Mercurial > repos > rnateam > bctools
changeset 55:4bedd35bcdff draft
Move deps from macros to individual tools
| author | rnateam |
|---|---|
| date | Fri, 12 Feb 2016 08:37:33 -0500 |
| parents | 7a05b21c5629 |
| children | b0d5cd8e4c6b |
| files | convert_bc_to_binary_RY.xml coords2clnt.xml extract_aln_ends.xml extract_bcs.xml macros.xml merge_pcr_duplicates.py merge_pcr_duplicates.xml remove_tail.xml rm_spurious_events.xml tool_dependencies.xml |
| diffstat | 10 files changed, 50 insertions(+), 75 deletions(-) [+] |
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--- a/convert_bc_to_binary_RY.xml Mon Feb 01 10:05:34 2016 -0500 +++ b/convert_bc_to_binary_RY.xml Fri Feb 12 08:37:33 2016 -0500 @@ -1,9 +1,13 @@ <tool id="convert_bc_to_binary_RY.py" name="Create binary barcodes" version="0.1.0"> <description>from regular barcodes.</description> + <xml name="requirements"> + <requirements> + <requirement type="package" version="1.66">biopython</requirement> + </requirements> + </xml> <macros> <import>macros.xml</import> </macros> - <expand macro="requirements" /> <expand macro="stdio" /> <version_command>python $__tool_directory__/convert_bc_to_binary_RY.py --version</version_command> <command interpreter="python"><![CDATA[
--- a/coords2clnt.xml Mon Feb 01 10:05:34 2016 -0500 +++ b/coords2clnt.xml Fri Feb 12 08:37:33 2016 -0500 @@ -1,9 +1,13 @@ <tool id="coords2clnt.py" name="Get crosslinked nucleotides" version="0.1.0"> <description>from full alignments</description> + <xml name="requirements"> + <requirements> + <requirement type="package" version="0.6.9">pybedtools</requirement> + </requirements> + </xml> <macros> <import>macros.xml</import> </macros> - <expand macro="requirements" /> <expand macro="stdio" /> <stdio> <exit_code level="fatal" range="1:"/>
--- a/extract_aln_ends.xml Mon Feb 01 10:05:34 2016 -0500 +++ b/extract_aln_ends.xml Fri Feb 12 08:37:33 2016 -0500 @@ -1,9 +1,14 @@ <tool id="extract_aln_ends.py" name="Extract alignment ends." version="0.2.0"> <description>from SAM or BAM.</description> + <xml name="requirements"> + <requirements> + <requirement type="package" version="0.6.9">pybedtools</requirement> + <requirement type="package" version="0.8.3">pysam</requirement> + </requirements> + </xml> <macros> <import>macros.xml</import> </macros> - <expand macro="requirements" /> <expand macro="stdio" /> <version_command>python $__tool_directory__/extract_aln_ends.py --version</version_command> <command interpreter="python"><![CDATA[
--- a/extract_bcs.xml Mon Feb 01 10:05:34 2016 -0500 +++ b/extract_bcs.xml Fri Feb 12 08:37:33 2016 -0500 @@ -1,9 +1,13 @@ <tool id="extract_bcs.py" name="Extract barcodes" version="1.0.0"> <description>using pattern.</description> + <xml name="requirements"> + <requirements> + <requirement type="package" version="1.66">biopython</requirement> + </requirements> + </xml> <macros> <import>macros.xml</import> </macros> - <expand macro="requirements" /> <expand macro="stdio" /> <version_command>python $__tool_directory__/extract_bcs.py --version</version_command> <command interpreter="python"><![CDATA[
--- a/macros.xml Mon Feb 01 10:05:34 2016 -0500 +++ b/macros.xml Fri Feb 12 08:37:33 2016 -0500 @@ -1,18 +1,4 @@ <macros> - <xml name="requirements"> - <requirements> - <requirement type="package" version="1.66">biopython</requirement> - <!-- <requirement type="package" version="1.65">biopython</requirement> --> - <requirement type="package" version="0.16">pandas</requirement> - <!-- <requirement type="package" version="0.7.4">pybedtools</requirement> --> - <requirement type="package" version="0.6.9">pybedtools</requirement> - <!-- <requirement type="package" version="2.24">bedtools</requirement> --> - <requirement type="package" version="0.8.3">pysam</requirement> - <requirement type="package" version="4.1.0">gnu_awk</requirement> - <requirement type="package" version="8.22">gnu_coreutils</requirement> - <requirement type="package" version="5.18.1">perl</requirement> - </requirements> - </xml> <xml name="stdio"> <stdio> <exit_code level="fatal" range="1:"/>
