From 782dd657b2af206f589480e869206f071ec61968 Mon Sep 17 00:00:00 2001 From: Foivos Gypas Date: Wed, 7 Oct 2020 14:22:28 +0200 Subject: [PATCH] Add option to estimate TPMs based on different transcript/gene lengths per sample. Changed tests from genes to transcripts. Add tests for the zpca functions. Update documentation. (#7) --- README.md | 9 +- scripts/zpca | 21 +- setup.py | 2 +- test_data/gene_expression.tsv | 33975 ------- test_data/gene_length.tsv | 33975 ------- test_data/transcripts_counts.tsv | 133225 +++++++++++++++++++++++++++ test_data/transcripts_length.tsv | 133225 +++++++++++++++++++++++++++ test_data/transcripts_lengths.tsv | 133225 +++++++++++++++++++++++++++ test_data/transcripts_tpm.tsv | 133225 +++++++++++++++++++++++++++ tests/test.py | 77 + zpca/zpca.py | 21 + 11 files changed, 533024 insertions(+), 67956 deletions(-) delete mode 100644 test_data/gene_expression.tsv delete mode 100644 test_data/gene_length.tsv create mode 100644 test_data/transcripts_counts.tsv create mode 100644 test_data/transcripts_length.tsv create mode 100644 test_data/transcripts_lengths.tsv create mode 100644 test_data/transcripts_tpm.tsv diff --git a/README.md b/README.md index 4353187..693ab20 100644 --- a/README.md +++ b/README.md @@ -31,7 +31,13 @@ Perform PCA based on an expression matrix (rows are genes/transcripts, columns a optional arguments: -h, --help show this help message and exit --counts FILE Counts table (tsv). The first column should contain the gene/transcript id. The other columns should contain the counts for each sample. - --lengths FILE Table of feature lengths (tsv). The first column should contain the gene/transcript id. The second column should contain the corresponding lengths + --lengths FILE Table of feature lengths (tsv). + The file can have two types of formats. + First option: The first column should contain the gene/transcript id. + The second column should contain the corresponding lengths + Second option: The first column should contain the gene/transcript id. + The rest of the columns should contain the gene/transcript lengths for each of the samples + Note that the sample names should be the same the sample names of the counts. --pseudocount PSEUDOCOUNT Pseudocount to add in the count table. Default: 1 --tpm-filter TPM_FILTER @@ -39,6 +45,7 @@ optional arguments: --filter-not-expressed Filter not expressed genes/transcripts (0 counts for all samples). --out DIRECTORY Output directory + -v, --verbose Verbose ``` # Docker diff --git a/scripts/zpca b/scripts/zpca index fc70e9b..df921ef 100755 --- a/scripts/zpca +++ b/scripts/zpca @@ -12,7 +12,7 @@ import matplotlib.pyplot as plt from mpl_toolkits.mplot3d import Axes3D from argparse import ArgumentParser, RawTextHelpFormatter -from zpca.zpca import counts2tpm +from zpca.zpca import counts2tpm, counts2tpm_many def main(): """ Main function """ @@ -35,7 +35,14 @@ def main(): parser.add_argument( "--lengths", dest="lengths", - help="Table of feature lengths (tsv). The first column should contain the gene/transcript id. The second column should contain the corresponding lengths", + help="Table of feature lengths (tsv). " + os.linesep + + "The file can have two types of formats." + os.linesep + + "First option: The first column should contain the gene/transcript id." + os.linesep + + "The second column should contain the corresponding lengths" + os.linesep + + "Second option: The first column should contain the gene/transcript id." + os.linesep + + "The rest of the columns should