
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21 parser = argparse.ArgumentParser(description='Convert Alevin or Kallisto MTX outputs to 10X .mtx.')
fe0fd27aba50 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/salmon-kallisto-mtx-to-10x/.shed.yml commit 023431ca119829efbde33c94d54e051fac24a1d5
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22 parser.add_argument('mtx', help = 'MTX-format matrix file')
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23 parser.add_argument('genes', help = 'Gene names text file')
fe0fd27aba50 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/salmon-kallisto-mtx-to-10x/.shed.yml commit 023431ca119829efbde33c94d54e051fac24a1d5
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24 parser.add_argument('barcodes', help = 'Barcodes file')
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25 parser.add_argument('mtx_out', help = 'Output directory for converted results')
fe0fd27aba50 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/salmon-kallisto-mtx-to-10x/.shed.yml commit 023431ca119829efbde33c94d54e051fac24a1d5
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26 parser.add_argument('--cell_prefix', dest='cell_prefix', default='', help = 'Prefix to apply to cell barcodes')
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27 args = parser.parse_args()
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29 quant_file=args.mtx
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30 cb_file=args.barcodes
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31 gene_file=args.genes
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32 mtx_out=args.mtx_out
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33 cell_prefix=args.cell_prefix
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35 if not os.path.exists(quant_file):
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36 print("quant file {} doesn't exist".format( quant_file ))
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37 sys.exit(1)
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39 if not os.path.exists(cb_file):
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40 print("cell barcodes file: {} doesn't exist".format( cb_file ))
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41 sys.exit(1)
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43 if not os.path.exists(gene_file):
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44 print("genes file: {} doesn't exist".format( gene_file))
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45 sys.exit(1)
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47 # Read gene and cell labels, apply cell prefix
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49 cb_names = [cell_prefix + s for s in pd.read_csv(cb_file, header=None)[0].values]
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50 gene_names = pd.read_csv(gene_file, header=None)[0].values
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51 umi_counts = mmread( quant_file )
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53 # Write outputs to a .mtx file readable by tools expecting 10X outputs.
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54 # Barcodes file works as-is, genes need to be two-column, duplicating the
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55 # identifiers. Matrix itself needs to have genes by row, so we transpose.
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57 pathlib.Path(mtx_out).mkdir(parents=True, exist_ok=True)
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58 mmwrite('%s/matrix.mtx' % mtx_out, umi_counts.transpose())
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60 genes_frame = pd.DataFrame([ gene_names, gene_names]).transpose()
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61 genes_frame.to_csv(path_or_buf='%s/genes.tsv' % mtx_out, index=False, sep="\t", header = False)
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63 with open('%s/barcodes.tsv' % mtx_out, 'w') as f:
fe0fd27aba50 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/salmon-kallisto-mtx-to-10x/.shed.yml commit 023431ca119829efbde33c94d54e051fac24a1d5
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64 f.write("\n".join(cb_names))
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65 f.write("\n")