--- a/merge_pcr_duplicates.py Mon Feb 01 10:05:34 2016 -0500 +++ b/merge_pcr_duplicates.py Fri Feb 12 08:37:33 2016 -0500 @@ -3,7 +3,6 @@ import argparse import logging from sys import stdout -import pandas as pd from subprocess import check_call from shutil import rmtree from tempfile import mkdtemp @@ -16,8 +15,7 @@ tool_description = """ Merge PCR duplicates according to random barcode library. -Barcodes containing uncalled base 'N' are removed. By default output is written -to stdout. +Barcodes containing uncalled base 'N' are removed. Input: * bed6 file containing alignments with fastq read-id in name field @@ -30,7 +28,7 @@ Example usage: - read PCR duplicates from file duplicates.bed and write merged results to file merged.bed: -merge_pcr_duplicates.py duplicates.bed bclibrary.fa --out merged.bed +merge_pcr_duplicates.py duplicates.bed bclibrary.fa --outfile merged.bed """ epilog = """ @@ -55,6 +53,7 @@ # optional arguments parser.add_argument( "-o", "--outfile", + required=True, help="Write results to this file.") # misc arguments parser.add_argument( @@ -104,57 +103,14 @@ tmpdir = mkdtemp() logging.debug("tmpdir: " + tmpdir) - # prepare barcode library - syscall1 = "cat " + args.bclib + " | awk 'BEGIN{OFS=\"\\t\"}NR%4==1{gsub(/^@/,\"\"); id=$1}NR%4==2{bc=$1}NR%4==3{print id,bc}' | sort -k1,1 > " + tmpdir + "/bclib.csv" - check_call(syscall1, shell=True) - # prepare alinments - syscall2 = "cat " + args.alignments + " | awk -F \"\\t\" 'BEGIN{OFS=\"\\t\"}{split($4, a, \" \"); $4 = a[1]; print}'| sort -k4,4 > " + tmpdir + "/alns.csv" + syscall2 = "cat " + args.alignments + " | awk -F \"\\t\" 'BEGIN{OFS=\"\\t\"}{split($4, a, \" \"); $4 = a[1]; print}'| sort --compress-program=gzip -k4,4 > " + tmpdir + "/alns.csv" check_call(syscall2, shell=True) # join barcode library and alignments - syscall3 = "join -1 1 -2 4 " + tmpdir + "/bclib.csv " + tmpdir + "/alns.csv " + " | awk 'BEGIN{OFS=\"\\t\"}{print $3,$4,$5,$2,$6,$7}' > " + tmpdir + "/bcalib.csv" + syscall3 = "cat " + args.bclib + " | awk 'BEGIN{OFS=\"\\t\"}NR%4==1{gsub(/^@/,\"\"); id=$1}NR%4==2{bc=$1}NR%4==3{print id,bc}' | sort --compress-program=gzip -k1,1 | join -1 1 -2 4 - " + tmpdir + "/alns.csv " + " | awk 'BEGIN{OFS=\"\\t\"}$4!~/N/{print $3,$4,$5,$2,$6,$7}' | datamash --sort -g 1,2,3,4,6 count 4 | awk 'BEGIN{OFS=\"\\t\"}$4!~/N/{print $1,$2,$3,$4,$6,$5}' > " + args.outfile + # 'chrom', 'start', 'stop', 'bc', 'ndupes', 'strand' check_call(syscall3, shell=True) - - # get alignments combined with barcodes - bcalib = pd.read_csv( - tmpdir + "/bcalib.csv", - sep="\t", - names=["chrom", "start", "stop", "bc", "score", "strand"]) finally: logging.debug("removed tmpdir: " + tmpdir) rmtree(tmpdir) - -# fail if alignments given but combined library is empty -if bcalib.empty: - raise Exception("ERROR: no common entries for alignments and barcode library found. Please check your input files.") - -# warn if not all alignments could be assigned a barcode -n_bcalib = len(bcalib.index) -if n_bcalib < n_alns: - logging.warning( - "{} of {} alignments could not be associated with a random barcode.".format(n_alns - n_bcalib, n_alns)) - -# remove entries with barcodes that has uncalled base N -bcalib_cleaned = bcalib.drop(bcalib[bcalib.bc.str.contains("N")].index) -n_bcalib_cleaned = len(bcalib_cleaned) -# if n_bcalib_cleaned < n_bcalib: -# msg = "{} of {} alignments had random barcodes containing uncalled bases and were dropped.".format( -# n_bcalib - n_bcalib_cleaned, n_bcalib) -# if n_bcalib_cleaned < (0.8 * n_bcalib): -# logging.warning(msg) -# else: -# logging.info(msg) - -# count and merge pcr duplicates -# grouping sorts by keys, so the ouput will be properly sorted -merged = bcalib_cleaned.groupby(['chrom', 'start', 'stop', 'strand', 'bc']).size().reset_index() -merged.rename(columns={0: 'ndupes'}, copy=False, inplace=True) - -# write coordinates of crosslinking event alignments -eventalnout = (open(args.outfile, "w") if args.outfile is not None else stdout) -merged.to_csv( - eventalnout, - columns=['chrom', 'start', 'stop', 'bc', 'ndupes', 'strand'], - sep="\t", index=False, header=False) -eventalnout.close()