contain the gene/transcript lengths for each of the samples" + os.linesep + + "Note that the sample names should be the same the sample names of the counts." + , required=True, metavar="FILE" ) @@ -106,6 +113,10 @@ def main(): sys.stdout.write(f"Reading: {options.lengths} {os.linesep}") lengths = pd.read_csv(options.lengths, header=0, index_col=0, sep="\t") + mode_lengths = "one" + if int(lengths.shape[1])>2: + mode_lengths = "many" + if options.filter_not_expressed: if options.verbose: sys.stdout.write(f"Filtering not expressed genes/transcripts {os.linesep}") @@ -117,7 +128,10 @@ def main(): if options.verbose: sys.stdout.write(f"Converting the data to TPM {os.linesep}") - tpm = counts2tpm(df, lengths) + if mode_lengths == "one": + tpm = counts2tpm(df, lengths) + elif mode_lengths == "many": + tpm = counts2tpm_many(df, lengths) if options.verbose: sys.stdout.write(f"Log2 transform the data {os.linesep}") @@ -263,7 +277,6 @@ def main(): # Call the Main function and catch Keyboard interrups # ----------------------------------------------------------------------------- - if __name__ == '__main__': try: main() diff --git a/setup.py b/setup.py index ec7bcb9..000b04d 100755 --- a/setup.py +++ b/setup.py @@ -13,7 +13,7 @@ setup( name='zpca', - version='0.3', + version='0.4', description="PCA analysis for genes or transcripts.", author="Foivos Gypas", author_email='fgypas@gmail.com', diff --git a/test_data/gene_expression.tsv b/test_data/gene_expression.tsv deleted file mode 100644 index 9b122d0..0000000 --- a/test_data/gene_expression.tsv +++ /dev/null @@ -1,33975 +0,0 @@ -Name cond1_rep1 cond1_rep2 cond2_rep1 cond2_rep2 cond2_rep3 cond3_rep1 cond3_rep2 cond3_rep3 -ENSG00000251214 0.082265 0 0 0.076778 0.03858 0 0 0.054041 -ENSG00000269886 0.628526 0.936157 0.713989 0.981109 0.286032 1.54953 1.62135 1.23102 -ENSG00000236687 0.26673 0.422927 0.439576 0.186699 0.36119 0.691466 0.599255 0.264577 -ENSG00000251421 0.047635 0.081111 0.056567 0 0 0.066918 0.031571 0.031017 -ENSG00000111305 0.07612 0.283408 0.186367 0.117149 0.200591 0.29465 0.231218 0.19041 -ENSG00000251538 0.064626 0.023291 0.018141 0.021085 0 0.03298 0.015051 0.014988 -ENSG00000186866 14.7054 13.9618 14.2064 15.0707 14.9917 15.8457 17.0727 16.8145 -ENSG00000163930 93.4195 96.2348 99.7083 101.233 105.415 90.6901 93.8713 97.5056 -ENSG00000133997 59.1173 57.8644 59.4449 50.615 53.9758 51.6868 50.3957 54.9751 -ENSG00000121413 54.4628 54.0021 48.4328 49.2271 49.2229 54.6316 60.6181 57.0383 -ENSG00000249621 0.054431 0 0.085871 0 0 0.077365 0 0 -ENSG00000100938 230.374 217.667 216.336 207.555 197.887 243.959 237.744 250.275 -ENSG00000272139 0.56785 0.866531 0.332732 0.518487 0.389424 1.17647 0.940532 0.745777 -ENSG00000168454 0.120813 0.064532 0.104513 0.075639 0.06992 0.206847 0.244357 0.207386 -ENSG00000167157 0.536337 0.587404 0.613873 0.489205 0.419606 0.604765 0.512463 0.648669 -ENSG00000151304 7.36909 7.21294 7.92991 6.95662 7.81487 6.62122 5.66886 5.89147 -ENSG00000248927 0 0.023614 0.027382 0.047885 0.016054 0.024898 0.067523 0 -ENSG00000184838 0.01788 0.02406 0.027971 0.016249 0.016328 0.074048 0 0 -ENSG00000164334 0.049854 0 0 0 0 0 0.051333 0 -ENSG00000056487 3.364 3.42135 2.50158 2.59516 2.29263 2.95104 3.87426 3.18928 -ENSG00000145779 12.1696 14.0337 13.0945 14.1809 11.7026 15.7992 14.7547 15.0774 -ENSG00000172869 13.7433 12.5846 14.1349 12.4115 12.9986 19.3785 18.6598 13.3167 -ENSG00000228505 0 0 0 0 0 0 0 0 -ENSG00000261467 0.284443 0.279632 0.206289 0.304185 0.240051 0.237562 0.346644 0.167863 -ENSG00000234622 0.065575 0.046407 0 0.059722 0 0.27544 0.425892 0.255688 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0.113846 0 +ENST00000553969 2.70927 0.856022 1.45206 1.5863 1.56352 2.5576 2.29114 2.29795 +ENST00000259631 0 0.207203 0 0 0 0 0 0 +ENST00000545043 0 0 0 0.24856 0 0.312901 0 0 +ENST00000564224 0.087951 0.058861 0.111831 0.161464 0.133381 0.176794 0.114609 0.123636 +ENST00000577222 0 0 0.043118 0.051379 0.102916 0.068106 0.26769 0 +ENST00000416454 0.831226 0.187085 0 0.742086 0.801008 0 0.816231 0.969425 diff --git a/tests/test.py b/tests/test.py index 58fc06a..a5fb655 100644 --- a/tests/test.py +++ b/tests/test.py @@ -3,6 +3,83 @@ import os import shutil import hashlib +import pandas as pd + +from zpca.zpca import counts2tpm, counts2tpm_many + +TRANSCRIPT_COUNTS = "test_data/transcripts_counts.tsv" +TRANSCRIPT_LENGTHS = "test_data/transcripts_lengths.tsv" +TRANSCRIPT_TPM = "test_data/transcripts_tpm.tsv" +TRANSCRIPT_LENGTH = "test_data/transcripts_length.tsv" + +def test_counts2tpm(): + + counts = pd.read_csv( + TRANSCRIPT_COUNTS, + header=0, + sep="\t" + )[["Name", "cond1_rep1"]] + counts.set_index("Name", inplace=True) + + length = pd.read_csv( + TRANSCRIPT_LENGTHS, + header=0, + sep="\t" + )[["Name", "cond1_rep1"]] + length.set_index("Name", inplace=True) + length.columns = ["Length"] + + tpm = pd.read_csv( + TRANSCRIPT_TPM, + header=0, + sep="\t" + )[["Name", "cond1_rep1"]] + tpm.set_index("Name", inplace=True) + tpm.columns = ["original"] + + tpm_estimated = counts2tpm(counts, length) + tpm_estimated.columns = ["estimated"] + + print(tpm_estimated.head()) + print(tpm.head()) + df = pd.merge(tpm, + tpm_estimated, + left_index=True, + right_index=True) + + corr = df.corr(method="pearson").iloc[0,1] + + assert corr > 0.99 + +def test_counts2tpm_many(): + + counts = pd.read_csv( + TRANSCRIPT_COUNTS, + header=0, + sep="\t" + ) + counts.set_index("Name", inplace=True) + + length = pd.read_csv( + TRANSCRIPT_LENGTHS, + header=0, + sep="\t" + ) + length.set_index("Name", inplace=True) + + tpm = pd.read_csv( + TRANSCRIPT_TPM, + header=0, + sep="\t" + ) + tpm.set_index("Name", inplace=True) + + tpm_estimated = counts2tpm_many(counts, length) + + corr = pd.DataFrame(tpm_estimated.corrwith(tpm, axis = 0)) + + for i, row in corr.T.iteritems(): + assert row[0] > 0.99 def test_zpca_path(script_runner): ret = script_runner.run('zpca', '--help') diff --git a/zpca/zpca.py b/zpca/zpca.py index 7061571..0416ade 100644 --- a/zpca/zpca.py +++ b/zpca/zpca.py @@ -1,4 +1,5 @@ import pandas as pd +from functools import reduce def counts2tpm(counts_df, lengths_df): """Convert a table of raw counts to TPM @@ -11,4 +12,24 @@ def counts2tpm(counts_df, lengths_df): rate = (counts).div(df.iloc[:,0], axis=0) denom = rate.sum() tpm = rate/denom*1e6 + return tpm + +def counts2tpm_many(counts_df, lengths_df): + """Convert a table of raw counts to TPM + Input-1: pandas dataframe of counts (the id should be the index) + Input-2: pandas dataframe of lengths (the id should be the index) + Each sample has a different length column + Output: pandas dataframe of TPMs + """ + columns = counts_df.columns + tpms = [] + for column in columns: + temp_counts = pd.DataFrame(counts_df[column]) + temp_length = pd.DataFrame(lengths_df[column]) + temp_length.columns = ["Length"] + tpms.append(counts2tpm(temp_counts, temp_length)) + tpm = reduce(lambda left,right: pd.merge(left, + right, + left_index=True, + right_index=True), tpms) return tpm \ No newline at end of file