--- a/merge_pcr_duplicates.xml Mon Feb 01 10:05:34 2016 -0500 +++ b/merge_pcr_duplicates.xml Fri Feb 12 08:37:33 2016 -0500 @@ -1,9 +1,15 @@ <tool id="merge_pcr_duplicates.py" name="Merge PCR duplicates" version="0.2.0"> <description>according to random barcode library.</description> + <xml name="requirements"> + <requirements> + <requirement type="package" version="4.1.0">gnu_awk</requirement> + <requirement type="package" version="8.22">gnu_coreutils</requirement> + <requirement type="package" version="1.0.6">datamash</requirement> + </requirements> + </xml> <macros> <import>macros.xml</import> </macros> - <expand macro="requirements" /> <expand macro="stdio" /> <version_command>python $__tool_directory__/merge_pcr_duplicates.py --version</version_command> <command interpreter="python"><![CDATA[merge_pcr_duplicates.py @@ -15,7 +21,7 @@ $positional_2 #end if -> $default]]></command> +--outfile $default]]></command> <inputs> <param area="false" label="bed6 file containing alignments." name="positional_1" type="data" format="bed"/> <param area="false" label="fastaq barcode library." name="positional_2" type="data" format="fastq"/>
--- a/remove_tail.xml Mon Feb 01 10:05:34 2016 -0500 +++ b/remove_tail.xml Fri Feb 12 08:37:33 2016 -0500 @@ -1,9 +1,13 @@ <tool id="remove_tail.py" name="Remove 3'-end nts" version="0.1.0"> <description>from FASTQ</description> + <xml name="requirements"> + <requirements> + <requirement type="package" version="1.66">biopython</requirement> + </requirements> + </xml> <macros> <import>macros.xml</import> </macros> - <expand macro="requirements" /> <expand macro="stdio" /> <version_command>python $__tool_directory__/remove_tail.py --version</version_command> <command interpreter="python"><![CDATA[remove_tail.py
--- a/rm_spurious_events.xml Mon Feb 01 10:05:34 2016 -0500 +++ b/rm_spurious_events.xml Fri Feb 12 08:37:33 2016 -0500 @@ -1,9 +1,14 @@ <tool id="rm_spurious_events.py" name="Remove spurious" version="0.1.0"> <description>crosslinking events</description> + <xml name="requirements"> + <requirements> + <requirement type="package" version="8.22">gnu_coreutils</requirement> + <requirement type="package" version="5.18.1">perl</requirement> + </requirements> + </xml> <macros> <import>macros.xml</import> </macros> - <expand macro="requirements" /> <expand macro="stdio" /> <version_command>python $__tool_directory__/rm_spurious_events.py --version</version_command> <command interpreter="python"><![CDATA[rm_spurious_events.py
--- a/tool_dependencies.xml Mon Feb 01 10:05:34 2016 -0500 +++ b/tool_dependencies.xml Fri Feb 12 08:37:33 2016 -0500 @@ -6,9 +6,6 @@ <!-- <package name="biopython" version="1.65"> <repository name="package_biopython_1_65" owner="biopython"/> </package> --> - <package name="pandas" version="0.16"> - <repository changeset_revision="67abd81bd3ac" name="package_python_2_7_pandas_0_16" owner="iuc" toolshed="https://testtoolshed.g2.bx.psu.edu" /> - </package> <!-- <package name="pybedtools" version="0.7.4"> <repository name="package_python_2_7_pybedtools_0_7_4" owner="iuc"/> </package> --> @@ -30,4 +27,8 @@ <package name="perl" version="5.18.1"> <repository changeset_revision="6f144bd786a8" name="package_perl_5_18" owner="iuc" toolshed="https://testtoolshed.g2.bx.psu.edu" /> </package> + <package name="datamash" version="1.0.6"> + <repository changeset_revision="df06a5e1ed6f" name="package_datamash_1_0_6" owner="agordon" toolshed="https://testtoolshed.g2.bx.psu.edu" /> + </package> + </tool_dependency>